sbuild (Debian sbuild) 0.91.5 (17 December 2025) on carme.larted.org.uk +==============================================================================+ | kmer 0~20150903+r2013-10 (amd64) Mon, 27 Apr 2026 01:37:28 +0000 | +==============================================================================+ Package: kmer Version: 0~20150903+r2013-10 Source Version: 0~20150903+r2013-10 Distribution: perl-5.42-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Mon, 27 Apr 2026 01:37:29 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup kmer_0~20150903+r2013-10 perl-5.42-throwaway amd64 ------------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup kmer_0~20150903+r2013-10 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Mon, 27 Apr 2026 01:37:29 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://deb.debian.org/debian sid InRelease Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B] Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Mon, 27 Apr 2026 01:37:31 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/kmer_0~20150903+r2013-10.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 27 Apr 2026 01:37:31 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-exec, dh-sequence-python3, python3-dev, build-essential Filtered Build-Depends: debhelper-compat (= 13), dh-exec, dh-sequence-python3, python3-dev, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/kmer-8W5TPl/resolver-SJFyOK/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/kmer-8W5TPl/resolver-SJFyOK/apt_archive ./ InRelease Get:2 copy:/build/kmer-8W5TPl/resolver-SJFyOK/apt_archive ./ Release [609 B] Ign:3 copy:/build/kmer-8W5TPl/resolver-SJFyOK/apt_archive ./ Release.gpg Get:4 copy:/build/kmer-8W5TPl/resolver-SJFyOK/apt_archive ./ Sources [643 B] Get:5 copy:/build/kmer-8W5TPl/resolver-SJFyOK/apt_archive ./ Packages [682 B] Fetched 1934 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libjs-sphinxdoc libmagic-mgc libmagic1t64 libpipeline1 libpython3-dev libpython3-stdlib libpython3.13 libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib libtool libuchardet0 libxml2-16 m4 man-db media-types netbase po-debconf python3 python3-dev python3-minimal python3.13 python3.13-dev python3.13-minimal sensible-utils tzdata zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build python3-installer python3-wheel gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.13-venv python3.13-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl ca-certificates The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libjs-sphinxdoc libmagic-mgc libmagic1t64 libpipeline1 libpython3-dev libpython3-stdlib libpython3.13 libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib libtool libuchardet0 libxml2-16 m4 man-db media-types netbase po-debconf python3 python3-dev python3-minimal python3.13 python3.13-dev python3.13-minimal sbuild-build-depends-main-dummy sensible-utils tzdata zlib1g-dev 0 upgraded, 50 newly installed, 0 to remove and 0 not upgraded. Need to get 26.4 MB of archives. After this operation, 104 MB of additional disk space will be used. Get:1 copy:/build/kmer-8W5TPl/resolver-SJFyOK/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [880 B] Get:2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.8.0-1 [116 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.12-1 [866 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.12-1 [2267 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.9-3 [27.6 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 media-types all 14.0.0 [30.8 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2026b-1 [260 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.12-1 [1974 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.12-1 [776 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.9-3 [10.5 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.9-3 [27.6 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5+b2 [337 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5+b2 [109 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5+b2 [42.6 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.2-2 [242 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b1 [68.8 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42-5 [99.4 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-6 [494 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.2-2 [770 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.31 [75.7 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:34 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.2+dfsg-0.1 [641 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.2-2 [1684 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.31 [932 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 dh-exec amd64 0.31 [26.1 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 dh-python all 7.20260309 [114 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.8.0-1 [171 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-12 [27.9 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.12-1 [2187 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.12-1 [5298 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.9-3 [10.8 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.12-1 [504 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.9-3 [26.0 kB] Preconfiguring packages ... Fetched 26.4 MB in 0s (147 MB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... 23451 files and directories currently installed.) Preparing to unpack .../libexpat1_2.8.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.8.0-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.12-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.12-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.12-1_amd64.deb ... Unpacking python3.13-minimal (3.13.12-1) ... Setting up libpython3.13-minimal:amd64 (3.13.12-1) ... Setting up libexpat1:amd64 (2.8.0-1) ... Setting up python3.13-minimal (3.13.12-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 23785 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.9-3_amd64.deb ... Unpacking python3-minimal (3.13.9-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_14.0.0_all.deb ... Unpacking media-types (14.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2026b-1_all.deb ... Unpacking tzdata (2026b-1) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../4-libpython3.13-stdlib_3.13.12-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.12-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../5-python3.13_3.13.12-1_amd64.deb ... Unpacking python3.13 (3.13.12-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.13.9-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.9-3) ... Setting up python3-minimal (3.13.9-3) ... Selecting previously unselected package python3. (Reading database ... 24764 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.9-3_amd64.deb ... Unpacking python3 (3.13.9-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5+b2_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5+b2) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5+b2_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5+b2) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5+b2_amd64.deb ... Unpacking file (1:5.46-5+b2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.2-2_amd64.deb ... Unpacking gettext-base (0.23.2-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-2+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.24.1-1_amd64.deb ... Unpacking groff-base (1.24.1-1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.42-5_amd64.deb ... Unpacking bsdextrautils (2.42-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.8-3_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-3) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.21-1_amd64.deb ... Unpacking m4 (1.4.21-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-6_all.deb ... Unpacking autoconf (2.72-6) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20240727.1+nmu1_all.deb ... Unpacking autotools-dev (20240727.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.18.1-4_all.deb ... Unpacking automake (1:1.18.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.23.2-2_all.deb ... Unpacking autopoint (0.23.2-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.31_all.deb ... Unpacking libdebhelper-perl (13.31) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-11_all.deb ... Unpacking libtool (2.5.4-11) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_22_all.deb ... Unpacking dh-autoreconf (22) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../22-libelf1t64_0.195-1_amd64.deb ... Unpacking libelf1t64:amd64 (0.195-1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.16-4_amd64.deb ... Unpacking dwz (0.16-4) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../24-libxml2-16_2.15.2+dfsg-0.1_amd64.deb ... Unpacking libxml2-16:amd64 (2.15.2+dfsg-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.2-2_amd64.deb ... Unpacking gettext (0.23.2-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.22_all.deb ... Unpacking po-debconf (1.0.22) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.31_all.deb ... Unpacking debhelper (13.31) ... Selecting previously unselected package dh-exec. Preparing to unpack .../29-dh-exec_0.31_amd64.deb ... Unpacking dh-exec (0.31) ... Selecting previously unselected package dh-python. Preparing to unpack .../30-dh-python_7.20260309_all.deb ... Unpacking dh-python (7.20260309) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../31-libexpat1-dev_2.8.0-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.8.0-1) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../32-libjs-sphinxdoc_8.2.3-12_all.deb ... Unpacking libjs-sphinxdoc (8.2.3-12) ... Selecting previously unselected package libpython3.13:amd64. Preparing to unpack .../33-libpython3.13_3.13.12-1_amd64.deb ... Unpacking libpython3.13:amd64 (3.13.12-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../34-zlib1g-dev_1%3a1.3.dfsg+really1.3.2-3_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-3) ... Selecting previously unselected package libpython3.13-dev:amd64. Preparing to unpack .../35-libpython3.13-dev_3.13.12-1_amd64.deb ... Unpacking libpython3.13-dev:amd64 (3.13.12-1) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../36-libpython3-dev_3.13.9-3_amd64.deb ... Unpacking libpython3-dev:amd64 (3.13.9-3) ... Selecting previously unselected package python3.13-dev. Preparing to unpack .../37-python3.13-dev_3.13.12-1_amd64.deb ... Unpacking python3.13-dev (3.13.12-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../38-python3-dev_3.13.9-3_amd64.deb ... Unpacking python3-dev (3.13.9-3) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../39-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up media-types (14.0.0) ... Setting up libpipeline1:amd64 (1.5.8-3) ... Setting up bsdextrautils (2.42-5) ... Setting up libmagic-mgc (1:5.46-5+b2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.15.2+dfsg-0.1) ... Setting up libdebhelper-perl (13.31) ... Setting up libmagic1t64:amd64 (1:5.46-5+b2) ... Setting up gettext-base (0.23.2-2) ... Setting up m4 (1.4.21-1) ... Setting up file (1:5.46-5+b2) ... Setting up libelf1t64:amd64 (0.195-1) ... Setting up tzdata (2026b-1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Apr 27 01:37:39 UTC 2026. Universal Time is now: Mon Apr 27 01:37:39 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1+nmu1) ... Setting up libexpat1-dev:amd64 (2.8.0-1) ... Setting up autopoint (0.23.2-2) ... Setting up libjs-sphinxdoc (8.2.3-12) ... Setting up autoconf (2.72-6) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-3) ... Setting up dwz (0.16-4) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2+b1) ... Setting up netbase (6.5) ... Configuration file '/etc/protocols' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Configuration file '/etc/services' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Setting up libpython3.13-stdlib:amd64 (3.13.12-1) ... Setting up libpython3-stdlib:amd64 (3.13.9-3) ... Setting up libpython3.13:amd64 (3.13.12-1) ... Setting up automake (1:1.18.1-4) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.2-2) ... Setting up libtool (2.5.4-11) ... Setting up python3.13 (3.13.12-1) ... Setting up python3 (3.13.9-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (22) ... Setting up libpython3.13-dev:amd64 (3.13.12-1) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.24.1-1) ... Setting up dh-python (7.20260309) ... Setting up libpython3-dev:amd64 (3.13.9-3) ... Setting up python3.13-dev (3.13.12-1) ... Setting up po-debconf (1.0.22) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-dev (3.13.9-3) ... Setting up debhelper (13.31) ... Setting up dh-exec (0.31) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.42-15) ... +------------------------------------------------------------------------------+ | Check architectures Mon, 27 Apr 2026 01:37:40 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Mon, 27 Apr 2026 01:37:40 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.18.5+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.18.5-1 (2026-01-16) amd64 (x86_64) Toolchain package versions: binutils_2.46-3 dpkg-dev_1.23.7 g++-14_14.3.0-14 g++-15_15.2.0-17 gcc-14_14.3.0-14 gcc-15_15.2.0-17 libc6-dev_2.42-15 libstdc++-14-dev_14.3.0-14 libstdc++-15-dev_15.2.0-17 libstdc++6_16-20260425-1 linux-libc-dev_6.19.14-1 Package versions: adduser_3.155 apt_3.2.0 autoconf_2.72-6 automake_1:1.18.1-4 autopoint_0.23.2-2 autotools-dev_20240727.1+nmu1 base-files_14 base-passwd_3.6.8 bash_5.3-2 binutils_2.46-3 binutils-common_2.46-3 binutils-gold_2.44-3 binutils-gold-x86-64-linux-gnu_2.44-3 binutils-x86-64-linux-gnu_2.46-3 bsdextrautils_2.42-5 bsdutils_1:2.42-5 build-essential_12.12 bzip2_1.0.8-6+b2 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-14_14.3.0-14 cpp-14-x86-64-linux-gnu_14.3.0-14 cpp-15_15.2.0-17 cpp-15-x86-64-linux-gnu_15.2.0-17 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_13.31 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_22 dh-exec_0.31 dh-python_7.20260309 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 dirmngr_2.4.9-4 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 eatmydata_131-2 file_1:5.46-5+b2 findutils_4.10.0-3 g++_4:15.2.0-5+b1 g++-14_14.3.0-14 g++-14-x86-64-linux-gnu_14.3.0-14 g++-15_15.2.0-17 g++-15-x86-64-linux-gnu_15.2.0-17 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-14_14.3.0-14 gcc-14-base_14.3.0-14 gcc-14-x86-64-linux-gnu_14.3.0-14 gcc-15_15.2.0-17 gcc-15-base_15.2.0-17 gcc-15-x86-64-linux-gnu_15.2.0-17 gcc-16-base_16-20260425-1 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_0.23.2-2 gettext-base_0.23.2-2 gnupg_2.4.9-4 gnupg-l10n_2.4.9-4 gpg_2.4.9-4 gpg-agent_2.4.9-4 gpgconf_2.4.9-4 gpgsm_2.4.9-4 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-3 libapt-pkg7.0_3.2.0 libarchive-zip-perl_1.68-1 libasan8_16-20260425-1 libassuan9_3.0.2-2+b2 libatomic1_16-20260425-1 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46-3 libblkid1_2.42-5 libbsd0_0.12.2-2+b2 libbz2-1.0_1.0.8-6+b2 libc-bin_2.42-15 libc-dev-bin_2.42-15 libc-gconv-modules-extra_2.42-15 libc-l10n_2.42-15 libc6_2.42-15 libc6-dev_2.42-15 libcap-ng0_0.9.3-1 libcap2_1:2.78-1 libcc1-0_16-20260425-1 libcrypt-dev_1:4.5.1-1+b1 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46-3 libctf0_2.46-3 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.282+b3 libdebhelper-perl_13.31 libdpkg-perl_1.23.7 libeatmydata1_131-2+b2 libelf1t64_0.195-1 libexpat1_2.8.0-1 libexpat1-dev_2.8.0-1 libffi8_3.5.2-4 libfile-stripnondeterminism-perl_1.15.0-1 libgcc-14-dev_14.3.0-14 libgcc-15-dev_15.2.0-17 libgcc-s1_16-20260425-1 libgcrypt20_1.12.2-1 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgnutls30t64_3.8.12-3 libgomp1_16-20260425-1 libgpg-error0_1.59-4 libgprofng0_2.46-3 libhogweed6t64_3.10.2-1+b1 libhwasan0_16-20260425-1 libidn2-0_2.3.8-4+b1 libisl23_0.27-2 libitm1_16-20260425-1 libjansson4_2.14-2+b4 libjs-sphinxdoc_8.2.3-12 libksba8_1.6.8-2 liblastlog2-2_2.42-5 libldap2_2.6.10+dfsg-1+b2 liblsan0_16-20260425-1 liblz4-1_1.10.0-10 liblzma5_5.8.3-1 libmagic-mgc_1:5.46-5+b2 libmagic1t64_1:5.46-5+b2 libmd0_1.1.0-2+b2 libmount1_2.42-5 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncursesw6_6.6+20251231-1 libnettle8t64_3.10.2-1+b1 libnpth0t64_1.8-3+b1 libp11-kit0_0.26.2-2 libpam-modules_1.7.0-5+b1 libpam-modules-bin_1.7.0-5+b1 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5+b1 libpcre2-8-0_10.46-1+b1 libperl5.40_5.40.1-7+b2 libperl5.42_5.42.2-1 libpipeline1_1.5.8-3 libpython3-dev_3.13.9-3 libpython3-stdlib_3.13.9-3 libpython3.13_3.13.12-1 libpython3.13-dev_3.13.12-1 libpython3.13-minimal_3.13.12-1 libpython3.13-stdlib_3.13.12-1 libquadmath0_16-20260425-1 libreadline8t64_8.3-4 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.0-2+b1 libselinux1_3.10-1 libsemanage-common_3.10-1 libsemanage2_3.10-1 libsepol2_3.10-1 libsframe2_2.45.50.20251209-1+b1 libsframe3_2.46-3 libsmartcols1_2.42-5 libsqlite3-0_3.46.1-9+b1 libssl3t64_3.6.2-1 libstdc++-14-dev_14.3.0-14 libstdc++-15-dev_15.2.0-17 libstdc++6_16-20260425-1 libsystemd0_260.1-1 libtasn1-6_4.21.0-2 libtinfo6_6.6+20251231-1 libtool_2.5.4-11 libtsan2_16-20260425-1 libubsan1_16-20260425-1 libuchardet0_0.0.8-2+b1 libudev1_260.1-1 libunistring5_1.4.2-1 libuuid1_2.42-5 libxml2-16_2.15.2+dfsg-0.1 libxxhash0_0.8.3-2+b1 libzstd1_1.5.7+dfsg-3+b1 linux-libc-dev_6.19.14-1 locales-all_2.42-15 login.defs_1:4.19.3-2 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 media-types_14.0.0 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1 netbase_6.5 openssl-provider-legacy_3.6.2-1 passwd_1:4.19.3-2 patch_2.8-2 perl_5.42.2-1 perl-base_5.42.2-1 perl-modules-5.40_5.40.1-7 perl-modules-5.42_5.42.2-1 pinentry-curses_1.3.2-4 po-debconf_1.0.22 python3_3.13.9-3 python3-dev_3.13.9-3 python3-minimal_3.13.9-3 python3.13_3.13.12-1 python3.13-dev_3.13.12-1 python3.13-minimal_3.13.12-1 readline-common_8.3-4 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.3.0-5+b1 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 tzdata_2026b-1 util-linux_2.42-5 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Mon, 27 Apr 2026 01:37:41 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: kmer Binary: kmer, libkmer-dev, meryl, libmeryl-dev, leaff, sim4db, atac, kmer-examples Architecture: any all Version: 0~20150903+r2013-10 Maintainer: Debian Med Packaging Team Uploaders: Afif Elghraoui Homepage: http://kmer.sourceforge.net Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/kmer Vcs-Git: https://salsa.debian.org/med-team/kmer.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-exec, dh-sequence-python3, python3-dev Package-List: atac deb science optional arch=any kmer deb science optional arch=all kmer-examples deb science optional arch=all leaff deb science optional arch=any libkmer-dev deb libdevel optional arch=any libmeryl-dev deb libdevel optional arch=any meryl deb science optional arch=any sim4db deb science optional arch=any Checksums-Sha1: 6da7324491e761437f27207f0b9135d767452e7a 1251653 kmer_0~20150903+r2013.orig.tar.gz f2b1d45b3a88f7311b0af09fbe6575a4af63b140 2381852 kmer_0~20150903+r2013-10.debian.tar.xz Checksums-Sha256: 8fd9c289244e69e38bb7709f3523d39edf1c2ced2cbcc687fcf00ecfca78ea47 1251653 kmer_0~20150903+r2013.orig.tar.gz b222a57be520cb861ac1afb05e2ffce75aaa175bdcf53446285c96213b8f1c44 2381852 kmer_0~20150903+r2013-10.debian.tar.xz Files: 30b66a10ddc64022509dd8b85425880f 1251653 kmer_0~20150903+r2013.orig.tar.gz a04e15bc3d55a1433b30db886cef8efd 2381852 kmer_0~20150903+r2013-10.debian.tar.xz Dgit: 83efb528c56c5ae49c8a9c0b36cc618739a8cf30 debian archive/debian/0_20150903+r2013-10 https://git.dgit.debian.org/kmer Git-Tag-Info: tag=ad1610a6ae9cbca7ebde4f40dacf0062260e41e2 fp=724d609337113c710550d7473c26763f6c67e6e2 Git-Tag-Tagger: Michael R. Crusoe -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEN02M5NuW6cvUwJcqYG0ITkaDwHkFAmia9Q4ACgkQYG0ITkaD wHm7+xAAggl10/Dx5E5vI8gnS6AdqL8pkhWJzum0JTgG1tLPv0fHaZM5JKOfvH4E BkYfSX/VT+vJRDe46RGrlUhpcLwosu/9iWmOPltPf6uSJvB54FenJpNdIGX9pUIb 3Vb3hjKhwH13n7FyzRXgk8xEKEaafJo/ICygJbLPKHPAn2R3+V1a+r44O4wBl/kM +csG2GsmeeVtbu2IuIaIlH+rIv6qn5Vy1swBbyWqhxhL7UqzndAyWC+DvoxZY5ay URh/Ha/Of6ige9R4l6aYfAhbfeyrfAvn04Di+xvwSelMPGCnJVAWItiQ61/C2XRY aSZZRh52gf4v4PX+QUFLKnR/AXE5+u0wd7aPXh+No8DtWxyzofypjOBpLjSeXmAj qC3O2zm2XQjNBj3GtzMjqKdXrc7SrdaLA0wVSlyIkW31C7GLELZonNsF2tkpzpkW N67/hgFrtokJIPDyA0I6hhxjddQcU8/VqcBIfd5iQDrdShG0aNa/PgiLlZ9hO7LS XnMFhJV8zJcDq4s7TTjq8bMhN2Bc++owYwKhR+8ddTh/XeF8apFk0b7tW65Ey3q5 nJVCrYQ+2F7Uys+O9AKUUTOCD86JUay3Yd4qLPHF0VG75U+SRUNTxDdW5dLB2QoX yz9gN1Hgf5Xj6d50f7IsOOIZ5PiT5b6vjArPDqYt65RDwOt75k4= =oHCi -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./kmer_0~20150903+r2013-10.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./kmer_0~20150903+r2013-10.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting kmer in /build/kmer-8W5TPl/kmer-0~20150903+r2013 dpkg-source: info: unpacking kmer_0~20150903+r2013.orig.tar.gz dpkg-source: info: unpacking kmer_0~20150903+r2013-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying allow-freebsd-build.patch dpkg-source: info: applying atac-helper-script-paths.patch dpkg-source: info: applying atac-readme.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying linux-cflags.patch dpkg-source: info: applying fix_wrong_evaluation_order.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying drop_distutils clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Mon, 27 Apr 2026 01:37:41 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network kmer_0~20150903+r2013-10 perl-5.42-throwaway amd64 ------------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network kmer_0~20150903+r2013-10 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/kmer-8W5TPl/kmer-0~20150903+r2013 SCHROOT_ALIAS_NAME=perl-5.42-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.42-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.42-amd64-debomatic-e4f40b4c-bd7d-486a-821d-9e32015b62f0 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package kmer dpkg-buildpackage: info: source version 0~20150903+r2013-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/kmer-8W5TPl/kmer-0~20150903+r2013' /usr/bin/make real-clean make[2]: Entering directory '/build/kmer-8W5TPl/kmer-0~20150903+r2013' rm -f ESTmapper/*.o ESTmapper/mergeCounts ESTmapper/terminate ESTmapper/Make.depends ESTmapper/mergeCounts.C.d ESTmapper/terminate.C.d ESTmapper/mergeCounts ESTmapper/terminate rm -f atac-driver/libatac/*.o atac-driver/libatac/*~ atac-driver/libatac/libatac.a atac-driver/libatac/Make.depends atac-driver/libatac/atacFeature.C.d atac-driver/libatac/atacFeatureList.C.d atac-driver/libatac/atacFile.C.d atac-driver/libatac/atacFileStreamMerge.C.d atac-driver/libatac/atacMatch.C.d atac-driver/libatac/atacMatchList.C.d atac-driver/libatac/atacMatchOrder.C.d rm -f atac-driver/alignOverlap/*.o atac-driver/alignOverlap/*~ atac-driver/alignOverlap/core atac-driver/alignOverlap/overlap-process1.C atac-driver/alignOverlap/overlap-process2.C atac-driver/alignOverlap/overlap atac-driver/alignOverlap/Make.depends atac-driver/alignOverlap/overlap.C.d atac-driver/alignOverlap/overlap-sort.C.d atac-driver/alignOverlap/overlap-printAnno.C.d atac-driver/alignOverlap/overlap-find.C.d rm -f atac-driver/gapShifter/*.o atac-driver/gapShifter/*~ atac-driver/gapShifter/core atac-driver/gapShifter/gapShifter atac-driver/gapShifter/extractSequence atac-driver/gapShifter/extractUnmapped atac-driver/gapShifter/coalesceMatches atac-driver/gapShifter/correctGaps atac-driver/gapShifter/testAtac atac-driver/gapShifter/cleanAtac atac-driver/gapShifter/projectFeatures atac-driver/gapShifter/Make.depends atac-driver/gapShifter/gapShifter.C.d atac-driver/gapShifter/extractSequence.C.d atac-driver/gapShifter/extractUnmapped.C.d atac-driver/gapShifter/coalesceMatches.C.d atac-driver/gapShifter/correctGaps.C.d atac-driver/gapShifter/testAtac.C.d atac-driver/gapShifter/cleanAtac.C.d atac-driver/gapShifter/projectFeatures.C.d rm -f atac-driver/lengthFilter/*.o atac-driver/lengthFilter/*~ atac-driver/lengthFilter/core atac-driver/lengthFilter/lengthFilter atac-driver/lengthFilter/Make.depends atac-driver/lengthFilter/lengthFilter.C.d rm -f atac-driver/matchExtender/*.o atac-driver/matchExtender/*~ atac-driver/matchExtender/core atac-driver/matchExtender/matchExtender atac-driver/matchExtender/Make.depends atac-driver/matchExtender/matchExtender.C.d atac-driver/matchExtender/matchExtender-dump.C.d atac-driver/matchExtender/matchExtender-func.C.d rm -f atac-driver/mismatchCounter/*.o atac-driver/mismatchCounter/*~ atac-driver/mismatchCounter/core atac-driver/mismatchCounter/mismatchCounter atac-driver/mismatchCounter/Make.depends atac-driver/mismatchCounter/mismatchCounter.C.d rm -f atac-driver/statsGenerator/*.o atac-driver/statsGenerator/*~ atac-driver/statsGenerator/core atac-driver/statsGenerator/statsGenerator atac-driver/statsGenerator/Make.depends atac-driver/statsGenerator/statsGenerator.C.d rm -f atac-driver/uniqueFilter/*.o atac-driver/uniqueFilter/*~ atac-driver/uniqueFilter/core atac-driver/uniqueFilter/uniqueFilter atac-driver/uniqueFilter/Make.depends atac-driver/uniqueFilter/uniqueFilter.C.d rm -f atac-driver/clumpMaker/*.o atac-driver/clumpMaker/*~ atac-driver/clumpMaker/core atac-driver/clumpMaker/clumpMaker atac-driver/clumpMaker/Make.depends atac-driver/clumpMaker/clumpMaker.C.d rm -f atac-driver/chainer/*.o atac-driver/chainer/*/*.o atac-driver/chainer/*.so atac-driver/chainer/python/*.pyc atac-driver/chainer/localAlignerInterfacemodule.so atac-driver/chainer/halignmodule.so atac-driver/chainer/Make.depends atac-driver/chainer/localalign/GF_ALN_dpaligner.C.d atac-driver/chainer/localalign/GF_ALN_local.C.d atac-driver/chainer/localalign/GF_ALN_overlap.C.d atac-driver/chainer/localalign/GF_ALN_loverlapper.C.d atac-driver/chainer/localalign/GF_ALN_pieceOlap.C.d atac-driver/chainer/localalign/localAlignerInterfacemodule.C.d atac-driver/chainer/halign/halign.C.d atac-driver/chainer/halign/halignmodule.C.d rm -f atac-driver/chimera/*.o atac-driver/chimera/*~ atac-driver/chimera/core atac-driver/chimera/happy-clones-span-clumps atac-driver/chimera/Make.depends atac-driver/chimera/happy-clones-span-clumps.C.d rm -f atac-driver/Make.depends rm -f seatac/*.o seatac/seatac seatac/heavychains seatac/filter-nop.so seatac/filter-heavychains.so seatac/Make.depends seatac/seatac.C.d seatac/configuration.C.d seatac/encodedQuery.C.d seatac/hitMatrix.C.d seatac/thr-search.C.d seatac/thr-loader.C.d seatac/thr-deadlock.C.d seatac/hitMatrix-sort.C.d rm -f leaff/*.o leaff/leaff leaff/Make.depends leaff/leaff.C.d leaff/blocks.C.d leaff/dups.C.d leaff/gc.C.d leaff/partition.C.d leaff/simseq.C.d leaff/stats.C.d rm -f meryl/*.o meryl/meryl meryl/simple meryl/mapMers meryl/mapMers-depth meryl/kmer-mask meryl/libmerylguts.a meryl/Make.depends meryl/args.C.d meryl/binaryOp.C.d meryl/build.C.d meryl/build-threads.C.d meryl/dump.C.d meryl/estimate.C.d meryl/merge.C.d meryl/unaryOp.C.d meryl/meryl.C.d meryl/simple.C.d meryl/mapMers.C.d meryl/mapMers-depth.C.d meryl/kmer-mask.C.d rm -f seagen/*.o seagen/seagen seagen/hitConverter seagen/filterEST seagen/filterMRNA seagen/filterNULL seagen/filtertest seagen/sortHits seagen/filterESTsimple seagen/Make.depends seagen/searchGENOME.C.d seagen/configuration.C.d seagen/encodedQuery.C.d seagen/thr-deadlock.C.d seagen/thr-loader.C.d seagen/thr-search.C.d seagen/thr-output.C.d seagen/hitMatrix-sort.C.d seagen/aHit.C.d seagen/hitConverter.C.d seagen/filterEST.C.d seagen/filterEST-complicated.C.d seagen/filterMRNA.C.d seagen/filterNULL.C.d seagen/sortHits.C.d seagen/filtertest.C.d seagen/hitReader.C.d seagen/hitMatrix.C.d rm -f sim4dbutils/*.o sim4dbutils/cleanPolishes sim4dbutils/fixPolishesIID sim4dbutils/comparePolishes sim4dbutils/convertToAtac sim4dbutils/convertToExtent sim4dbutils/convertPolishes sim4dbutils/detectChimera sim4dbutils/depthOfPolishes sim4dbutils/filterPolishes sim4dbutils/headPolishes sim4dbutils/mappedCoverage sim4dbutils/mergePolishes sim4dbutils/parseSNP sim4dbutils/pickBestPolish sim4dbutils/pickBestPair sim4dbutils/pickUniquePolish sim4dbutils/plotCoverageVsIdentity sim4dbutils/removeDuplicate sim4dbutils/sortPolishes sim4dbutils/summarizePolishes sim4dbutils/uniqPolishes sim4dbutils/vennPolishes sim4dbutils/realignPolishes sim4dbutils/removeRedundant sim4dbutils/reportAlignmentDifferences sim4dbutils/Make.depends sim4dbutils/cleanPolishes.C.d sim4dbutils/fixPolishesIID.C.d sim4dbutils/comparePolishes.C.d sim4dbutils/convertToAtac.C.d sim4dbutils/convertToExtent.C.d sim4dbutils/convertPolishes.C.d sim4dbutils/detectChimera.C.d sim4dbutils/depthOfPolishes.C.d sim4dbutils/filterPolishes.C.d sim4dbutils/headPolishes.C.d sim4dbutils/mappedCoverage.C.d sim4dbutils/mergePolishes.C.d sim4dbutils/parseSNP.C.d sim4dbutils/pickBestPolish.C.d sim4dbutils/pickBestPair.C.d sim4dbutils/pickUniquePolish.C.d sim4dbutils/plotCoverageVsIdentity.C.d sim4dbutils/removeDuplicate.C.d sim4dbutils/sortPolishes.C.d sim4dbutils/summarizePolishes.C.d sim4dbutils/uniqPolishes.C.d sim4dbutils/vennPolishes.C.d sim4dbutils/realignPolishes.C.d sim4dbutils/removeRedundant.C.d sim4dbutils/reportAlignmentDifferences.C.d sim4dbutils/s4p_overlap.C.d rm -f sim4db/*.o sim4db/sim4db sim4db/Make.depends sim4db/sim4th.C.d rm -f snapper/*.o snapper/snapper2 snapper/Make.depends snapper/snapper2.C.d snapper/configuration.C.d snapper/thr-search.C.d snapper/thr-filter.C.d snapper/thr-polish.C.d snapper/thr-polish-dp.C.d snapper/hitMatrix.C.d snapper/hitMatrix-sort.C.d rm -f tapper/*.o tapper/tagger tapper/tapper tapper/tapperconvert tapper/tappermerge tapper/tappersort tapper/tappererrorcorrect tapper/Make.depends tapper/tagger.C.d tapper/tapper.C.d tapper/tapperconvert.C.d tapper/tappermerge.C.d tapper/tappersort.C.d tapper/tappererrorcorrect.C.d rm -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/*.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/*.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/*.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/Make.depends /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/align.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/extend.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/greedy.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/poly.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/splice.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/table.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/util.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.C.d rm -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/*.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/Make.depends /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-dump.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-existDB.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C.d rm -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/*.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/Make.depends /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C.d rm -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/*.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/Make.depends /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet.c.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.c.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet-colorspace.c.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/halign.c.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/reversecomplement.c.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/kmer.C.d rm -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/*.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/Make.depends /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaStdin.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqStdin.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/sffFile.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqFactory.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqCache.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/merStream.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C.d rm -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/*.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/test.c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/diffs /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/libmt19937ar.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/Make.depends /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.c.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/test.c.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/*.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/test.c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/diffs /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test rm -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/*.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/libkaz.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/Make.depends /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/dict.c.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/except.c.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/hash.c.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/list.c.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/sfx.c.d rm -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/*.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/Make.depends /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/file.c.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/md5.c.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/palloc.c.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/qsort_mt.c.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.c.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bigQueue.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/fibonacciNumbers.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/readBuffer.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/speedCounter.C.d /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.C.d rm -f Make.depends Make.compilers make[2]: Leaving directory '/build/kmer-8W5TPl/kmer-0~20150903+r2013' rm -rf installdir make[1]: Leaving directory '/build/kmer-8W5TPl/kmer-0~20150903+r2013' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building kmer using existing ../kmer_0~20150903+r2013.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building kmer in ../kmer_0~20150903+r2013-10.debian.tar.xz dpkg-source: info: building kmer in ../kmer_0~20150903+r2013-10.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/kmer-8W5TPl/kmer-0~20150903+r2013' # The Makefile apparently doesn't use regular LDFLAGS. # It defines CLDFLAGS and CXXLDFLAGS as empty strings, so let's # use them here. /usr/bin/make install \ CLDFLAGS="-Wl,-z,relro -Wl,-z,now" \ CXXLDFLAGS="-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/kmer-8W5TPl/kmer-0~20150903+r2013' making ESTmapper/mergeCounts.C.d making ESTmapper/terminate.C.d making atac-driver/libatac/atacFeature.C.d making atac-driver/libatac/atacFeatureList.C.d making atac-driver/libatac/atacFile.C.d making atac-driver/libatac/atacFileStreamMerge.C.d making atac-driver/libatac/atacMatch.C.d making atac-driver/libatac/atacMatchList.C.d making atac-driver/libatac/atacMatchOrder.C.d making atac-driver/alignOverlap/overlap.C.d making atac-driver/alignOverlap/overlap-sort.C.d making atac-driver/alignOverlap/overlap-printAnno.C.d making atac-driver/alignOverlap/overlap-find.C.d making atac-driver/gapShifter/gapShifter.C.d making atac-driver/gapShifter/extractSequence.C.d making atac-driver/gapShifter/extractUnmapped.C.d making atac-driver/gapShifter/coalesceMatches.C.d making atac-driver/gapShifter/correctGaps.C.d making atac-driver/gapShifter/testAtac.C.d making atac-driver/gapShifter/cleanAtac.C.d making atac-driver/gapShifter/projectFeatures.C.d making atac-driver/lengthFilter/lengthFilter.C.d making atac-driver/matchExtender/matchExtender.C.d making atac-driver/matchExtender/matchExtender-dump.C.d making atac-driver/matchExtender/matchExtender-func.C.d making atac-driver/mismatchCounter/mismatchCounter.C.d making atac-driver/statsGenerator/statsGenerator.C.d making atac-driver/uniqueFilter/uniqueFilter.C.d making atac-driver/clumpMaker/clumpMaker.C.d making atac-driver/chainer/localalign/GF_ALN_dpaligner.C.d making atac-driver/chainer/localalign/GF_ALN_local.C.d making atac-driver/chainer/localalign/GF_ALN_overlap.C.d making atac-driver/chainer/localalign/GF_ALN_loverlapper.C.d making atac-driver/chainer/localalign/GF_ALN_pieceOlap.C.d making atac-driver/chainer/localalign/localAlignerInterfacemodule.C.d making atac-driver/chainer/halign/halign.C.d making atac-driver/chainer/halign/halignmodule.C.d making atac-driver/chimera/happy-clones-span-clumps.C.d making seatac/seatac.C.d making seatac/configuration.C.d making seatac/encodedQuery.C.d making seatac/hitMatrix.C.d making seatac/thr-search.C.d making seatac/thr-loader.C.d making seatac/thr-deadlock.C.d making seatac/hitMatrix-sort.C.d making leaff/leaff.C.d making leaff/blocks.C.d making leaff/dups.C.d making leaff/gc.C.d making leaff/partition.C.d making leaff/simseq.C.d making leaff/stats.C.d making meryl/args.C.d making meryl/binaryOp.C.d making meryl/build.C.d making meryl/build-threads.C.d making meryl/dump.C.d making meryl/estimate.C.d making meryl/merge.C.d making meryl/unaryOp.C.d making meryl/meryl.C.d making meryl/simple.C.d making meryl/mapMers.C.d making meryl/mapMers-depth.C.d making meryl/kmer-mask.C.d making seagen/searchGENOME.C.d making seagen/configuration.C.d making seagen/encodedQuery.C.d making seagen/thr-deadlock.C.d making seagen/thr-loader.C.d making seagen/thr-search.C.d making seagen/thr-output.C.d making seagen/hitMatrix-sort.C.d making seagen/aHit.C.d making seagen/hitConverter.C.d making seagen/filterEST.C.d making seagen/filterEST-complicated.C.d making seagen/filterMRNA.C.d making seagen/filterNULL.C.d making seagen/sortHits.C.d making seagen/filtertest.C.d making seagen/hitReader.C.d making seagen/hitMatrix.C.d making sim4dbutils/cleanPolishes.C.d making sim4dbutils/fixPolishesIID.C.d making sim4dbutils/comparePolishes.C.d making sim4dbutils/convertToAtac.C.d making sim4dbutils/convertToExtent.C.d making sim4dbutils/convertPolishes.C.d making sim4dbutils/detectChimera.C.d making sim4dbutils/depthOfPolishes.C.d making sim4dbutils/filterPolishes.C.d making sim4dbutils/headPolishes.C.d making sim4dbutils/mappedCoverage.C.d making sim4dbutils/mergePolishes.C.d making sim4dbutils/parseSNP.C.d making sim4dbutils/pickBestPolish.C.d making sim4dbutils/pickBestPair.C.d making sim4dbutils/pickUniquePolish.C.d making sim4dbutils/plotCoverageVsIdentity.C.d making sim4dbutils/removeDuplicate.C.d making sim4dbutils/sortPolishes.C.d making sim4dbutils/summarizePolishes.C.d making sim4dbutils/uniqPolishes.C.d making sim4dbutils/vennPolishes.C.d making sim4dbutils/realignPolishes.C.d making sim4dbutils/removeRedundant.C.d making sim4dbutils/reportAlignmentDifferences.C.d making sim4dbutils/s4p_overlap.C.d making sim4db/sim4th.C.d making snapper/snapper2.C.d making snapper/configuration.C.d making snapper/thr-search.C.d making snapper/thr-filter.C.d making snapper/thr-polish.C.d making snapper/thr-polish-dp.C.d making snapper/hitMatrix.C.d making snapper/hitMatrix-sort.C.d making tapper/tagger.C.d making tapper/tapper.C.d making tapper/tapperconvert.C.d making tapper/tappermerge.C.d making tapper/tappersort.C.d making tapper/tappererrorcorrect.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/align.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/extend.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/greedy.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/poly.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/splice.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/table.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/util.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-dump.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-existDB.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet.c.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.c.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet-colorspace.c.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/halign.c.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/reversecomplement.c.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/kmer.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaStdin.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqStdin.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/sffFile.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqFactory.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqCache.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/merStream.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/file.c.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/md5.c.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/palloc.c.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/qsort_mt.c.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.c.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bigQueue.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/fibonacciNumbers.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/readBuffer.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/speedCounter.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.C.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.c.d gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.c: In function ‘mtRandomGaussian’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.c:166:34: warning: variable ‘y2’ set but not used [-Wunused-but-set-variable] 166 | double x1=0, x2=0, w=0, y1=0, y2=0; | ^~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test.c gcc -Wl,-z,relro -Wl,-z,now -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test.o -pthread -ldl -lm /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test | diff - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.out > /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/diffs 2>&1 if test -s /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/diffs ; then echo 'MT19937: TEST FAILED'; else echo 'MT19937: Test Passed'; fi MT19937: Test Passed touch /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/test.c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar-test | diff - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.out making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/test.c.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/dict.c.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/except.c.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/hash.c.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/list.c.d making /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/sfx.c.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ESTmapper/mergeCounts.o -c ESTmapper/mergeCounts.C ESTmapper/mergeCounts.C: In function ‘int main(int, char**)’: ESTmapper/mergeCounts.C:33:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 33 | fgets(buf, 256, Fs[i]); | ~~~~~^~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o ESTmapper/mergeCounts ESTmapper/mergeCounts.o -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ESTmapper/terminate.o -c ESTmapper/terminate.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from ESTmapper/terminate.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ ESTmapper/terminate.C: In member function ‘void iidReaderWriter::load(uint32)’: ESTmapper/terminate.C:82:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 82 | fscanf(inFile, uint32FMT, &iid); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ ESTmapper/terminate.C:85:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85 | fscanf(inFile, uint32FMT, &iid); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C: In member function ‘void sim4command::finalize()’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C:147:6: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 147 | if (_genLo > _genHi) | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C: In member function ‘char* sim4command::getESTheader()’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C:184:22: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 184 | static char *xxx = "anonymous cDNA sequence"; | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C: In member function ‘char* sim4command::getGENheader()’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.C:222:15: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 222 | char *xxx = "anonymous genomic sequence"; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.H:8, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.C:2: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C: In member function ‘void Sim4::IDISPLAY(sim4polishBuilder&, char*, char*, char*, char*, int, int, int*, int, int, int, Exon*)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C:681:30: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 681 | builder.addExonAlignment("Empty exon list; no alignment possible!", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C:682:30: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 682 | "Empty exon list; no alignment possible!"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C:694:30: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 694 | builder.addExonAlignment("Alignment fragment not found; no alignment possible!", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.C:695:30: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 695 | "Alignment fragment not found; no alignment possible!"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/align.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/align.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/align.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/align.C: In member function ‘void Sim4::path(int, int, char, int, int, char, int, edit_script**, edit_script**)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/align.C:777:13: warning: ‘head2’ may be used uninitialized [-Wmaybe-uninitialized] 777 | if (head2) *tail = tail2; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/align.C:557:38: note: ‘head2’ declared here 557 | edit_script *head1, *tail1, *head2, *tail2; | ^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/extend.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/extend.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/extend.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C: In function ‘void readModel(Fixed_Length_ICM_t*, const char*)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C:53:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 53 | fread (line, sizeof (char), ID_STRING_LEN, fp); // skip the text header line | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.C:84:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 84 | fread ((*fixed).permutation, sizeof (int), (*fixed).length, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/greedy.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/greedy.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/greedy.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.C:2: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/poly.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/poly.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/poly.C:2: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites.C:4: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites.C: In function ‘int readtree(Sim4*, char*, tree*, int)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites.C:452:6: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] 452 | int len; | ^~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites.C: In function ‘int Is_Cod_NonCod(const int*, double*, int)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites.C:751:12: warning: ‘scores’ may be used uninitialized [-Wmaybe-uninitialized] 751 | double *scores; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/splice.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/splice.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/splice.C:2: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/table.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/table.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/table.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/table.C: In member function ‘void Sim4::bld_table(char*, int, mss_t, int)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/table.C:112:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 112 | if (emer < 0) | ^~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/table.C:115:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 115 | ecode <<= 2; | ^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/util.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/util.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/util.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C:249:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 249 | fprintf(stderr, "s4p_compareExons()-- Can't allocate "uint32FMT" + "uint32FMT" words for counting exons.\n%s\n", A->_numExons, B->_numExons, strerror(errno)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C:249:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 249 | fprintf(stderr, "s4p_compareExons()-- Can't allocate "uint32FMT" + "uint32FMT" words for counting exons.\n%s\n", A->_numExons, B->_numExons, strerror(errno)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C:365:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 365 | fprintf(stderr, "s4p_compareExons()-- Can't allocate "uint32FMT" + "uint32FMT" words for counting exons.\n%s\n", A->_numExons, B->_numExons, strerror(errno)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.C:365:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 365 | fprintf(stderr, "s4p_compareExons()-- Can't allocate "uint32FMT" + "uint32FMT" words for counting exons.\n%s\n", A->_numExons, B->_numExons, strerror(errno)); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:58:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | sprintf(gpp, "%c"uint32FMT" ", gaptyp, gapcnt); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:68:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | sprintf(gpp, "%c"uint32FMT" ", gaptyp, gapcnt); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:80:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 80 | sprintf(gpp, "%c"uint32FMT" ", gaptyp, gapcnt); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:91:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | sprintf(gpp, "%c"uint32FMT"", gaptyp, gapcnt); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:163:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 163 | fprintf(stderr, "sim4reader: Unknown matchOrientation '"uint32FMT"' in printPolish()\n", _matchOrientation); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:176:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 176 | fprintf(stderr, "sim4reader: Unknown strandOrientation '"uint32FMT"' in printPolish()\n", _matchOrientation); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:88: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:100: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:181:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | sprintf(outc, "sim4begin\n"uint32FMT"["uint32FMT"-"uint32FMT"-"uint32FMT"] "uint32FMT"["uint32FMT"-"uint32FMT"] <"uint32FMT"-"uint32FMT"-"uint32FMT"-%s-%s>\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:212:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | sprintf(outc, ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">%s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:323:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 323 | fprintf(stderr, "sim4reader: Unknown strandOrientation '"uint32FMT"' in printPolishGFF3()\n", _matchOrientation); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:346:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 346 | sprintf(outc, uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:346:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 346 | sprintf(outc, uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:346:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 346 | sprintf(outc, uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:350:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 350 | sprintf(outc, "ID=sim4db"uint32FMT";Name="uint32FMT":%s;Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:350:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 350 | sprintf(outc, "ID=sim4db"uint32FMT";Name="uint32FMT":%s;Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:350:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 350 | sprintf(outc, "ID=sim4db"uint32FMT";Name="uint32FMT":%s;Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:350:76: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 350 | sprintf(outc, "ID=sim4db"uint32FMT";Name="uint32FMT":%s;Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:350:91: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 350 | sprintf(outc, "ID=sim4db"uint32FMT";Name="uint32FMT":%s;Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:354:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 354 | sprintf(outc, "targetLen="uint32FMT";pA="uint32FMT";pT="uint32FMT";genRegion="uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:354:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 354 | sprintf(outc, "targetLen="uint32FMT";pA="uint32FMT";pT="uint32FMT";genRegion="uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:354:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 354 | sprintf(outc, "targetLen="uint32FMT";pA="uint32FMT";pT="uint32FMT";genRegion="uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:354:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 354 | sprintf(outc, "targetLen="uint32FMT";pA="uint32FMT";pT="uint32FMT";genRegion="uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:354:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 354 | sprintf(outc, "targetLen="uint32FMT";pA="uint32FMT";pT="uint32FMT";genRegion="uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:363:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 363 | sprintf(outc, uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:363:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 363 | sprintf(outc, uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:363:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 363 | sprintf(outc, uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:368:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 368 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;Gap=%s;nMatches="uint32FMT"", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:368:45: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 368 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;Gap=%s;nMatches="uint32FMT"", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:368:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 368 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;Gap=%s;nMatches="uint32FMT"", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:368:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 368 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;Gap=%s;nMatches="uint32FMT"", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:368:91: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 368 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;Gap=%s;nMatches="uint32FMT"", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:371:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;nMatches="uint32FMT"", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:371:45: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;nMatches="uint32FMT"", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:371:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;nMatches="uint32FMT"", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:371:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;nMatches="uint32FMT"", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.C:371:91: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | sprintf(outc, "Parent=sim4db"uint32FMT";Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c;nMatches="uint32FMT"", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C:46:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(stderr, "sim4reader: Got '%s', expecting 'sim4begin' at byte "uint64FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C:65:2: warning: #warning LAZY PROGRAMMER did not extend an array [-Wcpp] 65 | #warning LAZY PROGRAMMER did not extend an array | ^~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C:126:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 126 | fprintf(stderr, "sim4reader: Got '%s', expecting GFF3 mRNA line at byte "uint64FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.C:150:2: warning: #warning LAZY PROGRAMMER did not extend an array [-Wcpp] 150 | #warning LAZY PROGRAMMER did not extend an array | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:104: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:42:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | uint32 r = sscanf(lines[cl], ""uint32FMT"["uint32FMT" "uint32FMT" "uint32FMT"] "uint32FMT"["uint32FMT" "uint32FMT"] <"uint32FMT" "uint32FMT" "uint32FMT" %s %s>", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:55:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "sim4polish::s4p_linesToPolishS4DB()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:72:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 72 | fprintf(stderr, "sim4polish::s4p_linesToPolishS4DB()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "sim4polish::s4p_linesToPolishS4DB()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:76: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:127:102: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | while (sscanf(lines[cl], ""uint32FMT"-"uint32FMT" ("uint32FMT"-"uint32FMT") <"uint32FMT"-"uint32FMT"-"uint32FMT">", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:169:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(stderr, "sim4polish::s4p_linesToPolishS4DB()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:243:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:243:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:243:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:243:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\tmRNA\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:246:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 246 | fprintf(stderr, "sim4polish::s4p_linesToPolishGFF3()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:275:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 275 | r = sscanf(crttok, "ID=sim4db"uint32FMT"", &matchID); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:280:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 280 | r = sscanf(crttok, "Name="uint32FMT":%s", &_estID, _estDefLine); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:285:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 285 | r = sscanf(crttok, "Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c", &_estID, _estDefLine, &dummy1, &dummy2, &mOri); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:285:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 285 | r = sscanf(crttok, "Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c", &_estID, _estDefLine, &dummy1, &dummy2, &mOri); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:285:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 285 | r = sscanf(crttok, "Target="uint32FMT":%s "uint32FMT" "uint32FMT" %c", &_estID, _estDefLine, &dummy1, &dummy2, &mOri); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:293:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 293 | r = sscanf(crttok, "targetLen="uint32FMT"", &_estLen); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:296:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 296 | r = sscanf(crttok, "pA="uint32FMT"", &_estPolyA); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:299:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 299 | r = sscanf(crttok, "pT="uint32FMT"", &_estPolyT); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:302:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 302 | r = sscanf(crttok, "genRegion="uint32FMT"-"uint32FMT"", &_genRegionOffset, &dummy1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:302:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 302 | r = sscanf(crttok, "genRegion="uint32FMT"-"uint32FMT"", &_genRegionOffset, &dummy1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:313:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 313 | fprintf(stderr, "sim4polish::s4p_linesToPolishGFF3()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:339:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:339:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:339:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:339:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | r = sscanf(lines[cl], ""uint32FMT":%s\tsim4db\texon\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t.\t", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:342:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 342 | fprintf(stderr, "sim4polish::s4p_linesToPolishGFF3()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:366:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 366 | r = sscanf(crttok, "Parent=sim4db"uint32FMT"", &dummy1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:370:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 370 | r = sscanf(crttok, "Target=%s "uint32FMT" "uint32FMT" %c", &dummybuf, &exon._estFrom, &exon._estTo, &mOri); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:370:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 370 | r = sscanf(crttok, "Target=%s "uint32FMT" "uint32FMT" %c", &dummybuf, &exon._estFrom, &exon._estTo, &mOri); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:377:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 377 | r = sscanf(crttok, "nMatches="uint32FMT"", &exon._numMatches); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:403:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 403 | fprintf(stderr, "sim4polish::s4p_linesToPolishGFF3()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:437:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 437 | fprintf(stderr, "sim4polish::s4p_linesToPolishGFF3()-- byte "uint32FMT": '%s'\n", startPosition, lines[cl]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C: In member function ‘void sim4polish::s4p_linesToPolishS4DB(uint32, uint32, char**, uint32*)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:140:13: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class sim4polishExon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 140 | memcpy(nnn, _exons, sizeof(sim4polishExon) * _numExons); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:49:7: note: ‘class sim4polishExon’ declared here 49 | class sim4polishExon { | ^~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C: In member function ‘void sim4polish::s4p_linesToPolishGFF3(uint32, uint32, char**, uint32*)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:261:5: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 261 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:261:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 261 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:262:5: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 262 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:262:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 262 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:263:5: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 263 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:263:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 263 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:264:5: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 264 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:264:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 264 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:265:5: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 265 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:265:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 265 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:266:5: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 266 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:266:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 266 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:267:5: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 267 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:267:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 267 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:268:5: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 268 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:268:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 268 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:346:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32’ {aka ‘unsigned int’} [-Wsign-compare] 346 | if ((dummy1 != _genID) || strcmp(dummybuf, _genDefLine) || | ~~~~~~~^~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:347:40: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 347 | (sOri != '+') && (sOri != '-') && (sOri != '.')) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:352:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 352 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:352:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 352 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:353:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 353 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:353:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 353 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:354:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 354 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:354:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 354 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:355:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 355 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:355:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 355 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:356:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 356 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:356:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 356 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:357:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 357 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:357:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 357 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:358:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 358 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:358:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 358 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:359:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 359 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:359:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 359 | while (*clptr!='\t') clptr++; clptr++; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:370:30: warning: format ‘%s’ expects argument of type ‘char*’, but argument 3 has type ‘char (*)[1000]’ [-Wformat=] 370 | r = sscanf(crttok, "Target=%s "uint32FMT" "uint32FMT" %c", &dummybuf, &exon._estFrom, &exon._estTo, &mOri); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ | | | char (*)[1000] /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:383:39: warning: format ‘%s’ expects argument of type ‘char*’, but argument 3 has type ‘char (*)[1000]’ [-Wformat=] 383 | r = sscanf(crttok, "intron=%s", &dummybuf); | ~^ ~~~~~~~~~ | | | | | char (*)[1000] | char* /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.C:414:13: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class sim4polishExon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 414 | memcpy(nnn, _exons, sizeof(sim4polishExon) * _numExons); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:49:7: note: ‘class sim4polishExon’ declared here 49 | class sim4polishExon { | ^~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.C:2: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C: In member function ‘sim4polish* sim4polishBuilder::release()’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C:246:11: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class sim4polishExon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 246 | memcpy(it->_exons + i, ex[i], sizeof(sim4polishExon)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:49:7: note: ‘class sim4polishExon’ declared here 49 | class sim4polishExon { | ^~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Failed to reposition %s to record "uint32FMT", only "uint32FMT" records\n", _path, ordinal, _polishRecordLen), exit(1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:120:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Failed to reposition %s to record "uint32FMT", only "uint32FMT" records\n", _path, ordinal, _polishRecordLen), exit(1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:248:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stderr, "polishes: "uint32FMT"\r", _polishRecordLen); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C: In member function ‘void sim4polishFile::loadIndex()’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:141:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 141 | fread(&magic, sizeof(char), 8, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:145:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 145 | fread(&_polishRecordLen, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:151:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 151 | fread( _polishRecord, sizeof(polishRecord), _polishRecordLen, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:152:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 152 | fread( _polishRecordEST, sizeof(uint32), _polishRecordLen, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:153:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 153 | fread( _polishRecordGEN, sizeof(uint32), _polishRecordLen, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:155:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | fread(&_maxEST, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:156:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 156 | fread(&_maxGEN, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:161:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 161 | fread( _ESTiidLocation, sizeof(uint32), _maxEST, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.C:162:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 162 | fread( _GENiidLocation, sizeof(uint32), _maxGEN, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ rm -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a && ar ruvs /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/align.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/extend.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/greedy.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/poly.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/splice.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/table.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/util.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4command.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4parameters.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4string.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/Xtend1.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/align.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/exon_cores.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/extend.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/glimmerSplice.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/greedy.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/mspManager.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/pluri_align.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/poly.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1a.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-1.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-2.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-3.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1-4.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sim4b1_s.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_donor.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_acceptor.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/sites_score.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/splice.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/table.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4core/util.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-compare.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-copy.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-deleteexon.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-exons.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-polishtostring.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-read.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-stringtopolish.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish-updatescores.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishList.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishBuilder.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishFile.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishReader.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polishWriter.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.C:151:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 151 | fprintf(stderr, "fastaFile::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.C:151:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 151 | fprintf(stderr, "fastaFile::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.C:252:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 252 | fprintf(stderr, "fastaFile::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.C:252:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 252 | fprintf(stderr, "fastaFile::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.C: In member function ‘void fastaFile::loadIndex(char*)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.C:357:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 357 | fread(&_header, sizeof(fastaFileHeader), 1, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.C:379:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 379 | fread(_index, sizeof(fastaFileIndex), _header._numberOfSequences, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.C:380:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 380 | fread(_names, sizeof(char), _header._namesLength, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaStdin.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaStdin.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaStdin.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaStdin.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaStdin.C: In member function ‘virtual bool fastaStdin::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaStdin.C:110:9: warning: unused variable ‘ret’ [-Wunused-variable] 110 | bool ret = true; | ^~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.C:141:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 141 | fprintf(stderr, "fastqFile::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.C:141:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 141 | fprintf(stderr, "fastqFile::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.C:253:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 253 | fprintf(stderr, "fastqFile::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.C:253:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 253 | fprintf(stderr, "fastqFile::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.C:533:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 533 | fprintf(stderr, "REALLOC len="uint32FMT" from "uint32FMT" to "uint32FMT"\n", indexLen, indexMax, indexMax * 2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.C:533:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 533 | fprintf(stderr, "REALLOC len="uint32FMT" from "uint32FMT" to "uint32FMT"\n", indexLen, indexMax, indexMax * 2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.C:533:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 533 | fprintf(stderr, "REALLOC len="uint32FMT" from "uint32FMT" to "uint32FMT"\n", indexLen, indexMax, indexMax * 2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.C: In member function ‘void fastqFile::loadIndex(char*)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.C:354:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 354 | fread(&_header, sizeof(fastqFileHeader), 1, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.C:374:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 374 | fread(_index, sizeof(fastqFileIndex), _header._numberOfSequences, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.C:375:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 375 | fread(_names, sizeof(char), _header._namesLength, I); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqStdin.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqStdin.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqStdin.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqStdin.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqStdin.C: In member function ‘virtual bool fastqStdin::getSequence(uint32, char*&, uint32&, uint32&, char*&, uint32&, uint32&)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqStdin.C:110:9: warning: unused variable ‘ret’ [-Wunused-variable] 110 | bool ret = true; | ^~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:2: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:129:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "seqStore::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:129:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "seqStore::getSequence(full)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:197:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 197 | fprintf(stderr, "seqStore::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:197:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 197 | fprintf(stderr, "seqStore::getSequence(part)-- iid "uint32FMT" more than number of sequences "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:203:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "seqStore::getSequence(part)-- for iid "uint32FMT"; invalid bgn="uint32FMT" end="uint32FMT"; seqLen="uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:203:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "seqStore::getSequence(part)-- for iid "uint32FMT"; invalid bgn="uint32FMT" end="uint32FMT"; seqLen="uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:203:96: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "seqStore::getSequence(part)-- for iid "uint32FMT"; invalid bgn="uint32FMT" end="uint32FMT"; seqLen="uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:203:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "seqStore::getSequence(part)-- for iid "uint32FMT"; invalid bgn="uint32FMT" end="uint32FMT"; seqLen="uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:463:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 463 | fprintf(stderr, "constructSeqStore()-- sequence %s too long, must be shorter than "uint64FMT" Gbp.\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:467:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 467 | fprintf(stderr, "constructSeqStore()-- too many sequences, must be fewer than "uint64FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:620:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 620 | fprintf(stderr, "constructSeqStore()-- seqStore '%s' constructed ("uint32FMT" sequences, "uint64FMT" ACGT letters, "uint32FMT" ACGT blocks, "uint32FMT" GAP blocks).\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:620:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 620 | fprintf(stderr, "constructSeqStore()-- seqStore '%s' constructed ("uint32FMT" sequences, "uint64FMT" ACGT letters, "uint32FMT" ACGT blocks, "uint32FMT" GAP blocks).\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:620:102: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 620 | fprintf(stderr, "constructSeqStore()-- seqStore '%s' constructed ("uint32FMT" sequences, "uint64FMT" ACGT letters, "uint32FMT" ACGT blocks, "uint32FMT" GAP blocks).\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:620:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 620 | fprintf(stderr, "constructSeqStore()-- seqStore '%s' constructed ("uint32FMT" sequences, "uint64FMT" ACGT letters, "uint32FMT" ACGT blocks, "uint32FMT" GAP blocks).\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C: In function ‘void constructSeqStore(char*, seqCache*)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:410:9: warning: ‘memset’ used with constant zero length parameter; this could be due to transposed parameters [-Wmemset-transposed-args] 410 | memset(&HEAD, sizeof(seqStoreHeader), 0); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C: In constructor ‘seqStore::seqStore(const char*)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:21:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 21 | fread(&_header, sizeof(seqStoreHeader), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C: In member function ‘virtual seqFile* seqStore::openFile(const char*)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:73:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 73 | fread(&magic1, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:74:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 74 | fread(&magic2, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C: In member function ‘void seqStore::loadIndex()’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:318:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 318 | fread(&_header, sizeof(seqStoreHeader), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:329:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 329 | fread( _index, sizeof(seqStoreIndex), _header._numberOfSequences, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:343:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 343 | fread( _block, sizeof(seqStoreBlock), _header._numberOfBlocks, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.C:347:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 347 | fread( _names, sizeof(char), _header._namesLength, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/sffFile.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/sffFile.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/sffFile.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/sffFile.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqFactory.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqFactory.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqFactory.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqFactory.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqFactory.C:3: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqCache.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqCache.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqCache.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqCache.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqCache.C:171:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stderr, "seqCache::loadAllSequences()-- Failed to load iid "uint32FMT".\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqFactory.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.C:2: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.C:236:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 236 | fprintf(stderr, "seqStream::setRange()-- ERROR: range ("uint64FMT","uint64FMT") too big; only "uint64FMT" positions.\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.C:236:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 236 | fprintf(stderr, "seqStream::setRange()-- ERROR: range ("uint64FMT","uint64FMT") too big; only "uint64FMT" positions.\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.C:236:82: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 236 | fprintf(stderr, "seqStream::setRange()-- ERROR: range ("uint64FMT","uint64FMT") too big; only "uint64FMT" positions.\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.C:268:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 268 | fprintf(stderr, "seqStream::sequenceNumberOfPosition()-- WARNING: position p="uint64FMT" too big; only "uint64FMT" positions.\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.C:268:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 268 | fprintf(stderr, "seqStream::sequenceNumberOfPosition()-- WARNING: position p="uint64FMT" too big; only "uint64FMT" positions.\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.C:340:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 340 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #1 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.C:340:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 340 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #1 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.C:340:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 340 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #1 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.C:386:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 386 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #2 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.C:386:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 386 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #2 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.C:386:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 386 | fprintf(stderr, "seqStream::fillBuffer()-- Failed to getSequence(part) #2 iid="uint32FMT" bgn="uint32FMT" end="uint32FMT"\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/merStream.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/merStream.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/merStream.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/merStream.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqCache.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C:3: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-correctSequence.H:33:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stderr, "generateCorrectSequence()-- Using seed "uint32FMT"\n", seed); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C:15:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 15 | fprintf(stderr, "testID:"uint32FMT" - empty sequence\n", testID); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C:22:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 22 | fprintf(stderr, "testID:"uint32FMT" - header differs '%s' vs '%s'\n", testID, S->header(), correctSequence[sid].header); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C:26:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 26 | fprintf(stderr, "testID:"uint32FMT" - header length differs "uint32FMT" vs "uint32FMT"\n", testID, S->headerLength(), correctSequence[sid].headerLength); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C:26:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 26 | fprintf(stderr, "testID:"uint32FMT" - header length differs "uint32FMT" vs "uint32FMT"\n", testID, S->headerLength(), correctSequence[sid].headerLength); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C:26:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 26 | fprintf(stderr, "testID:"uint32FMT" - header length differs "uint32FMT" vs "uint32FMT"\n", testID, S->headerLength(), correctSequence[sid].headerLength); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C:30:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 30 | fprintf(stderr, "testID:"uint32FMT" - sequence differs\n", testID); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C:34:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs strlen "uint32FMT" vs "uint32FMT"\n", testID, (uint32)strlen(S->sequence()), correctSequence[sid].sequenceLength); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C:34:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs strlen "uint32FMT" vs "uint32FMT"\n", testID, (uint32)strlen(S->sequence()), correctSequence[sid].sequenceLength); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C:34:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs strlen "uint32FMT" vs "uint32FMT"\n", testID, (uint32)strlen(S->sequence()), correctSequence[sid].sequenceLength); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C:38:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 38 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs "uint32FMT" vs "uint32FMT"\n", testID, S->sequenceLength(), correctSequence[sid].sequenceLength); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C:38:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 38 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs "uint32FMT" vs "uint32FMT"\n", testID, S->sequenceLength(), correctSequence[sid].sequenceLength); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.C:38:77: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 38 | fprintf(stderr, "testID:"uint32FMT" - sequence length differs "uint32FMT" vs "uint32FMT"\n", testID, S->sequenceLength(), correctSequence[sid].sequenceLength); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqCache.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:3: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-correctSequence.H:33:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stderr, "generateCorrectSequence()-- Using seed "uint32FMT"\n", seed); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:17:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | fprintf(stderr, "testIndexing()-- numSeq="uint32FMT" sep=%c sepLen="uint32FMT"\n", numSeq, sep, sepLen); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:17:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | fprintf(stderr, "testIndexing()-- numSeq="uint32FMT" sep=%c sepLen="uint32FMT"\n", numSeq, sep, sepLen); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:55:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "lengthOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:55:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "lengthOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:55:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "lengthOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:60:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 60 | fprintf(stderr, "startOf "uint32FMT" returned "uint64FMT", not correct "uint64FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:60:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 60 | fprintf(stderr, "startOf "uint32FMT" returned "uint64FMT", not correct "uint64FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:60:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 60 | fprintf(stderr, "startOf "uint32FMT" returned "uint64FMT", not correct "uint64FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:65:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(stderr, "IIDOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:65:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(stderr, "IIDOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:65:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(stderr, "IIDOf "uint32FMT" returned "uint32FMT", not correct "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:74:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 74 | fprintf(stderr, "sequenceNumberOfPosition "uint64FMT" returned "uint32FMT", not correct "uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:74:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 74 | fprintf(stderr, "sequenceNumberOfPosition "uint64FMT" returned "uint32FMT", not correct "uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:74:82: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 74 | fprintf(stderr, "sequenceNumberOfPosition "uint64FMT" returned "uint32FMT", not correct "uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:95:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 95 | fprintf(stderr, "wrong separator at sep "uint32FMT" got %d expected %d\n", x, s, sep); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:124:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- letter wrong got'%c'\n", sp, si, st, ch, chainSeq[sib]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:124:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- letter wrong got'%c'\n", sp, si, st, ch, chainSeq[sib]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:124:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- letter wrong got'%c'\n", sp, si, st, ch, chainSeq[sib]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:128:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqPos wrong got "uint32FMT"\n", sp, si, st, ch, chainSeqPos[sib]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:128:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqPos wrong got "uint32FMT"\n", sp, si, st, ch, chainSeqPos[sib]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:128:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqPos wrong got "uint32FMT"\n", sp, si, st, ch, chainSeqPos[sib]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:128:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqPos wrong got "uint32FMT"\n", sp, si, st, ch, chainSeqPos[sib]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:132:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqIID wrong got"uint32FMT"\n", sp, si, st, ch, chainSeqIID[sib]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:132:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqIID wrong got"uint32FMT"\n", sp, si, st, ch, chainSeqIID[sib]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:132:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqIID wrong got"uint32FMT"\n", sp, si, st, ch, chainSeqIID[sib]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:132:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- seqIID wrong got"uint32FMT"\n", sp, si, st, ch, chainSeqIID[sib]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:136:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- strPos wrong got "uint64FMT"\n", sp, si, st, ch, chainStrPos[sib]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:136:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- strPos wrong got "uint64FMT"\n", sp, si, st, ch, chainStrPos[sib]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:136:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- strPos wrong got "uint64FMT"\n", sp, si, st, ch, chainStrPos[sib]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:136:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "sp="uint32FMT" si="uint32FMT" st="uint64FMT" ch=%c -- strPos wrong got "uint64FMT"\n", sp, si, st, ch, chainStrPos[sib]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:145:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 145 | fprintf(stderr, "iterated length wrong; sib="uint32FMT" sie="uint32FMT"\n", sib, sie); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:145:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 145 | fprintf(stderr, "iterated length wrong; sib="uint32FMT" sie="uint32FMT"\n", sib, sie); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:159:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 159 | fprintf(stderr, "testChaining()-- numSeq="uint32FMT" sep=%c sepLen="uint32FMT"\n", numSeq, sep, sepLen); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.C:159:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 159 | fprintf(stderr, "testChaining()-- numSeq="uint32FMT" sep=%c sepLen="uint32FMT"\n", numSeq, sep, sepLen); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqCache.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:3: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-correctSequence.H:33:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stderr, "generateCorrectSequence()-- Using seed "uint32FMT"\n", seed); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-correctSequence.H:34:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(stderr, "generateCorrectSequence()-- Generating "uint32FMT" sequences of length "uint32FMT" to "uint32FMT"\n", numSeq, minLen, maxLen); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:11:2: warning: #warning HOW DO WE TEST IF WE GET ALL THE MERS? [-Wcpp] 11 | #warning HOW DO WE TEST IF WE GET ALL THE MERS? | ^~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:33:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stdout, "MS pos="uint32FMT" posInSeq="uint64FMT" posInStr="uint64FMT" seqNum="uint64FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:33:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stdout, "MS pos="uint32FMT" posInSeq="uint64FMT" posInStr="uint64FMT" seqNum="uint64FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:33:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stdout, "MS pos="uint32FMT" posInSeq="uint64FMT" posInStr="uint64FMT" seqNum="uint64FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:33:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 33 | fprintf(stdout, "MS pos="uint32FMT" posInSeq="uint64FMT" posInStr="uint64FMT" seqNum="uint64FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:39:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(stdout, "MS pos="uint32FMT" failed '%s' != '%s'.\n", pos, testmer, seq + pos); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:124:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "mer stream position out of range; at "uint32FMT", range "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:124:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "mer stream position out of range; at "uint32FMT", range "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:124:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "mer stream position out of range; at "uint32FMT", range "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C: In function ‘int main(int, char**)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:223:33: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 223 | testMerStreamSimple(MS, 20, "GGGTCAACTCCGCCCGCACTCTAGC", SP); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:225:33: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 225 | testMerStreamSimple(MS, 20, "GGGTCAACTCCGCCCGCACTCTAGC", SP); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:228:33: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 228 | testMerStreamSimple(MS, 20, "GGGTCAACTCCGCCCGCACTCTAGC", SP); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:243:33: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 243 | testMerStreamSimple(MS, 20, "GATCACTCGCGCACTCTAGCA", SP); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:245:33: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 245 | testMerStreamSimple(MS, 20, "GATCACTCGCGCACTCTAGCA", SP); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.C:248:33: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 248 | testMerStreamSimple(MS, 20, "GATCACTCGCGCACTCTAGCA", SP); | ^~~~~~~~~~~~~~~~~~~~~~~ rm -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a && ar ruvs /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaStdin.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqStdin.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/sffFile.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqFactory.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqCache.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/merStream.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaFile.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastaStdin.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqFile.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/fastqStdin.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStore.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/sffFile.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqFactory.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqCache.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/seqStream.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/merStream.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet-colorspace.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet-colorspace.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/halign.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/halign.c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/halign.c: In function ‘align_path’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/halign.c:385:7: warning: ‘head2’ may be used uninitialized [-Wmaybe-uninitialized] 385 | if (head2) *tail = tail2; | ^~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/halign.c:163:32: note: ‘head2’ declared here 163 | edit_script *head1, *tail1, *head2, *tail2; | ^~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/reversecomplement.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/reversecomplement.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/kmer.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/kmer.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/kmer.H:28, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/kmer.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/kmer.H:29: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ rm -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a && ar ruvs /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet-colorspace.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/halign.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/reversecomplement.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/kmer.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet-acgtspace.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/alphabet-colorspace.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/halign.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/reversecomplement.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/kmer.o gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/file.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/file.c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/file.c: In function ‘openFile’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/file.c:382:9: warning: variable ‘isRW’ set but not used [-Wunused-but-set-variable] 382 | int isRW = 1; | ^~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/md5.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/md5.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/palloc.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/palloc.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/qsort_mt.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/qsort_mt.c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/qsort_mt.c: In function ‘swapfunc’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/qsort_mt.c:72:1: warning: old-style function definition [-Wold-style-definition] 72 | swapfunc(a, b, n, swaptype) | ^~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/qsort_mt.c: In function ‘qsort_algo’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/qsort_mt.c:264:13: warning: variable ‘id’ set but not used [-Wunused-but-set-variable] 264 | pthread_t id; | ^~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/qsort_mt.c: In function ‘qsort_thread’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/qsort_mt.c:370:13: warning: variable ‘id’ set but not used [-Wunused-but-set-variable] 370 | pthread_t id; | ^~ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bigQueue.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bigQueue.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bigQueue.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bigQueue.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bigQueue.C: In member function ‘void bigQueue::mergeTemporaryFiles()’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bigQueue.C:204:16: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 204 | fread(thing, _objectSize, 1, _temporaryFiles[i]); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bigQueue.C:255:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 255 | fread(thing, _objectSize, 1, _temporaryFiles[fileid]); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bigQueue.C: In member function ‘bool bigQueue::next()’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bigQueue.C:302:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 302 | fread(_thingBuffer, _objectSize, 1, _temporaryFiles[0]); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.C:8: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.C:35:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(stderr, "bitPackedArray::get()-- element index "uint64FMT" is out of range, only "uint64FMT" elements.\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.C:35:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(stderr, "bitPackedArray::get()-- element index "uint64FMT" is out of range, only "uint64FMT" elements.\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.C:168:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 168 | fprintf(stderr, " at position "uint64HEX"\n", file_offset); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.C:367:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 367 | fprintf(stderr, "bitPackedFile::seekNormal() '%s' seek to pos="uint64FMT" failed: %s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.C:376:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 376 | fprintf(stderr, "bitPackedFile::seekNormal() '%s' read of "uint64FMT" bytes failed': %s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.C: In constructor ‘bitPackedFile::bitPackedFile(const char*, uint64, bool)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.C:109:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 109 | write(_file, t, sizeof(char) * 16); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.C:110:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 110 | write(_file, &at, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.C:111:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | write(_file, &bt, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.C: In member function ‘void bitPackedFile::flushDirty()’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.C:232:8: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 232 | write(_file, _bfr, sizeof(uint64) * _bfrmax); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/fibonacciNumbers.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/fibonacciNumbers.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/fibonacciNumbers.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/readBuffer.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/readBuffer.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/readBuffer.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/readBuffer.C:132:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "readBuffer::fillBuffer()-- only read "uint64FMT" bytes, couldn't read "uint64FMT" bytes from '%s': %s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/readBuffer.C:132:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "readBuffer::fillBuffer()-- only read "uint64FMT" bytes, couldn't read "uint64FMT" bytes from '%s': %s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/readBuffer.C:165:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 165 | fprintf(stderr, "readBuffer()-- '%s' couldn't seek to position "int64FMT": %s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/readBuffer.C:228:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 228 | fprintf(stderr, "readBuffer()-- couldn't read "uint64FMT" bytes from '%s': n%s\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:227:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 227 | fprintf(stderr, "recordFile::seek() '%s' seek to record="uint64FMT" at fileposition="uint64FMT" failed: %s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:227:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 227 | fprintf(stderr, "recordFile::seek() '%s' seek to record="uint64FMT" at fileposition="uint64FMT" failed: %s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:233:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 233 | fprintf(stderr, "recordFile::seek() '%s' read of "uint64FMT" bytes failed at record "uint64FMT", fileposition "uint64FMT"': %s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:233:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 233 | fprintf(stderr, "recordFile::seek() '%s' read of "uint64FMT" bytes failed at record "uint64FMT", fileposition "uint64FMT"': %s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:233:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 233 | fprintf(stderr, "recordFile::seek() '%s' read of "uint64FMT" bytes failed at record "uint64FMT", fileposition "uint64FMT"': %s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C: In constructor ‘recordFile::recordFile(const char*, uint32, uint32, char)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:68:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 68 | write(_file, &recordFileMagic1, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:69:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | write(_file, &recordFileMagic2, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:70:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | write(_file, &_numRecords, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:71:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 71 | write(_file, &_recordSize, sizeof(uint32)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:72:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | write(_file, &_headerSize, sizeof(uint32)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:73:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 73 | write(_file, _header, sizeof(char) * _headerSize); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:112:9: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 112 | read(_file, &m1, sizeof(uint64)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:113:9: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 113 | read(_file, &m2, sizeof(uint64)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:114:9: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 114 | read(_file, &_numRecords, sizeof(uint64)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:115:9: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 115 | read(_file, &_recordSize, sizeof(uint32)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:116:9: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 116 | read(_file, &_headerSize, sizeof(uint32)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:117:9: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 117 | read(_file, _header, sizeof(char) * _headerSize); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C: In destructor ‘recordFile::~recordFile()’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:151:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 151 | write(_file, &recordFileMagic1, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:152:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 152 | write(_file, &recordFileMagic2, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:153:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 153 | write(_file, &_numRecords, sizeof(uint64)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:154:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 154 | write(_file, &_recordSize, sizeof(uint32)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:155:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | write(_file, &_headerSize, sizeof(uint32)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:156:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 156 | write(_file, _header, sizeof(char) * _headerSize); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C: In member function ‘void recordFile::flushDirty()’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:197:8: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 197 | write(_file, _bfr, _recordSize * _rec); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C: In member function ‘void recordFile::seek(uint64, bool)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.C:231:7: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 231 | read(_file, _bfr, _recordSize * _bfrmax); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/speedCounter.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/speedCounter.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/speedCounter.C:4: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.H:7, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.C:127:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "sweatShop::setThreadData()-- worker ID "uint32FMT" more than number of workers="uint32FMT"\n", t, _numberOfWorkers), exit(1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.C:127:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "sweatShop::setThreadData()-- worker ID "uint32FMT" more than number of workers="uint32FMT"\n", t, _numberOfWorkers), exit(1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.C:390:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" loaded; "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" written; "uint64FMTW(8)" queued for output)\r", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.C:390:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" loaded; "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" written; "uint64FMTW(8)" queued for output)\r", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.C:390:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" loaded; "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" written; "uint64FMTW(8)" queued for output)\r", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.C:390:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" loaded; "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" written; "uint64FMTW(8)" queued for output)\r", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.C:390:135: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" loaded; "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" written; "uint64FMTW(8)" queued for output)\r", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.C:425:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 425 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" queued for output)\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.C:425:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 425 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" queued for output)\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.C:425:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 425 | fprintf(stderr, " %6.1f/s - "uint64FMTW(8)" queued for compute; "uint64FMTW(8)" finished; "uint64FMTW(8)" queued for output)\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.C:560:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 560 | fprintf(stderr, "sweatShop::run()-- Failed to launch worker thread "uint32FMT": %s.\n", i, strerror(err)), exit(1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.C:580:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 580 | fprintf(stderr, "sweatShop::run()-- Failed to join worker thread "uint32FMT": %s.\n", i, strerror(err)), exit(1); | ^ gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/dict.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/dict.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/except.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/except.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/hash.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/hash.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/list.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/list.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/sfx.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/sfx.c rm -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a && ar ruvs /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/file.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/md5.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/palloc.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/qsort_mt.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bigQueue.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/fibonacciNumbers.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/readBuffer.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/speedCounter.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/dict.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/except.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/hash.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/list.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/sfx.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/file.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/md5.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/palloc.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/qsort_mt.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bigQueue.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/fibonacciNumbers.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/readBuffer.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/speedCounter.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/sweatShop.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/dict.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/except.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/hash.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/list.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/sfx.o g++ -Wl,-z,relro -Wl,-z,now -o ESTmapper/terminate ESTmapper/terminate.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacFeature.o -c atac-driver/libatac/atacFeature.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacFeature.C:23: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacFeature.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.C:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "Feature longer than sequence (by "uint32FMT"bp): seqLen="uint32FMTW(8)" %s\n", | ^ atac-driver/libatac/atacFeature.C:109:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "Feature longer than sequence (by "uint32FMT"bp): seqLen="uint32FMTW(8)" %s\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacFeatureList.o -c atac-driver/libatac/atacFeatureList.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacFeatureList.C:23: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacFeatureList.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacFeatureList.C: In member function ‘void atacFeatureList::add(atacFeature&)’: atac-driver/libatac/atacFeatureList.C:50:52: warning: operation on ‘((atacFeatureList*)this)->atacFeatureList::_featuresLen’ may be undefined [-Wsequence-point] 50 | _features[_featuresLen].featureiid = _featuresLen++; | ~~~~~~~~~~~~^~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacFile.o -c atac-driver/libatac/atacFile.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacFile.C:23: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacFile.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacFile.C: In member function ‘void atacFileBase::readHeader(char*, FILE*)’: atac-driver/libatac/atacFile.C:255:7: warning: the address of ‘atacFileBase::_fileA’ will never be NULL [-Waddress] 255 | if (_fileA && _fileA[0]) { | ^~~~~~ atac-driver/libatac/atac.H:59:22: note: ‘atacFileBase::_fileA’ declared here 59 | char _fileA[1024]; // The name of our genome files | ^~~~~~ atac-driver/libatac/atacFile.C:262:7: warning: the address of ‘atacFileBase::_fileB’ will never be NULL [-Waddress] 262 | if (_fileB && _fileB[0]) { | ^~~~~~ atac-driver/libatac/atac.H:60:22: note: ‘atacFileBase::_fileB’ declared here 60 | char _fileB[1024]; | ^~~~~~ atac-driver/libatac/atacFile.C: In member function ‘atacMatch* atacFileStream::nextMatch(char)’: atac-driver/libatac/atacFile.C:76:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | fgets(_inLine, 1024, _inFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ atac-driver/libatac/atacFile.C: In member function ‘atacFeature* atacFileStream::nextFeature(char*)’: atac-driver/libatac/atacFile.C:105:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 105 | fgets(_inLine, 1024, _inFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ atac-driver/libatac/atacFile.C: In constructor ‘atacFile::atacFile(const char*)’: atac-driver/libatac/atacFile.C:171:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 171 | fgets(inLine, 1024, inFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ atac-driver/libatac/atacFile.C: In member function ‘void atacFileBase::readHeader(char*, FILE*)’: atac-driver/libatac/atacFile.C:206:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 206 | fgets(inLine, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~~~ atac-driver/libatac/atacFile.C:245:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 245 | fgets(inLine, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacFileStreamMerge.o -c atac-driver/libatac/atacFileStreamMerge.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacFileStreamMerge.C:23: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacFileStreamMerge.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacFileStreamMerge.C: In member function ‘void atacFileStreamMerge::addFile(const char*)’: atac-driver/libatac/atacFileStreamMerge.C:86:11: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class afsm’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 86 | memcpy(F, _files, sizeof(afsm) * _filesLen); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ atac-driver/libatac/atacFileStreamMerge.C:27:7: note: ‘class afsm’ declared here 27 | class afsm { | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacMatch.o -c atac-driver/libatac/atacMatch.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atac.H:26, from atac-driver/libatac/atacMatch.C:19: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacMatch.C:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "Match longer than sequence (by "uint32FMT"bp) in 1: seqLen="uint32FMTW(8)" %s\n", | ^ atac-driver/libatac/atacMatch.C:131:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "Match longer than sequence (by "uint32FMT"bp) in 1: seqLen="uint32FMTW(8)" %s\n", | ^ atac-driver/libatac/atacMatch.C:139:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(stderr, "Match longer than sequence (by "uint32FMT"bp) in 2: seqLen="uint32FMTW(8)" %s\n", | ^ atac-driver/libatac/atacMatch.C:139:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(stderr, "Match longer than sequence (by "uint32FMT"bp) in 2: seqLen="uint32FMTW(8)" %s\n", | ^ atac-driver/libatac/atacMatch.C: In constructor ‘atacMatch::atacMatch(char*, char*, uint32, char*, uint32, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: atac-driver/libatac/atacMatch.C:50:10: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 16 equals destination size [-Wstringop-truncation] 50 | strncpy(matchuid, muid, 16); | ^ atac-driver/libatac/atacMatch.C: In member function ‘void atacMatch::decode(char*)’: atac-driver/libatac/atacMatch.C:100:10: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 16 equals destination size [-Wstringop-truncation] 100 | strncpy(matchuid, S[2], 16); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacMatchList.o -c atac-driver/libatac/atacMatchList.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacMatchList.C:23: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacMatchList.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/libatac/atacMatchOrder.o -c atac-driver/libatac/atacMatchOrder.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/libatac/atacMatchOrder.C:23: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from atac-driver/libatac/atac.H:30, from atac-driver/libatac/atacMatchOrder.C:24: atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from atac-driver/libatac/atac.H:34: atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from atac-driver/libatac/atac.H:37: atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/libatac/atacMatchOrder.C:38:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 38 | sprintf(n.matchuid, "merge"uint32FMT, mergeuid); | ^ rm -f atac-driver/libatac/libatac.a && ar ruvs atac-driver/libatac/libatac.a atac-driver/libatac/atacFeature.o atac-driver/libatac/atacFeatureList.o atac-driver/libatac/atacFile.o atac-driver/libatac/atacFileStreamMerge.o atac-driver/libatac/atacMatch.o atac-driver/libatac/atacMatchList.o atac-driver/libatac/atacMatchOrder.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating atac-driver/libatac/libatac.a a - atac-driver/libatac/atacFeature.o a - atac-driver/libatac/atacFeatureList.o a - atac-driver/libatac/atacFile.o a - atac-driver/libatac/atacFileStreamMerge.o a - atac-driver/libatac/atacMatch.o a - atac-driver/libatac/atacMatchList.o a - atac-driver/libatac/atacMatchOrder.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap.o -c atac-driver/alignOverlap/overlap.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap.C:19: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ atac-driver/alignOverlap/overlap.C:123:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 123 | fprintf(stderr, "unmapped: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.unmapped.getSum(), statsB.unmapped.getSum()); | ^ atac-driver/alignOverlap/overlap.C:123:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 123 | fprintf(stderr, "unmapped: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.unmapped.getSum(), statsB.unmapped.getSum()); | ^ atac-driver/alignOverlap/overlap.C:124:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "unique mapping 1: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.map1unique.getSum(), statsB.map1unique.getSum()); | ^ atac-driver/alignOverlap/overlap.C:124:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 124 | fprintf(stderr, "unique mapping 1: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.map1unique.getSum(), statsB.map1unique.getSum()); | ^ atac-driver/alignOverlap/overlap.C:125:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 125 | fprintf(stderr, "unique mapping 2: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.map2unique.getSum(), statsB.map2unique.getSum()); | ^ atac-driver/alignOverlap/overlap.C:125:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 125 | fprintf(stderr, "unique mapping 2: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.map2unique.getSum(), statsB.map2unique.getSum()); | ^ atac-driver/alignOverlap/overlap.C:126:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 126 | fprintf(stderr, "different: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.different.getSum(), statsB.different.getSum()); | ^ atac-driver/alignOverlap/overlap.C:126:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 126 | fprintf(stderr, "different: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.different.getSum(), statsB.different.getSum()); | ^ atac-driver/alignOverlap/overlap.C:127:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "wild diff: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.wilddiff.getSum(), statsB.wilddiff.getSum()); | ^ atac-driver/alignOverlap/overlap.C:127:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "wild diff: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.wilddiff.getSum(), statsB.wilddiff.getSum()); | ^ atac-driver/alignOverlap/overlap.C:128:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "same: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.same.getSum(), statsB.same.getSum()); | ^ atac-driver/alignOverlap/overlap.C:128:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "same: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.same.getSum(), statsB.same.getSum()); | ^ atac-driver/alignOverlap/overlap.C:129:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "inconsistent: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.inconsistent.getSum(), statsB.inconsistent.getSum()); | ^ atac-driver/alignOverlap/overlap.C:129:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "inconsistent: A:"uint32FMTW(10)" B:"uint32FMTW(10)"\n", statsA.inconsistent.getSum(), statsB.inconsistent.getSum()); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-find.o -c atac-driver/alignOverlap/overlap-find.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-find.C:19: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ atac-driver/alignOverlap/overlap-find.C:45:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 45 | fprintf(stderr, "isolated Unique: map1: "uint32FMT" map2: "uint32FMT"\n", sumA, sumB); | ^ atac-driver/alignOverlap/overlap-find.C:45:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 45 | fprintf(stderr, "isolated Unique: map1: "uint32FMT" map2: "uint32FMT"\n", sumA, sumB); | ^ atac-driver/alignOverlap/overlap-find.C:59:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 59 | fprintf(stderr, "got invalid type; "uint32FMT" -- %c\n", type, (char)type), exit(1); | ^ atac-driver/alignOverlap/overlap-find.C:91:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(stderr, "%s: "uint32FMT" len:"uint32FMT"\n", msg, count, len); | ^ atac-driver/alignOverlap/overlap-find.C:91:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(stderr, "%s: "uint32FMT" len:"uint32FMT"\n", msg, count, len); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-matchTree.o -c atac-driver/alignOverlap/overlap-matchTree.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-matchTree.C:19: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-printAnno.o -c atac-driver/alignOverlap/overlap-printAnno.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-printAnno.C:19: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ atac-driver/alignOverlap/overlap-printAnno.C:46:14: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(F, "%c "uint32FMTW(4)":"uint32FMTW(09)"-"uint32FMTW(09)"["uint32FMTW(6)"] ", | ^ atac-driver/alignOverlap/overlap-printAnno.C:46:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(F, "%c "uint32FMTW(4)":"uint32FMTW(09)"-"uint32FMTW(09)"["uint32FMTW(6)"] ", | ^ atac-driver/alignOverlap/overlap-printAnno.C:46:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(F, "%c "uint32FMTW(4)":"uint32FMTW(09)"-"uint32FMTW(09)"["uint32FMTW(6)"] ", | ^ atac-driver/alignOverlap/overlap-printAnno.C:46:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(F, "%c "uint32FMTW(4)":"uint32FMTW(09)"-"uint32FMTW(09)"["uint32FMTW(6)"] ", | ^ atac-driver/alignOverlap/overlap-printAnno.C:63:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 63 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:63:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 63 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:63:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 63 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:65:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid1, m1->pos1 + off1, m1->pos1 + off1 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:65:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid1, m1->pos1 + off1, m1->pos1 + off1 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:65:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m1->iid1, m1->pos1 + off1, m1->pos1 + off1 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:69:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 69 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ atac-driver/alignOverlap/overlap-printAnno.C:69:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 69 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ atac-driver/alignOverlap/overlap-printAnno.C:69:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 69 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ atac-driver/alignOverlap/overlap-printAnno.C:85:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 85 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:85:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 85 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:85:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 85 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid2, sta, end); | ^ atac-driver/alignOverlap/overlap-printAnno.C:87:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid1, m2->pos1 + off2, m2->pos1 + off2 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:87:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid1, m2->pos1 + off2, m2->pos1 + off2 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:87:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", m2->iid1, m2->pos1 + off2, m2->pos1 + off2 + len); | ^ atac-driver/alignOverlap/overlap-printAnno.C:91:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ atac-driver/alignOverlap/overlap-printAnno.C:91:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ atac-driver/alignOverlap/overlap-printAnno.C:91:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(F, "("uint32FMTW(8)": "uint32FMTW(9)"-"uint32FMTW(9)") ", uint32ZERO, uint32ZERO, uint32ZERO); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-sort.o -c atac-driver/alignOverlap/overlap-sort.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-sort.C:19: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ ln -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/alignOverlap/overlap-process.C /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/alignOverlap/overlap-process1.C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -DINDEX=1 -DNAME=process1 -DPOS1=pos1 -DPOS2=pos2 -DLEN2=len2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-process1.o -c atac-driver/alignOverlap/overlap-process1.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-process1.C:19: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ ln -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/alignOverlap/overlap-process.C /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/alignOverlap/overlap-process2.C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -DINDEX=2 -DNAME=process2 -DPOS1=pos2 -DPOS2=pos1 -DLEN2=len1 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/alignOverlap/overlap-process2.o -c atac-driver/alignOverlap/overlap-process2.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/alignOverlap/overlap.H:26, from atac-driver/alignOverlap/overlap-process2.C:19: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/alignOverlap/overlap.H:28: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ In file included from atac-driver/alignOverlap/overlap.H:41: atac-driver/alignOverlap/overlap-span.H:75:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ atac-driver/alignOverlap/overlap-span.H:75:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | fprintf(stderr, "span_t::split()-- _beg="uint32FMT" _end="uint32FMT" postition="uint32FMT"?\n", _beg, _end, position); | ^ In file included from atac-driver/alignOverlap/overlap.H:45: atac-driver/alignOverlap/overlap-stats.H:64:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(out, uint32FMT" "uint32FMT"\n", i, hist[i]); | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/alignOverlap/overlap atac-driver/alignOverlap/overlap.o atac-driver/alignOverlap/overlap-find.o atac-driver/alignOverlap/overlap-matchTree.o atac-driver/alignOverlap/overlap-printAnno.o atac-driver/alignOverlap/overlap-sort.o atac-driver/alignOverlap/overlap-process1.o atac-driver/alignOverlap/overlap-process2.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/gapShifter.o -c atac-driver/gapShifter/gapShifter.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:26, from atac-driver/gapShifter/gapShifter.C:23: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:203:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "iid1 "uint32FMT", iid2 "uint32FMT"\n", iid1, iid2); | ^ atac-driver/gapShifter/gapShifter.C:203:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stderr, "iid1 "uint32FMT", iid2 "uint32FMT"\n", iid1, iid2); | ^ atac-driver/gapShifter/gapShifter.C:223:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 223 | fprintf(stderr, "iid1 "uint32FMT", iid2 "uint32FMT"\n", iid1, iid2); | ^ atac-driver/gapShifter/gapShifter.C:223:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 223 | fprintf(stderr, "iid1 "uint32FMT", iid2 "uint32FMT"\n", iid1, iid2); | ^ atac-driver/gapShifter/gapShifter.C:510:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 510 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:510:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 510 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:510:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 510 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:510:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 510 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:510:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 510 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:515:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 515 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:515:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 515 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:515:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 515 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:515:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 515 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:515:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 515 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:523:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 523 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:523:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 523 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:523:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 523 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:523:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 523 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:523:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 523 | fprintf(logFile, "%s\t%s\t%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\t", | ^ atac-driver/gapShifter/gapShifter.C:528:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 528 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:528:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 528 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:528:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 528 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:528:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 528 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:528:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 528 | fprintf(logFile, "%s:"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t->\t"uint32FMT"\t"uint32FMT"\n", | ^ atac-driver/gapShifter/gapShifter.C:738:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 738 | fprintf(stderr, "Shifting gaps of length at most "uint32FMT" bases, to the %s.\n", gapLimit, (shiftRight) ? "right" : "left"); | ^ atac-driver/gapShifter/gapShifter.C:750:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 750 | fprintf(stderr, "numShifted = "uint32FMT"\n", numShifted); | ^ atac-driver/gapShifter/gapShifter.C:751:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 751 | fprintf(stderr, "numNotShifted = "uint32FMT"\n", numNotShifted); | ^ atac-driver/gapShifter/gapShifter.C:752:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 752 | fprintf(stderr, "numDiffSeq = "uint32FMT"\n", numDiffSeq); | ^ atac-driver/gapShifter/gapShifter.C:753:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 753 | fprintf(stderr, "numDiffOri = "uint32FMT"\n", numDiffOri); | ^ atac-driver/gapShifter/gapShifter.C:754:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 754 | fprintf(stderr, "numZeroLen = "uint32FMT"\n", numZeroLen); | ^ atac-driver/gapShifter/gapShifter.C:755:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 755 | fprintf(stderr, "numOutOfOrder = "uint32FMT"\n", numOutOfOrder); | ^ atac-driver/gapShifter/gapShifter.C:756:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 756 | fprintf(stderr, "numNotAdjacent = "uint32FMT"\n", numNotAdjacent); | ^ atac-driver/gapShifter/gapShifter.C:757:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 757 | fprintf(stderr, "numNoGap = "uint32FMT"\n", numNoGap); | ^ atac-driver/gapShifter/gapShifter.C:758:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 758 | fprintf(stderr, "numGapTooBig = "uint32FMT"\n", numGapTooBig); | ^ atac-driver/gapShifter/gapShifter.C:759:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 759 | fprintf(stderr, "numOverlapping = "uint32FMT"\n", numOverlapping); | ^ atac-driver/gapShifter/gapShifter.C:762:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "amountShifted["uint32FMT"] = "uint32FMT" (number of gaps shifted by [number of bases])\n", x, amountShifted[x]); | ^ atac-driver/gapShifter/gapShifter.C:762:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "amountShifted["uint32FMT"] = "uint32FMT" (number of gaps shifted by [number of bases])\n", x, amountShifted[x]); | ^ atac-driver/gapShifter/gapShifter.C:764:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 764 | fprintf(stderr, "shifted "uint32FMT" out of "uint32FMT" (%6.2f%%)\n", gapsShifted, ML.numMatches(), (double)gapsShifted / (double)ML.numMatches() * 100.0); | ^ atac-driver/gapShifter/gapShifter.C:764:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 764 | fprintf(stderr, "shifted "uint32FMT" out of "uint32FMT" (%6.2f%%)\n", gapsShifted, ML.numMatches(), (double)gapsShifted / (double)ML.numMatches() * 100.0); | ^ atac-driver/gapShifter/gapShifter.C:780:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/gapShifter.C:780:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/gapShifter.C:780:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/gapShifter.C:780:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/gapShifter.C:780:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/gapShifter.C:780:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 780 | fprintf(stdout, "M u %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/gapShifter atac-driver/gapShifter/gapShifter.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/extractSequence.o -c atac-driver/gapShifter/extractSequence.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:26, from atac-driver/gapShifter/extractSequence.C:23: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/extractSequence.C:110:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(Aoutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ atac-driver/gapShifter/extractSequence.C:110:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(Aoutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ atac-driver/gapShifter/extractSequence.C:110:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(Aoutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ atac-driver/gapShifter/extractSequence.C:121:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 121 | fprintf(Boutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ atac-driver/gapShifter/extractSequence.C:121:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 121 | fprintf(Boutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ atac-driver/gapShifter/extractSequence.C:121:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 121 | fprintf(Boutput, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" match %s(%s)\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/extractSequence atac-driver/gapShifter/extractSequence.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/extractUnmapped.o -c atac-driver/gapShifter/extractUnmapped.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/extractUnmapped.C:23: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/extractUnmapped.C:24: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/extractUnmapped.C:105:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 105 | fprintf(output, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" between match %s(%s) and %s(%s)\n", | ^ atac-driver/gapShifter/extractUnmapped.C:105:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 105 | fprintf(output, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" between match %s(%s) and %s(%s)\n", | ^ atac-driver/gapShifter/extractUnmapped.C:105:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 105 | fprintf(output, "%s extracted from iid "uint32FMT" pos "uint32FMT" "uint32FMT" between match %s(%s) and %s(%s)\n", | ^ atac-driver/gapShifter/extractUnmapped.C:583:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 583 | fprintf(stderr, "Done masking. "uint32FMT" in A, "uint32FMT" in B.\n", stats[0], stats[1]); | ^ atac-driver/gapShifter/extractUnmapped.C:583:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 583 | fprintf(stderr, "Done masking. "uint32FMT" in A, "uint32FMT" in B.\n", stats[0], stats[1]); | ^ atac-driver/gapShifter/extractUnmapped.C: In function ‘int main(int, char**)’: atac-driver/gapShifter/extractUnmapped.C:541:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fgets(L, 1024, F); | ~~~~~^~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/extractUnmapped atac-driver/gapShifter/extractUnmapped.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/coalesceMatches.o -c atac-driver/gapShifter/coalesceMatches.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/coalesceMatches.C:23: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/coalesceMatches.C:24: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/coalesceMatches atac-driver/gapShifter/coalesceMatches.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/correctGaps.o -c atac-driver/gapShifter/correctGaps.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/correctGaps.C:23: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/correctGaps.C:24: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/correctGaps.C:138:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 138 | fprintf(logFile, "HEY! F gap of size "uint32FMT" not in a run?\n", gap1); | ^ atac-driver/gapShifter/correctGaps.C:200:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 200 | fprintf(logFile, "HEY! R gap of size "uint32FMT" not in a run?\n", gap1); | ^ atac-driver/gapShifter/correctGaps.C:222:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(logFile, "CLOSE "uint32FMT"----------------------------------------\n", gap1); | ^ atac-driver/gapShifter/correctGaps.C:235:22: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 235 | fprintf(logFile, "At gapSize="uint32FMT" closed "uint32FMT" f-gaps and "uint32FMT" r-gaps.\n", gapsize, fgaps, rgaps); | ^ atac-driver/gapShifter/correctGaps.C:235:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 235 | fprintf(logFile, "At gapSize="uint32FMT" closed "uint32FMT" f-gaps and "uint32FMT" r-gaps.\n", gapsize, fgaps, rgaps); | ^ atac-driver/gapShifter/correctGaps.C:235:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 235 | fprintf(logFile, "At gapSize="uint32FMT" closed "uint32FMT" f-gaps and "uint32FMT" r-gaps.\n", gapsize, fgaps, rgaps); | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/correctGaps atac-driver/gapShifter/correctGaps.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/testAtac.o -c atac-driver/gapShifter/testAtac.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/testAtac.C:23: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/testAtac.C:24: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/testAtac.C:89:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 89 | fprintf(stderr, "match "uint32FMT" is only %6.2f%% identity: ", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/testAtac atac-driver/gapShifter/testAtac.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/cleanAtac.o -c atac-driver/gapShifter/cleanAtac.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/cleanAtac.C:23: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/cleanAtac.C:24: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/cleanAtac.C:149:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 149 | fprintf(stderr, "match "uint32FMT" is only %6.2f%% identity and "uint32FMT" long: ", | ^ atac-driver/gapShifter/cleanAtac.C:149:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 149 | fprintf(stderr, "match "uint32FMT" is only %6.2f%% identity and "uint32FMT" long: ", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/cleanAtac atac-driver/gapShifter/cleanAtac.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/gapShifter/projectFeatures.o -c atac-driver/gapShifter/projectFeatures.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/gapShifter/projectFeatures.C:23: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/gapShifter/projectFeatures.C:24: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/gapShifter/projectFeatures.C:72:2: warning: #warning BROKEN [-Wcpp] 72 | #warning BROKEN | ^~~~~~~ atac-driver/gapShifter/projectFeatures.C:132:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:132:124: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "M u Aprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:146:124: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 146 | fprintf(stdout, "M u Bprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:171:124: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "M u Cprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:112: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/gapShifter/projectFeatures.C:192:124: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u Dprojected"uint32FMT" %s.%s %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/gapShifter/projectFeatures atac-driver/gapShifter/projectFeatures.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/lengthFilter/lengthFilter.o -c atac-driver/lengthFilter/lengthFilter.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from atac-driver/lengthFilter/lengthFilter.C:24: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ atac-driver/lengthFilter/lengthFilter.C:46:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | sprintf(inLine, "/globalMatchMinSize="uint32FMT"\n", minLength); | ^ atac-driver/lengthFilter/lengthFilter.C:57:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 57 | fprintf(stdout, "/globalMatchMinSize="uint32FMT"\n", minLength); | ^ atac-driver/lengthFilter/lengthFilter.C:114:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 114 | fprintf(stderr, "lengthFilter: Discarded "uint32FMTW(8)" matches with total length "uint32FMTW(10)", %7.3f%% of the sequence in matches.\n", | ^ atac-driver/lengthFilter/lengthFilter.C:114:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 114 | fprintf(stderr, "lengthFilter: Discarded "uint32FMTW(8)" matches with total length "uint32FMTW(10)", %7.3f%% of the sequence in matches.\n", | ^ atac-driver/lengthFilter/lengthFilter.C:116:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stderr, "lengthFilter: Saved "uint32FMTW(8)" matches with total length "uint32FMTW(10)", %7.3f%% of the sequence in matches.\n", | ^ atac-driver/lengthFilter/lengthFilter.C:116:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stderr, "lengthFilter: Saved "uint32FMTW(8)" matches with total length "uint32FMTW(10)", %7.3f%% of the sequence in matches.\n", | ^ atac-driver/lengthFilter/lengthFilter.C: In function ‘void readHeader(char*, FILE*, uint32&, FILE*)’: atac-driver/lengthFilter/lengthFilter.C:34:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 34 | fgets(inLine, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~~~ atac-driver/lengthFilter/lengthFilter.C:53:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 53 | fgets(inLine, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~~~ atac-driver/lengthFilter/lengthFilter.C: In function ‘int main(int, char**)’: atac-driver/lengthFilter/lengthFilter.C:111:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | fgets(inLine, 1024, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/lengthFilter/lengthFilter atac-driver/lengthFilter/lengthFilter.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/matchExtender/matchExtender.o -c atac-driver/matchExtender/matchExtender.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:26, from atac-driver/matchExtender/matchExtender.C:27: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/matchExtender/matchExtender.C:192:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:192:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:192:60: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:192:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:192:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:192:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 192 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" 1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:60: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ atac-driver/matchExtender/matchExtender.C:201:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stdout, "M u %s . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" -1\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/matchExtender/matchExtender-dump.o -c atac-driver/matchExtender/matchExtender-dump.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/matchExtender/matchExtender-dump.C:25: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/matchExtender/match.H:8, from atac-driver/matchExtender/matchExtender-dump.C:26: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:31:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 31 | fprintf(out, "%s: ID:%s range1:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT")\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:31:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 31 | fprintf(out, "%s: ID:%s range1:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT")\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:31:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 31 | fprintf(out, "%s: ID:%s range1:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT")\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:31:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 31 | fprintf(out, "%s: ID:%s range1:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT")\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:34:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(out, "%s ID:%s range2:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT") diag:"uint32FMT" %s\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:34:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(out, "%s ID:%s range2:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT") diag:"uint32FMT" %s\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:34:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(out, "%s ID:%s range2:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT") diag:"uint32FMT" %s\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:34:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(out, "%s ID:%s range2:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT") diag:"uint32FMT" %s\n", | ^ atac-driver/matchExtender/matchExtender-dump.C:34:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 34 | fprintf(out, "%s ID:%s range2:"uint32FMT","uint32FMT" _pos="uint32FMT" (seqlen="uint32FMT") diag:"uint32FMT" %s\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/matchExtender/matchExtender-func.o -c atac-driver/matchExtender/matchExtender-func.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/matchExtender/matchExtender-func.C:26: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/matchExtender/matchExtender-func.C:27: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/matchExtender/matchExtender atac-driver/matchExtender/matchExtender.o atac-driver/matchExtender/matchExtender-dump.o atac-driver/matchExtender/matchExtender-func.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/mismatchCounter/mismatchCounter.o -c atac-driver/mismatchCounter/mismatchCounter.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from atac-driver/mismatchCounter/mismatchCounter.C:23: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/mismatchCounter/mismatchCounter.C:25: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/mismatchCounter/mismatchCounter.C:197:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 197 | fprintf(stderr, "globalSequence = "uint32FMT"\n", globalSequence); | ^ atac-driver/mismatchCounter/mismatchCounter.C:198:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 198 | fprintf(stderr, "globalMismatches = "uint32FMT"\n", globalMismatches); | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/mismatchCounter/mismatchCounter atac-driver/mismatchCounter/mismatchCounter.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/statsGenerator/statsGenerator.o -c atac-driver/statsGenerator/statsGenerator.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:26, from atac-driver/statsGenerator/statsGenerator.C:26: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/statsGenerator/statsGenerator.C:91:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(stdout, "histogram %s "uint32FMT" items %8.3f average %8.3f std.dev.\n", | ^ atac-driver/statsGenerator/statsGenerator.C:102:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 102 | fprintf(out, uint64FMT" "uint32FMT"\n", i * _b, _h[i]); | ^ atac-driver/statsGenerator/statsGenerator.C:103:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 103 | fprintf(out, ">"uint64FMT" "uint32FMT"\n", _m, _l); | ^ atac-driver/statsGenerator/statsGenerator.C:103:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 103 | fprintf(out, ">"uint64FMT" "uint32FMT"\n", _m, _l); | ^ atac-driver/statsGenerator/statsGenerator.C:133:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 133 | fprintf(out, "plot [0:"uint64FMT"][0:"uint64FMT"] \"%s.%s.histogramdat\" using 2 with lines\n", | ^ atac-driver/statsGenerator/statsGenerator.C:133:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 133 | fprintf(out, "plot [0:"uint64FMT"][0:"uint64FMT"] \"%s.%s.histogramdat\" using 2 with lines\n", | ^ atac-driver/statsGenerator/statsGenerator.C:136:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(out, "plot [0:"uint64FMT"][0:"uint64FMT"] \"%s.%s.histogramdat\" using 2 with lines\n", | ^ atac-driver/statsGenerator/statsGenerator.C:136:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(out, "plot [0:"uint64FMT"][0:"uint64FMT"] \"%s.%s.histogramdat\" using 2 with lines\n", | ^ atac-driver/statsGenerator/statsGenerator.C:172:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 172 | fprintf(stdout, "totalLength %s "uint64FMT" %s "uint64FMT" # all letters, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:172:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 172 | fprintf(stdout, "totalLength %s "uint64FMT" %s "uint64FMT" # all letters, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:193:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "totalLength %s "uint64FMT" %s "uint64FMT" # ACGT only\n", | ^ atac-driver/statsGenerator/statsGenerator.C:193:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "totalLength %s "uint64FMT" %s "uint64FMT" # ACGT only\n", | ^ atac-driver/statsGenerator/statsGenerator.C:282:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 282 | fprintf(stdout, "numberOfItems "uint64FMT"\n", (uint64)ifa.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:283:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 283 | fprintf(stdout, "totalLength "uint64FMT" # sum of lengths of all features\n", ifa.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:285:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 285 | fprintf(stdout, "numberOfItems "uint64FMT" # after merging overlapping regions\n", (uint64)ifa.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:286:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "coveredLength "uint64FMT" # sequence covered by a feature, including N\n", ifa.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:287:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 287 | fprintf(stdout, "coveredLength "uint64FMT" # sequence covered by a feature, ACGT only\n", tandemRepeatACGTLength(ifa, offset1, A)); | ^ atac-driver/statsGenerator/statsGenerator.C:289:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 289 | fprintf(stdout, "numberOfItems "uint64FMT" # after merging overlapping regions, only in matches\n", (uint64)mma.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:290:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 290 | fprintf(stdout, "inMatches "uint64FMT" # sequence covered by a feature and in a match, including N\n", mma.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:291:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 291 | fprintf(stdout, "inMatches "uint64FMT" # sequence covered by a feature and in a match, ACGT only\n", tandemRepeatACGTLength(mma, offset1, A)); | ^ atac-driver/statsGenerator/statsGenerator.C:295:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 295 | fprintf(stdout, "numberOfItems "uint64FMT"\n", (uint64)ifb.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:296:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 296 | fprintf(stdout, "totalLength "uint64FMT" # sum of lengths of all features\n", ifb.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:298:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 298 | fprintf(stdout, "numberOfItems "uint64FMT" # after merging overlapping regions\n", (uint64)ifb.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:299:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 299 | fprintf(stdout, "coveredLength "uint64FMT" # sequence covered by a feature, including N\n", ifb.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:300:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 300 | fprintf(stdout, "coveredLength "uint64FMT" # sequence covered by a feature, ACGT only\n", tandemRepeatACGTLength(ifb, offset2, B)); | ^ atac-driver/statsGenerator/statsGenerator.C:302:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 302 | fprintf(stdout, "numberOfItems "uint64FMT" # after merging overlapping regions, only in matches\n", (uint64)mmb.numberOfIntervals()); | ^ atac-driver/statsGenerator/statsGenerator.C:303:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 303 | fprintf(stdout, "inMatches "uint64FMT" # sequence covered by a feature and in a match, including N\n", mmb.sumOfLengths()); | ^ atac-driver/statsGenerator/statsGenerator.C:304:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 304 | fprintf(stdout, "inMatches "uint64FMT" # sequence covered by a feature and in a match, ACGT only\n", tandemRepeatACGTLength(mmb, offset2, B)); | ^ atac-driver/statsGenerator/statsGenerator.C:335:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 335 | fprintf(stdout, "numberOfItems "uint64FMT"\n", (uint64)matches.numberOfMatches()); | ^ atac-driver/statsGenerator/statsGenerator.C:337:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 337 | fprintf(stdout, "matchLength %s "uint64FMT" %s "uint64FMT" # Sum of lengths of sequence in matches\n", | ^ atac-driver/statsGenerator/statsGenerator.C:337:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 337 | fprintf(stdout, "matchLength %s "uint64FMT" %s "uint64FMT" # Sum of lengths of sequence in matches\n", | ^ atac-driver/statsGenerator/statsGenerator.C:349:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 349 | fprintf(stdout, "coveredLength %s "uint64FMT" %s "uint64FMT" # sequence covered by a match, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:349:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 349 | fprintf(stdout, "coveredLength %s "uint64FMT" %s "uint64FMT" # sequence covered by a match, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:353:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 353 | fprintf(stdout, "coveredLength %s "uint64FMT" %s "uint64FMT" # sequence covered by a match, ACGT only (new)\n", | ^ atac-driver/statsGenerator/statsGenerator.C:353:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 353 | fprintf(stdout, "coveredLength %s "uint64FMT" %s "uint64FMT" # sequence covered by a match, ACGT only (new)\n", | ^ atac-driver/statsGenerator/statsGenerator.C:409:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 409 | fprintf(out, uint64FMT" "uint32FMT"\n", n, n50[iter-1]); | ^ atac-driver/statsGenerator/statsGenerator.C:507:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 507 | fprintf(stdout, "chrCoveredLength["uint32FMTW(2)"] %s "uint64FMT" "uint64FMT" %6.2f%% "uint64FMT" "uint64FMT" %6.2f%% # seqCov, totalSeq for both ALL and ACGTonly\n", | ^ atac-driver/statsGenerator/statsGenerator.C:507:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 507 | fprintf(stdout, "chrCoveredLength["uint32FMTW(2)"] %s "uint64FMT" "uint64FMT" %6.2f%% "uint64FMT" "uint64FMT" %6.2f%% # seqCov, totalSeq for both ALL and ACGTonly\n", | ^ atac-driver/statsGenerator/statsGenerator.C:507:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 507 | fprintf(stdout, "chrCoveredLength["uint32FMTW(2)"] %s "uint64FMT" "uint64FMT" %6.2f%% "uint64FMT" "uint64FMT" %6.2f%% # seqCov, totalSeq for both ALL and ACGTonly\n", | ^ atac-driver/statsGenerator/statsGenerator.C:507:82: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 507 | fprintf(stdout, "chrCoveredLength["uint32FMTW(2)"] %s "uint64FMT" "uint64FMT" %6.2f%% "uint64FMT" "uint64FMT" %6.2f%% # seqCov, totalSeq for both ALL and ACGTonly\n", | ^ atac-driver/statsGenerator/statsGenerator.C:507:104: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 507 | fprintf(stdout, "chrCoveredLength["uint32FMTW(2)"] %s "uint64FMT" "uint64FMT" %6.2f%% "uint64FMT" "uint64FMT" %6.2f%% # seqCov, totalSeq for both ALL and ACGTonly\n", | ^ atac-driver/statsGenerator/statsGenerator.C:516:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 516 | sprintf(label, "chr"uint32FMTW(02)"full", c); | ^ atac-driver/statsGenerator/statsGenerator.C:520:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | sprintf(label, "chr"uint32FMTW(02)"acgt", c); | ^ atac-driver/statsGenerator/statsGenerator.C:628:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 628 | fprintf(stdout, "runMissingFull %s "uint64FMT" %s "uint64FMT" # sequence in run, not covered, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:628:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 628 | fprintf(stdout, "runMissingFull %s "uint64FMT" %s "uint64FMT" # sequence in run, not covered, including N\n", | ^ atac-driver/statsGenerator/statsGenerator.C:631:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 631 | fprintf(stdout, "runMissingFull %s "uint64FMT" %s "uint64FMT" # sequence in run, not covered, ACGT only\n", | ^ atac-driver/statsGenerator/statsGenerator.C:631:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 631 | fprintf(stdout, "runMissingFull %s "uint64FMT" %s "uint64FMT" # sequence in run, not covered, ACGT only\n", | ^ atac-driver/statsGenerator/statsGenerator.C: In function ‘void tandemRepeatStats(atacFileStream&, atacFileStream&, atacFile&, seqCache*, seqCache*)’: atac-driver/statsGenerator/statsGenerator.C:267:37: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 267 | while ((f = featuresA.nextFeature("tr")) != 0L) | ^~~~ atac-driver/statsGenerator/statsGenerator.C:269:37: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 269 | while ((f = featuresB.nextFeature("tr")) != 0L) | ^~~~ atac-driver/statsGenerator/statsGenerator.C: In function ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’: atac-driver/statsGenerator/statsGenerator.C:99:29: warning: ‘.histogramdat’ directive writing 13 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 99 | sprintf(filename, "%s.%s.histogramdat", prefix, label); | ^~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from atac-driver/statsGenerator/statsGenerator.C:21: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void histogram::dump(const char*, const char*)’ at atac-driver/statsGenerator/statsGenerator.C:99:12, inlined from ‘void histogram::dump(const char*, const char*)’ at atac-driver/statsGenerator/statsGenerator.C:95:14, inlined from ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’ at atac-driver/statsGenerator/statsGenerator.C:517:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 15 or more bytes (assuming 1038) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ atac-driver/statsGenerator/statsGenerator.C: In function ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’: atac-driver/statsGenerator/statsGenerator.C:127:29: warning: ‘.histogram.gnuplot’ directive writing 18 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 127 | sprintf(filename, "%s.%s.histogram.gnuplot", prefix, label); | ^~~~~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void histogram::plot(const char*, const char*)’ at atac-driver/statsGenerator/statsGenerator.C:127:12, inlined from ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’ at atac-driver/statsGenerator/statsGenerator.C:518:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 20 or more bytes (assuming 1043) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ atac-driver/statsGenerator/statsGenerator.C: In function ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’: atac-driver/statsGenerator/statsGenerator.C:140:37: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1013 [-Wformat-overflow=] 140 | sprintf(filename, "gnuplot < %s.%s.histogram.gnuplot", prefix, label); | ^~ ...... 518 | hist1full[c]->plot(prefix, label); | ~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void histogram::plot(const char*, const char*)’ at atac-driver/statsGenerator/statsGenerator.C:140:12, inlined from ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’ at atac-driver/statsGenerator/statsGenerator.C:518:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 30 or more bytes (assuming 1053) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ atac-driver/statsGenerator/statsGenerator.C: In function ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’: atac-driver/statsGenerator/statsGenerator.C:99:29: warning: ‘.histogramdat’ directive writing 13 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 99 | sprintf(filename, "%s.%s.histogramdat", prefix, label); | ^~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void histogram::dump(const char*, const char*)’ at atac-driver/statsGenerator/statsGenerator.C:99:12, inlined from ‘void histogram::dump(const char*, const char*)’ at atac-driver/statsGenerator/statsGenerator.C:95:14, inlined from ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’ at atac-driver/statsGenerator/statsGenerator.C:521:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 15 or more bytes (assuming 1038) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ atac-driver/statsGenerator/statsGenerator.C: In function ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’: atac-driver/statsGenerator/statsGenerator.C:127:29: warning: ‘.histogram.gnuplot’ directive writing 18 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 127 | sprintf(filename, "%s.%s.histogram.gnuplot", prefix, label); | ^~~~~~~~~~~~~~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void histogram::plot(const char*, const char*)’ at atac-driver/statsGenerator/statsGenerator.C:127:12, inlined from ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’ at atac-driver/statsGenerator/statsGenerator.C:522:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 20 or more bytes (assuming 1043) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ atac-driver/statsGenerator/statsGenerator.C: In function ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’: atac-driver/statsGenerator/statsGenerator.C:140:37: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1013 [-Wformat-overflow=] 140 | sprintf(filename, "gnuplot < %s.%s.histogram.gnuplot", prefix, label); | ^~ ...... 522 | hist1acgt[c]->plot(prefix, label); | ~~~~~ In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘void histogram::plot(const char*, const char*)’ at atac-driver/statsGenerator/statsGenerator.C:140:12, inlined from ‘void MappedByChromosome(atacFile&, atacMatchList&, seqCache*, seqCache*, char*)’ at atac-driver/statsGenerator/statsGenerator.C:522:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output 30 or more bytes (assuming 1053) into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/statsGenerator/statsGenerator atac-driver/statsGenerator/statsGenerator.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/uniqueFilter/uniqueFilter.o -c atac-driver/uniqueFilter/uniqueFilter.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from atac-driver/uniqueFilter/uniqueFilter.C:23: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30, from atac-driver/uniqueFilter/uniqueFilter.C:24: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:226:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 226 | fprintf(stderr, "Sorting error -- have negative coverage (axis="uint32FMT" position="uint32FMT")!\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:226:80: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 226 | fprintf(stderr, "Sorting error -- have negative coverage (axis="uint32FMT" position="uint32FMT")!\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:236:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 236 | fprintf(stderr, "offsetsToCoverage()-- Found "uint64FMT" bases at coverage "uint32FMT" or greater.\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:236:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 236 | fprintf(stderr, "offsetsToCoverage()-- Found "uint64FMT" bases at coverage "uint32FMT" or greater.\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:370:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 370 | fprintf(stderr, "Got fwd intersection on i="uint32FMT" matchNumber="uint32FMT"\n", i, matchNumber); | ^ atac-driver/uniqueFilter/uniqueFilter.C:370:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 370 | fprintf(stderr, "Got fwd intersection on i="uint32FMT" matchNumber="uint32FMT"\n", i, matchNumber); | ^ atac-driver/uniqueFilter/uniqueFilter.C:371:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:371:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:371:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:371:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 371 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:374:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 374 | fprintf(stdout, "--key1 beg="uint32FMT" end="uint32FMT"\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:374:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 374 | fprintf(stdout, "--key1 beg="uint32FMT" end="uint32FMT"\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:379:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 379 | fprintf(stderr, "Got rev intersection on i="uint32FMT" matchNumber="uint32FMT"\n", i, matchNumber); | ^ atac-driver/uniqueFilter/uniqueFilter.C:379:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 379 | fprintf(stderr, "Got rev intersection on i="uint32FMT" matchNumber="uint32FMT"\n", i, matchNumber); | ^ atac-driver/uniqueFilter/uniqueFilter.C:380:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 380 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:380:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 380 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:380:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 380 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:380:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 380 | fprintf(stdout, "--"uint32FMT" "uint32FMT" 1 "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:383:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 383 | fprintf(stdout, "--key2 beg="uint32FMT" end="uint32FMT"\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:383:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 383 | fprintf(stdout, "--key2 beg="uint32FMT" end="uint32FMT"\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:418:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 418 | #define D08D2 uint32FMTW(8)" "uint32FMTW(8) | ^ atac-driver/uniqueFilter/uniqueFilter.C:419:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 419 | #define KEY1THING "key1 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:419:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 419 | #define KEY1THING "key1 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:419:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 419 | #define KEY1THING "key1 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:419:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 419 | #define KEY1THING "key1 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:419:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 419 | #define KEY1THING "key1 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:420:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 420 | #define KEY2THING "key2 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:420:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 420 | #define KEY2THING "key2 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:420:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 420 | #define KEY2THING "key2 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:420:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 420 | #define KEY2THING "key2 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:420:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 420 | #define KEY2THING "key2 = "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" thing = "D08D2" "D08D2"\n" | ^ atac-driver/uniqueFilter/uniqueFilter.C:818:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 818 | fprintf(stderr, "match "uint32FMT" is outside the extent!\n", i); | ^ atac-driver/uniqueFilter/uniqueFilter.C:828:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 828 | fprintf(stdout, "M %s %s."uint32FMT" . %s "uint32FMT" "uint32FMT" 1 %s "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:828:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 828 | fprintf(stdout, "M %s %s."uint32FMT" . %s "uint32FMT" "uint32FMT" 1 %s "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:828:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 828 | fprintf(stdout, "M %s %s."uint32FMT" . %s "uint32FMT" "uint32FMT" 1 %s "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:828:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 828 | fprintf(stdout, "M %s %s."uint32FMT" . %s "uint32FMT" "uint32FMT" 1 %s "uint32FMT" "uint32FMT" %d\n", | ^ atac-driver/uniqueFilter/uniqueFilter.C:828:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 828 | fprintf(stdout, "M %s %s."uint32FMT" . %s "uint32FMT" "uint32FMT" 1 %s "uint32FMT" "uint32FMT" %d\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/uniqueFilter/uniqueFilter atac-driver/uniqueFilter/uniqueFilter.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/clumpMaker/clumpMaker.o -c atac-driver/clumpMaker/clumpMaker.C In file included from atac-driver/clumpMaker/clumpMaker.C:4: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:26, from atac-driver/clumpMaker/clumpMaker.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:30: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacMatch.H:64:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(f, "M %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT" %d %s:"uint32FMT" "uint32FMT" "uint32FMT" %d\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atacFeature.H:71:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 71 | fprintf(f, "F %s %s %s %s:"uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/atac.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:12:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 12 | fprintf(stderr, "%s-- position "uint32FMT" larger than length "uint32FMT"\n", \ | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:107:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "FastAAccessor::setRange()-- base="uint32FMT" and length="uint32FMT" exceed sequence length of "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:127:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "operator[]-- Tried to access to "uint32FMT", but range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:144:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | fprintf(stderr, "setPosition()-- Tried to set to "uint32FMT", but range is "uint32FMT"-"uint32FMT".\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:166:136: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 166 | fprintf(stderr, "FastAAccessor::extendLeft()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/fasta-accessor.H:180:137: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "FastAAccessor::extendRight()-- extend by "int32FMT" makes invalid: length is "uint32FMT", new range is "uint32FMT"-"uint32FMT"\n", | ^ atac-driver/clumpMaker/clumpMaker.C:341:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 341 | sprintf(C.matchuid, "clump"int32FMTW(06), cc); | ^ atac-driver/clumpMaker/clumpMaker.C:377:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 377 | sprintf(hits[mm].match.parentuid, "clump"int32FMTW(06), cc); | ^ atac-driver/clumpMaker/clumpMaker.C: In function ‘int main(int, char**)’: atac-driver/clumpMaker/clumpMaker.C:220:12: warning: variable ‘isSorted’ set but not used [-Wunused-but-set-variable] 220 | bool isSorted = false; | ^~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/clumpMaker/clumpMaker atac-driver/clumpMaker/clumpMaker.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/localalign/GF_ALN_dpaligner.o -c atac-driver/chainer/localalign/GF_ALN_dpaligner.C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/localalign/GF_ALN_local.o -c atac-driver/chainer/localalign/GF_ALN_local.C atac-driver/chainer/localalign/GF_ALN_local.C: In function ‘void Align_Recursion(const char*, int, const char*, int, const Trapezoid*, int, int, int, double, int)’: atac-driver/chainer/localalign/GF_ALN_local.C:872:15: warning: variable ‘indel’ set but not used [-Wunused-but-set-variable] 872 | int j, mid, indel; | ^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/localalign/GF_ALN_overlap.o -c atac-driver/chainer/localalign/GF_ALN_overlap.C atac-driver/chainer/localalign/GF_ALN_overlap.C: In function ‘void AVLinit()’: atac-driver/chainer/localalign/GF_ALN_overlap.C:93:17: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 93 | OutOfMemory("Candidate list"); | ^~~~~~~~~~~~~~~~ atac-driver/chainer/localalign/GF_ALN_overlap.C: In function ‘AVLnode* NEW(AVLnode*, Candidate*, AVLnode*)’: atac-driver/chainer/localalign/GF_ALN_overlap.C:125:21: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 125 | OutOfMemory("Candidate list"); | ^~~~~~~~~~~~~~~~ atac-driver/chainer/localalign/GF_ALN_overlap.C: In function ‘Local_Overlap* Find_Local_Overlap(int, int, int, int, Local_Segment*, int, int, double)’: atac-driver/chainer/localalign/GF_ALN_overlap.C:396:19: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 396 | OutOfMemory("Overlap Trace Array"); | ^~~~~~~~~~~~~~~~~~~~~ atac-driver/chainer/localalign/GF_ALN_overlap.C:662:19: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 662 | OutOfMemory("Overlap descriptor"); | ^~~~~~~~~~~~~~~~~~~~ atac-driver/chainer/localalign/GF_ALN_overlap.C:614:20: warning: variable ‘beg’ set but not used [-Wunused-but-set-variable] 614 | int best, end, beg; | ^~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/localalign/GF_ALN_loverlapper.o -c atac-driver/chainer/localalign/GF_ALN_loverlapper.C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/localalign/GF_ALN_pieceOlap.o -c atac-driver/chainer/localalign/GF_ALN_pieceOlap.C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -I/usr/include/python3.13 -o atac-driver/chainer/localalign/localAlignerInterfacemodule.o -c atac-driver/chainer/localalign/localAlignerInterfacemodule.C atac-driver/chainer/localalign/localAlignerInterfacemodule.C: In function ‘PyObject* spam_syntenicSegments(PyObject*, PyObject*)’: atac-driver/chainer/localalign/localAlignerInterfacemodule.C:176:18: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 176 | char *Aseq = "undefined"; | ^~~~~~~~~~~ atac-driver/chainer/localalign/localAlignerInterfacemodule.C:179:18: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 179 | char *Bseq = "undefined"; | ^~~~~~~~~~~ rm -f atac-driver/chainer/localAlignerInterfacemodule.so && g++ -Wl,-z,relro -Wl,-z,now -shared -o atac-driver/chainer/localAlignerInterfacemodule.so atac-driver/chainer/localalign/GF_ALN_dpaligner.o atac-driver/chainer/localalign/GF_ALN_local.o atac-driver/chainer/localalign/GF_ALN_overlap.o atac-driver/chainer/localalign/GF_ALN_loverlapper.o atac-driver/chainer/localalign/GF_ALN_pieceOlap.o atac-driver/chainer/localalign/localAlignerInterfacemodule.o -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chainer/halign/halign.o -c atac-driver/chainer/halign/halign.C atac-driver/chainer/halign/halign.C: In function ‘int diff(const char*, const char*, int, int, int*, int*, int*, int*, int, int, int, int, int, int, int, int, int, EditScript**, EditScript**)’: atac-driver/chainer/halign/halign.C:295:9: warning: variable ‘cost1’ set but not used [-Wunused-but-set-variable] 295 | int cost1, cost2; | ^~~~~ atac-driver/chainer/halign/halign.C:295:16: warning: variable ‘cost2’ set but not used [-Wunused-but-set-variable] 295 | int cost1, cost2; | ^~~~~ atac-driver/chainer/halign/halign.C:345:9: warning: variable ‘cost1’ set but not used [-Wunused-but-set-variable] 345 | int cost1, cost2; | ^~~~~ atac-driver/chainer/halign/halign.C:345:16: warning: variable ‘cost2’ set but not used [-Wunused-but-set-variable] 345 | int cost1, cost2; | ^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -I/usr/include/python3.13 -o atac-driver/chainer/halign/halignmodule.o -c atac-driver/chainer/halign/halignmodule.C rm -f atac-driver/chainer/halignmodule.so && g++ -Wl,-z,relro -Wl,-z,now -shared -o atac-driver/chainer/halignmodule.so atac-driver/chainer/halign/halign.o atac-driver/chainer/halign/halignmodule.o -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o atac-driver/chimera/happy-clones-span-clumps.o -c atac-driver/chimera/happy-clones-span-clumps.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from atac-driver/chimera/happy-clones-span-clumps.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ atac-driver/chimera/happy-clones-span-clumps.C:202:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 202 | fprintf(stderr, "ERROR: increase scaffoldsMax "uint32FMT"\n", scaffoldid); | ^ atac-driver/chimera/happy-clones-span-clumps.C:229:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(stderr, "Deleted "uint32FMT" scaffolds with less than 2 clumps.\n", deleted); | ^ atac-driver/chimera/happy-clones-span-clumps.C:230:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 230 | fprintf(stderr, "Remain "uint32FMT" scaffolds with more than 2 clumps.\n", remain); | ^ atac-driver/chimera/happy-clones-span-clumps.C:248:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" begin "uint32FMT" end "uint32FMT"\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:248:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" begin "uint32FMT" end "uint32FMT"\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:248:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" begin "uint32FMT" end "uint32FMT"\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:248:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" begin "uint32FMT" end "uint32FMT"\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:255:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 255 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and clump "uint32FMT" OVERLAP\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:255:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 255 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and clump "uint32FMT" OVERLAP\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:255:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 255 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and clump "uint32FMT" OVERLAP\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:263:31: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 263 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and "uint32FMT" confirmed by "uint32FMT" clones.\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:263:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 263 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and "uint32FMT" confirmed by "uint32FMT" clones.\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:263:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 263 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and "uint32FMT" confirmed by "uint32FMT" clones.\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:263:85: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 263 | fprintf(stdout, "scaffold "uint32FMT" clump "uint32FMT" and "uint32FMT" confirmed by "uint32FMT" clones.\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:449:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 449 | fprintf(stdout, "%s spans clump in scaffold %s,"uint32FMT"\n", ina, A[7], scfa); | ^ atac-driver/chimera/happy-clones-span-clumps.C:453:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 453 | fprintf(stdout, "%s spans clump in scaffold %s,"uint32FMT" \n", inb, B[7], scfb); | ^ atac-driver/chimera/happy-clones-span-clumps.C:464:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 464 | fprintf(stdout, "scaffold %s,"uint32FMT" clump "uint32FMT" "uint32FMT" confirmed by %s\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:464:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 464 | fprintf(stdout, "scaffold %s,"uint32FMT" clump "uint32FMT" "uint32FMT" confirmed by %s\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C:464:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 464 | fprintf(stdout, "scaffold %s,"uint32FMT" clump "uint32FMT" "uint32FMT" confirmed by %s\n", | ^ atac-driver/chimera/happy-clones-span-clumps.C: In function ‘int main(int, char**)’: atac-driver/chimera/happy-clones-span-clumps.C:393:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 393 | char *uidmapName = "/project/huref6/assembly/fasta/HUREF6A.info"; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C: In function ‘atacClumpCoordTree* buildCoordTree(char*)’: atac-driver/chimera/happy-clones-span-clumps.C:313:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 313 | fgets(inl, 1024, inf); | ~~~~~^~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:340:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 340 | fgets(inl, 1024, inf); | ~~~~~^~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C: In function ‘int main(int, char**)’: atac-driver/chimera/happy-clones-span-clumps.C:402:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 402 | fgets(L, 1024, F); | ~~~~~^~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:409:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 409 | fgets(L, 1024, F); | ~~~~~^~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:426:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 426 | fgets(ina, 1024, inf); chomp(ina); | ~~~~~^~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:427:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 427 | fgets(inb, 1024, inf); chomp(inb); | ~~~~~^~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:473:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 473 | fgets(ina, 1024, inf); chomp(ina); | ~~~~~^~~~~~~~~~~~~~~~ atac-driver/chimera/happy-clones-span-clumps.C:474:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 474 | fgets(inb, 1024, inf); chomp(inb); | ~~~~~^~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o atac-driver/chimera/happy-clones-span-clumps atac-driver/chimera/happy-clones-span-clumps.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/atac-driver/libatac/libatac.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/seatac.o -c seatac/seatac.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/seatac.C:4: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/seatac.C:201:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | "O:"uint32FMTW(7)" S:"uint32FMTW(7)" I:"uint32FMTW(7)" T:"uint32FMTW(7)" (%5.1f%%; %8.3f/sec) Finish in %5.2f seconds.\r", | ^ seatac/seatac.C:201:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | "O:"uint32FMTW(7)" S:"uint32FMTW(7)" I:"uint32FMTW(7)" T:"uint32FMTW(7)" (%5.1f%%; %8.3f/sec) Finish in %5.2f seconds.\r", | ^ seatac/seatac.C:201:52: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | "O:"uint32FMTW(7)" S:"uint32FMTW(7)" I:"uint32FMTW(7)" T:"uint32FMTW(7)" (%5.1f%%; %8.3f/sec) Finish in %5.2f seconds.\r", | ^ seatac/seatac.C:201:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | "O:"uint32FMTW(7)" S:"uint32FMTW(7)" I:"uint32FMTW(7)" T:"uint32FMTW(7)" (%5.1f%%; %8.3f/sec) Finish in %5.2f seconds.\r", | ^ seatac/seatac.C:239:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "\n"uint32FMTW(7)" sequences (%5.1f%%; %8.3f/sec) %5.2f seconds.\n", | ^ seatac/filterObj.H: In member function ‘void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/filterObj.H:146:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seatac/hitMatrix.H:82:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/configuration.o -c seatac/configuration.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/configuration.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/configuration.C:259:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 259 | fprintf(out, "/seatacNumSearchThreads="uint32FMT"\n", _numSearchThreads); | ^ seatac/configuration.C:260:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 260 | fprintf(out, "/seatacLoaderHighWaterMark="uint32FMT"\n", _loaderHighWaterMark); | ^ seatac/configuration.C:264:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 264 | fprintf(out, "/seatacWriterHighWaterMark="uint32FMT"\n", _writerHighWaterMark); | ^ seatac/configuration.C:267:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 267 | fprintf(out, "/seatacMaxDiagonal="uint32FMT"\n", _maxDiagonal); | ^ seatac/configuration.C:268:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 268 | fprintf(out, "/seatacMaxGap="uint32FMT"\n", _maxGap); | ^ seatac/configuration.C:269:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(out, "/seatacQsOverlap="uint32FMT"\n", _qsOverlap); | ^ seatac/configuration.C:270:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 270 | fprintf(out, "/seatacDsOverlap="uint32FMT"\n", _dsOverlap); | ^ seatac/configuration.C:271:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 271 | fprintf(out, "/seatacMinLength="uint32FMT"\n", _minLength + _merSize); | ^ seatac/configuration.C:272:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 272 | fprintf(out, "/seatacMerSize="uint32FMT"\n", _merSize); | ^ seatac/configuration.C:273:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 273 | fprintf(out, "/seatacMerSkip="uint32FMT"\n", _merSkip); | ^ seatac/filterObj.H: In member function ‘void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/filterObj.H:146:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seatac/hitMatrix.H:82:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/encodedQuery.o -c seatac/encodedQuery.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/encodedQuery.C:3: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/filterObj.H: In member function ‘void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/filterObj.H:146:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seatac/hitMatrix.H:82:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/hitMatrix.o -c seatac/hitMatrix.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/hitMatrix.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/filterObj.H: In member function ‘void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/filterObj.H:146:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seatac/hitMatrix.H:82:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/thr-search.o -c seatac/thr-search.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/thr-search.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/thr-search.C:3:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 3 | char const *srchGbye = "[%ld] computed: "uint64FMTW(8)" blocked: "uint64FMTW(4)"/"uint64FMTW(4)" encodeTime: %7.2f searchTime: %7.2f processTime: %7.2f\n"; | ^ seatac/thr-search.C:3:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 3 | char const *srchGbye = "[%ld] computed: "uint64FMTW(8)" blocked: "uint64FMTW(4)"/"uint64FMTW(4)" encodeTime: %7.2f searchTime: %7.2f processTime: %7.2f\n"; | ^ seatac/thr-search.C:3:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 3 | char const *srchGbye = "[%ld] computed: "uint64FMTW(8)" blocked: "uint64FMTW(4)"/"uint64FMTW(4)" encodeTime: %7.2f searchTime: %7.2f processTime: %7.2f\n"; | ^ seatac/thr-search.C:130:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, uint64FMT" Blocked by output (idx = "uint32FMT", outputPos = "uint32FMT").\n", (long)U, idx, outputPos); | ^ seatac/thr-search.C:130:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, uint64FMT" Blocked by output (idx = "uint32FMT", outputPos = "uint32FMT").\n", (long)U, idx, outputPos); | ^ seatac/filterObj.H: In member function ‘void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/filterObj.H:146:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seatac/hitMatrix.H:82:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/thr-loader.o -c seatac/thr-loader.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/thr-loader.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/filterObj.H: In member function ‘void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/filterObj.H:146:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seatac/hitMatrix.H:82:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/thr-loader.C: In function ‘void* loaderThread(void*)’: seatac/thr-loader.C:68:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 68 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/thr-deadlock.o -c seatac/thr-deadlock.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/seatac.H:20, from seatac/thr-deadlock.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/seatac.H:25: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10, from seatac/seatac.H:27: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/filterObj.H: In member function ‘void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/filterObj.H:146:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seatac/hitMatrix.H:82:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/hitMatrix-sort.o -c seatac/hitMatrix-sort.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from seatac/hitMatrix.H:8, from seatac/hitMatrix-sort.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/hitMatrix.H:9: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seatac/hitMatrix.H:10: seatac/filterObj.H:148:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:148:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT" bytes.\n", theOutputPos, theOutputMax); | ^ seatac/filterObj.H:157:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:157:111: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | "M x ############ . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filterObj.H:212:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "WARNING: there isn't enough space in the match to insert the match id "uint64FMT" '%s'!\n", | ^ seatac/hitMatrix.H:84:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/hitMatrix.H:84:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seatac/filterObj.H: In member function ‘void filterObj::addHit(char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/filterObj.H:146:21: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 146 | } catch (std::bad_alloc) { | ^~~~~~~~~ seatac/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seatac/hitMatrix.H:82:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 82 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB.H:7, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:136:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "existDB::createFromFastA()-- hashTable is "uint64FMT"MB\n", _hashTableWords >> 17); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:137:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | fprintf(stderr, "existDB::createFromFastA()-- buckets is "uint64FMT"MB\n", _bucketsWords >> 17); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:139:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(stderr, "existDB::createFromFastA()-- counts is "uint64FMT"MB\n", _countsWords >> 17); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:239:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:239:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.C:239:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB.H:7, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:27:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 27 | fprintf(stderr, "createFromMeryl()-- ERROR: requested merSize ("uint32FMT") is different than merSize in meryl database ("uint32FMT").\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:27:78: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 27 | fprintf(stderr, "createFromMeryl()-- ERROR: requested merSize ("uint32FMT") is different than merSize in meryl database ("uint32FMT").\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:54:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stderr, "createFromMeryl()-- tableSizeInEntries "uint64FMT"\n", tableSizeInEntries); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:55:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "createFromMeryl()-- count range "uint32FMT"-"uint32FMT"\n", lo, hi); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:55:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "createFromMeryl()-- count range "uint32FMT"-"uint32FMT"\n", lo, hi); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:104:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 104 | fprintf(stderr, "createFromMeryl()-- numberOfMers "uint64FMT"\n", numberOfMers); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:116:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stderr, "existDB::createFromMeryl()-- Found "uint64FMT" mers between count of "uint32FMT" and "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:116:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stderr, "existDB::createFromMeryl()-- Found "uint64FMT" mers between count of "uint32FMT" and "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:116:101: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stderr, "existDB::createFromMeryl()-- Found "uint64FMT" mers between count of "uint32FMT" and "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:135:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 135 | fprintf(stderr, "existDB::createFromMeryl()-- hashTable is "uint64FMT"MB\n", _hashTableWords >> 17); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:136:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "existDB::createFromMeryl()-- buckets is "uint64FMT"MB\n", _bucketsWords >> 17); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.C:138:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 138 | fprintf(stderr, "existDB::createFromMeryl()-- counts is "uint64FMT"MB\n", _countsWords >> 17); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB.H:7, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:136:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | fprintf(stderr, "existDB::createFromSequence()-- hashTable is "uint64FMT"MB\n", _hashTableWords >> 17); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:137:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | fprintf(stderr, "existDB::createFromSequence()-- buckets is "uint64FMT"MB\n", _bucketsWords >> 17); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:139:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(stderr, "existDB::createFromSequence()-- counts is "uint64FMT"MB\n", _countsWords >> 17); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:239:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:239:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.C:239:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 239 | fprintf(stderr, "Compressed from "uint64FMT" to "uint64FMT" ("uint64FMT" bits)\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB.H:7, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:169:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(stream, "merSizeInBases: "uint32FMT"\n", _merSizeInBases); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:170:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 170 | fprintf(stream, "tableBits "uint32FMT"\n", 2 * _merSizeInBases - _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:172:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 172 | fprintf(stream, "_hashTableWords "uint64FMT" ("uint64FMT" KB)\n", _hashTableWords, _hashTableWords >> 7); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:172:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 172 | fprintf(stream, "_hashTableWords "uint64FMT" ("uint64FMT" KB)\n", _hashTableWords, _hashTableWords >> 7); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:173:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 173 | fprintf(stream, "_bucketsWords "uint64FMT" ("uint64FMT" KB)\n", _bucketsWords, _bucketsWords >> 7); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:173:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 173 | fprintf(stream, "_bucketsWords "uint64FMT" ("uint64FMT" KB)\n", _bucketsWords, _bucketsWords >> 7); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:174:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 174 | fprintf(stream, "_countsWords "uint64FMT" ("uint64FMT" KB)\n", _countsWords, _countsWords >> 7); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:174:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 174 | fprintf(stream, "_countsWords "uint64FMT" ("uint64FMT" KB)\n", _countsWords, _countsWords >> 7); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:176:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 176 | fprintf(stream, "_shift1: "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:177:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 177 | fprintf(stream, "_shift2 "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:178:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stream, "_mask1 "uint64HEX"\n", _mask1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:179:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 179 | fprintf(stream, "_mask2 "uint64HEX"\n", _mask2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:183:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 183 | fprintf(stream, "_hshWidth "uint32FMT"\n", _hshWidth); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:191:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 191 | fprintf(stream, "_chkWidth "uint32FMT"\n", _chkWidth); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:199:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 199 | fprintf(stream, "_cntWidth "uint32FMT"\n", _cntWidth); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C: In member function ‘bool existDB::loadState(const char*, bool, bool)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:80:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80 | fread(cigam, sizeof(char), 16, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:124:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 124 | fread(&_merSizeInBases, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:125:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 125 | fread(&_shift1, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:126:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 126 | fread(&_shift2, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:127:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 127 | fread(&_mask1, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:128:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 128 | fread(&_mask2, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:129:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 129 | fread(&_hshWidth, sizeof(uint32), 1, F); // only valid if _compressedHash | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:130:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 130 | fread(&_chkWidth, sizeof(uint32), 1, F); // only valid if _compressedBucket | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:131:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | fread(&_cntWidth, sizeof(uint32), 1, F); // only valid if _compressedCounts | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:133:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 133 | fread(&_hashTableWords, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:134:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 134 | fread(&_bucketsWords, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:135:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 135 | fread(&_countsWords, sizeof(uint64), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:148:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 148 | fread(_hashTable, sizeof(uint64), _hashTableWords, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:149:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 149 | fread(_buckets, sizeof(uint64), _bucketsWords, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:152:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 152 | fread(_counts, sizeof(uint64), _countsWords, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C: In member function ‘void existDB::saveState(const char*)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.C:24:10: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation] 24 | strncpy(cigam, magic, 16); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB.H:7, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB.C:44:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 44 | fprintf(stderr, "existDB::existDB()-- Got "uint32FMT", expected "uint32FMT"\n", _merSizeInBases, merSize); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB.C:44:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 44 | fprintf(stderr, "existDB::existDB()-- Got "uint32FMT", expected "uint32FMT"\n", _merSizeInBases, merSize); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.C:2: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.C:22:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 22 | fprintf(stderr, "positionDB::get()-- Can't allocate space for more positions, requested "uint64FMT" uint64's.\n", posnMax); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.C:215:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 215 | fprintf(stderr, "positionDB::filter()-- Filtering out kmers less than "uint64FMT" and more than "uint64FMT"\n", lo, hi); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.C:215:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 215 | fprintf(stderr, "positionDB::filter()-- Filtering out kmers less than "uint64FMT" and more than "uint64FMT"\n", lo, hi); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.C:339:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | fprintf(stderr, "positionDB::filter()-- Filtered "uint64FMT" kmers less than "uint64FMT"\n", loCount, lo); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.C:339:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 339 | fprintf(stderr, "positionDB::filter()-- Filtered "uint64FMT" kmers less than "uint64FMT"\n", loCount, lo); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.C:340:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 340 | fprintf(stderr, "positionDB::filter()-- Filtered "uint64FMT" kmers more than "uint64FMT"\n", hiCount, hi); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.C:340:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 340 | fprintf(stderr, "positionDB::filter()-- Filtered "uint64FMT" kmers more than "uint64FMT"\n", hiCount, hi); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.C:341:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 341 | fprintf(stderr, "positionDB::filter()-- Saved "uint64FMT" kmers with acceptable count\n", okCount); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.C: In member function ‘void positionDB::filter(uint64, uint64)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.C:204:11: warning: unused variable ‘vv’ [-Wunused-variable] 204 | uint64 vv; | ^~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-dump.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-dump.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:5, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:4: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:25:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 25 | fprintf(F, "B "uint64FMT" "uint64FMT"-"uint64FMT"\n", h, st, ed); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:25:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 25 | fprintf(F, "B "uint64FMT" "uint64FMT"-"uint64FMT"\n", h, st, ed); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:25:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 25 | fprintf(F, "B "uint64FMT" "uint64FMT"-"uint64FMT"\n", h, st, ed); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:32:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(F, "%c chk="uint64HEX" pos="uint64FMT" siz="uint64FMT, | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:32:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(F, "%c chk="uint64HEX" pos="uint64FMT" siz="uint64FMT, | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:32:52: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(F, "%c chk="uint64HEX" pos="uint64FMT" siz="uint64FMT, | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-dump.C:40:22: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 40 | fprintf(F, " "uint64FMT, getDecodedValue(_positions, pos, _posnWidth)); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:5, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:197:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 197 | fprintf(stream, "merSizeInBases: "uint32FMT"\n", _merSizeInBases); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:198:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 198 | fprintf(stream, "merSkipInBases: "uint32FMT"\n", _merSkipInBases); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:199:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 199 | fprintf(stream, "tableSizeInBits: "uint32FMT"\n", _tableSizeInBits); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:200:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 200 | fprintf(stream, "tableSizeInEntries: "uint64FMT"\n", _tableSizeInEntries); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:201:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 201 | fprintf(stream, "hashWidth: "uint32FMT"\n", _hashWidth); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:202:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 202 | fprintf(stream, "chckWidth: "uint32FMT"\n", _chckWidth); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:203:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 203 | fprintf(stream, "posnWidth: "uint32FMT"\n", _posnWidth); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:204:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stream, "numberOfMers: "uint64FMT"\n", _numberOfMers); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:205:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 205 | fprintf(stream, "numberOfPositions: "uint64FMT"\n", _numberOfPositions); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:206:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 206 | fprintf(stream, "numberOfDistinct: "uint64FMT"\n", _numberOfDistinct); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:207:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 207 | fprintf(stream, "numberOfUnique: "uint64FMT"\n", _numberOfUnique); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:208:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 208 | fprintf(stream, "numberOfEntries: "uint64FMT"\n", _numberOfEntries); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:209:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 209 | fprintf(stream, "maximumEntries: "uint64FMT"\n", _maximumEntries); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C: In member function ‘void positionDB::saveState(const char*)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:63:22: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 63 | _hashTable_FW = (uint32 *)((_hashTable_FW) ? uint32ONE : uint32ZERO); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:37:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | write(F, magic, sizeof(char) * 16); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:39:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | write(F, faild, sizeof(char) * 16); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.C:95:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 95 | write(F, magic, sizeof(char) * 16); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:5, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.C:324:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 324 | fprintf(stderr, "positionDB::getUpToNMismatches()-- Can't allocate space for initial positions, requested "uint64FMT" uint64's.\n", posnMax); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:5, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:37:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 37 | fprintf(stdout, "ERROR: Bucket "uint64FMT" starts at "uint64FMT" ends at "uint64FMT"?\n", b, st, ed); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:37:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 37 | fprintf(stdout, "ERROR: Bucket "uint64FMT" starts at "uint64FMT" ends at "uint64FMT"?\n", b, st, ed); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:37:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 37 | fprintf(stdout, "ERROR: Bucket "uint64FMT" starts at "uint64FMT" ends at "uint64FMT"?\n", b, st, ed); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:78:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 78 | fprintf(stdout, "ERROR: unset posn bucket="uint64FMT" t="int64FMT" le="uint32FMT"\n", b, t, le); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:78:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 78 | fprintf(stdout, "ERROR: unset posn bucket="uint64FMT" t="int64FMT" le="uint32FMT"\n", b, t, le); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:78:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 78 | fprintf(stdout, "ERROR: unset posn bucket="uint64FMT" t="int64FMT" le="uint32FMT"\n", b, t, le); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:86:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 86 | fprintf(stdout, uint32FMTW(4)"] chck="uint64HEX" posn="uint64FMT"\n", t, _sortedChck[t], _sortedPosn[t]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:86:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 86 | fprintf(stdout, uint32FMTW(4)"] chck="uint64HEX" posn="uint64FMT"\n", t, _sortedChck[t], _sortedPosn[t]); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:110:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "ERROR: bucket="uint64FMT" t="uint32FMT" le="uint32FMT": "uint64HEX" > "uint64HEX"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:110:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "ERROR: bucket="uint64FMT" t="uint32FMT" le="uint32FMT": "uint64HEX" > "uint64HEX"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:110:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "ERROR: bucket="uint64FMT" t="uint32FMT" le="uint32FMT": "uint64HEX" > "uint64HEX"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:110:77: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "ERROR: bucket="uint64FMT" t="uint32FMT" le="uint32FMT": "uint64HEX" > "uint64HEX"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.C:110:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "ERROR: bucket="uint64FMT" t="uint32FMT" le="uint32FMT": "uint64HEX" > "uint64HEX"\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:46:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but mer size is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:46:107: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 46 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but mer size is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:52:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 52 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but mer skip is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:52:107: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 52 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but mer skip is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:58:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but max number of mismatches is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:58:123: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | fprintf(stderr, "positionDB()-- Tried to read state from '%s', but max number of mismatches is wrong (found "uint32FMT", wanted "uint32FMT").\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:127:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, " sm = "uint64FMT"\n", sm); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:128:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, " lg = "uint64FMT"\n", lg); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:129:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, " merSize = "uint32FMT" bits\n", 2 * merSize); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:130:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, " approxMers = "uint64FMT" mers\n", approxMers); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:131:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, " posnWidth = "uint64FMT" bits\n", posnWidth); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:142:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 142 | fprintf(stderr, "potential configurations for approximately "uint64FMT" "uint32FMT"-mers (posnW="uint64FMT").\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:142:77: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 142 | fprintf(stderr, "potential configurations for approximately "uint64FMT" "uint32FMT"-mers (posnW="uint64FMT").\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:142:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 142 | fprintf(stderr, "potential configurations for approximately "uint64FMT" "uint32FMT"-mers (posnW="uint64FMT").\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:200:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 200 | fprintf(stderr, "tblBits="uint64FMTW(2)" shifts="uint32FMTW(02)","uint32FMTW(02)" -- size %8.3fGB -- work %8.3f%s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:200:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 200 | fprintf(stderr, "tblBits="uint64FMTW(2)" shifts="uint32FMTW(02)","uint32FMTW(02)" -- size %8.3fGB -- work %8.3f%s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:200:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 200 | fprintf(stderr, "tblBits="uint64FMTW(2)" shifts="uint32FMTW(02)","uint32FMTW(02)" -- size %8.3fGB -- work %8.3f%s\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:217:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:217:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:217:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:217:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:217:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:217:122: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 217 | fprintf(stderr, "tblBits="uint32FMT" s1="uint32FMT" s2="uint32FMT" -- merSize="uint32FMT" bits + posnWidth="uint64FMT" bits (est "uint64FMT" mers) FINAL\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:326:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 326 | fprintf(stderr, "positionDB()-- bktAlloc = new uint64 ["uint64FMT"]\n", _tableSizeInEntries / 2 + 4); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:348:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 348 | fprintf(stderr, " Allocated bucket size counting space with total size "uint64FMT" KB\n", _tableSizeInEntries >> 8); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:392:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 392 | fprintf(stderr, " Found "uint64FMT" mers (max position = "uint64FMT")\n", _numberOfMers, _numberOfPositions); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:392:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 392 | fprintf(stderr, " Found "uint64FMT" mers (max position = "uint64FMT")\n", _numberOfMers, _numberOfPositions); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:430:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 430 | fprintf(stderr, " Allocated "uint64FMT"KB for buckets ("uint64FMT" 64-bit words)\n", bucketsSpace >> 7, bucketsSpace); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:430:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 430 | fprintf(stderr, " Allocated "uint64FMT"KB for buckets ("uint64FMT" 64-bit words)\n", bucketsSpace >> 7, bucketsSpace); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:435:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 435 | fprintf(stderr, "positionDB()-- _countingBuckets = new uint64 ["uint64FMT"]\n", bucketsSpace); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:553:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 553 | fprintf(stderr, " Sorting and repacking buckets ("uint64FMT" buckets).\n", _tableSizeInEntries); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:565:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 565 | " Found "uint64FMTW(12)" total mers\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:566:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 566 | " Found "uint64FMTW(12)" distinct mers\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:567:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 567 | " Found "uint64FMTW(12)" unique mers\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:568:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 568 | " Need "uint64FMT" non-unique position list entries ("uint64FMT" maximum count)\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:568:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 568 | " Need "uint64FMT" non-unique position list entries ("uint64FMT" maximum count)\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:637:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 637 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for hash table ("uint64FMT" 64-bit words)\n", hs >> 7, hs); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:637:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 637 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for hash table ("uint64FMT" 64-bit words)\n", hs >> 7, hs); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:643:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 643 | fprintf(stderr, "positionDB()-- _hashTable_BP = new uint64 ["uint64FMT"]\n", hs); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:662:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 662 | fprintf(stderr, " Reusing bucket space; Have: "uint64FMT" Need: "uint64FMT" (64-bit words)\n", bucketsSpace, bs); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:662:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 662 | fprintf(stderr, " Reusing bucket space; Have: "uint64FMT" Need: "uint64FMT" (64-bit words)\n", bucketsSpace, bs); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:669:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 669 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for buckets ("uint64FMT" 64-bit words)\n", bs >> 7, bs); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:669:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 669 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for buckets ("uint64FMT" 64-bit words)\n", bs >> 7, bs); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:674:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 674 | fprintf(stderr, "positionDB()-- _buckets = new uint64 ["uint64FMT"]\n", bs); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:680:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 680 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for positions ("uint64FMT" 64-bit words)\n", ps >> 7, ps); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:680:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 680 | fprintf(stderr, " Allocated "uint64FMTW(10)"KB for positions ("uint64FMT" 64-bit words)\n", ps >> 7, ps); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:685:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 685 | fprintf(stderr, "positionDB()-- _positions = new uint64 ["uint64FMT"\n", ps); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:695:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 695 | fprintf(stderr, " Transferring to final structure ("uint64FMT" buckets).\n", _tableSizeInEntries); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:878:31: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 878 | fprintf(stderr, "positionDB()-- ERROR: Got position "uint64FMT", but only "uint64FMT" available!\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:878:78: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 878 | fprintf(stderr, "positionDB()-- ERROR: Got position "uint64FMT", but only "uint64FMT" available!\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:916:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 916 | fprintf(stderr, " Avail: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (64-bit words)\n", bs, ps); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:916:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 916 | fprintf(stderr, " Avail: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (64-bit words)\n", bs, ps); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:917:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 917 | fprintf(stderr, " Avail: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (entries)\n", _numberOfDistinct, _numberOfEntries); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:917:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 917 | fprintf(stderr, " Avail: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (entries)\n", _numberOfDistinct, _numberOfEntries); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:918:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 918 | fprintf(stderr, " Used: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (64-bit words)\n", currentBbit / 64, currentPbit / 64); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:918:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 918 | fprintf(stderr, " Used: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (64-bit words)\n", currentBbit / 64, currentPbit / 64); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:928:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 928 | fprintf(stderr, " Used: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (entries)\n", _numberOfDistinct, _numberOfEntries); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:928:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 928 | fprintf(stderr, " Used: Bucket "uint64FMTW(12)" Position "uint64FMTW(12)" (entries)\n", _numberOfDistinct, _numberOfEntries); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:930:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 930 | " Found "uint64FMTW(12)" total mers\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:931:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 931 | " Found "uint64FMTW(12)" distinct mers\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:932:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 932 | " Found "uint64FMTW(12)" unique mers\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:933:13: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 933 | " Need "uint64FMT" non-unique position list entries ("uint64FMT" maximum count)\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:933:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 933 | " Need "uint64FMT" non-unique position list entries ("uint64FMT" maximum count)\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:955:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 955 | fprintf(stderr, " Rebuilding the hash table, from "uint32FMT" bits wide to "uint32FMT" bits wide.\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:955:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 955 | fprintf(stderr, " Rebuilding the hash table, from "uint32FMT" bits wide to "uint32FMT" bits wide.\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:990:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 990 | fprintf(stderr, " Loading "uint64FMT" mercounts.\n", counts->numberOfDistinctMers()); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:1013:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1013 | fprintf(stderr, " Loaded "uint64FMT" mercounts; largest is "uint64FMT".\n", countsLoaded, largestMerylCount); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:1013:45: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1013 | fprintf(stderr, " Loaded "uint64FMT" mercounts; largest is "uint64FMT".\n", countsLoaded, largestMerylCount); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:1017:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1017 | fprintf(stderr, " Compress sizes from "uint32FMT" bits to "uint32FMT" bits.\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:1017:60: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1017 | fprintf(stderr, " Compress sizes from "uint32FMT" bits to "uint32FMT" bits.\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C: In member function ‘void positionDB::build(merStream*, existDB*, existDB*, merylStreamReader*, uint32, uint32, bool)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:324:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 324 | } catch (std::bad_alloc) { | ^~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:433:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 433 | } catch (std::bad_alloc) { | ^~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:641:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 641 | } catch (std::bad_alloc) { | ^~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:672:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 672 | } catch (std::bad_alloc) { | ^~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.C:683:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 683 | } catch (std::bad_alloc) { | ^~~~~~~~~ rm -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a && ar ruvs /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-dump.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-fasta.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-meryl.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-create-from-sequence.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB-state.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-access.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-dump.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-file.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-mismatch.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB-sort.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C:72:2: warning: #warning not checking pmagic [-Wcpp] 72 | #warning not checking pmagic | ^~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C:134:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 134 | fprintf(stderr, "merylStreamReader()-- ERROR: User requested mersize "uint32FMT" but '%s' is mersize "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C:134:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 134 | fprintf(stderr, "merylStreamReader()-- ERROR: User requested mersize "uint32FMT" but '%s' is mersize "uint32FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C:6:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 6 | static char *ImagicV = "merylStreamIv03\n"; | ^~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C:7:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 7 | static char *ImagicX = "merylStreamIvXX\n"; | ^~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C:8:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 8 | static char *DmagicV = "merylStreamDv03\n"; | ^~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C:9:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 9 | static char *DmagicX = "merylStreamDvXX\n"; | ^~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C:10:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 10 | static char *PmagicV = "merylStreamPv03\n"; | ^~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C:11:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 11 | static char *PmagicX = "merylStreamPvXX\n"; | ^~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C: In constructor ‘merylStreamReader::merylStreamReader(const char*, uint32)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C:42:11: warning: variable ‘Pmagic’ set but not used [-Wunused-but-set-variable] 42 | char Pmagic[16] = {0}; | ^~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C: In member function ‘void merylStreamWriter::addMer(uint64, uint32, uint64, uint32, uint32, uint32*)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.C:469:31: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 469 | (prefix <= _thisMerPre) && (mer < _thisMerMer)) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ rm -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a && ar ruvs /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.o g++ -Wl,-z,relro -Wl,-z,now -o seatac/seatac seatac/seatac.o seatac/configuration.o seatac/encodedQuery.o seatac/hitMatrix.o seatac/thr-search.o seatac/thr-loader.o seatac/thr-deadlock.o seatac/hitMatrix-sort.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/heavychains-driver.o -c seatac/heavychains-driver.C In file included from seatac/heavychains.H:11, from seatac/heavychains-driver.C:24: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ seatac/heavychains.H: In member function ‘double DPTree::matchScore(kd_node, Match&)’: seatac/heavychains.H:374:19: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 374 | if ( (flo.X() && node[flo.intv].lo <= p.xlo || | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/heavychains.o -c seatac/heavychains.C In file included from seatac/heavychains.H:11, from seatac/heavychains.C:22: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ seatac/heavychains.C:96:22: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stderr,"HeavyChains: filtering strands "uint32FMT" "uint32FMT" "uint32FMT"\n", iid1, iid2, Plen); | ^ seatac/heavychains.C:96:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stderr,"HeavyChains: filtering strands "uint32FMT" "uint32FMT" "uint32FMT"\n", iid1, iid2, Plen); | ^ seatac/heavychains.C:96:76: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stderr,"HeavyChains: filtering strands "uint32FMT" "uint32FMT" "uint32FMT"\n", iid1, iid2, Plen); | ^ seatac/heavychains.C:164:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 164 | fprintf(stderr, "heavychains: out "uint32FMTW(8)" %8d %8d -- "uint32FMTW(8)" %8d %8d\n", | ^ seatac/heavychains.C:164:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 164 | fprintf(stderr, "heavychains: out "uint32FMTW(8)" %8d %8d -- "uint32FMTW(8)" %8d %8d\n", | ^ seatac/heavychains.C:169:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(outF, "M x H"uint64FMT" . %s:"uint32FMT" %d %d %d %s:"uint32FMT" %d %d %d > /hf=%.1f /hr=%.1f\n", | ^ seatac/heavychains.C:169:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(outF, "M x H"uint64FMT" . %s:"uint32FMT" %d %d %d %s:"uint32FMT" %d %d %d > /hf=%.1f /hr=%.1f\n", | ^ seatac/heavychains.C:169:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(outF, "M x H"uint64FMT" . %s:"uint32FMT" %d %d %d %s:"uint32FMT" %d %d %d > /hf=%.1f /hr=%.1f\n", | ^ seatac/heavychains.C:186:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 186 | fprintf(stderr, "HeavyChains: finished strands "uint32FMTW(8)" "uint32FMTW(8)" maxlen1=%f maxlen2=%f maxScoreFwd=%f maxScoreRef=%f\n", | ^ seatac/heavychains.C:186:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 186 | fprintf(stderr, "HeavyChains: finished strands "uint32FMTW(8)" "uint32FMTW(8)" maxlen1=%f maxlen2=%f maxScoreFwd=%f maxScoreRef=%f\n", | ^ seatac/heavychains.H: In member function ‘double DPTree::matchScore(kd_node, Match&)’: seatac/heavychains.H:374:19: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 374 | if ( (flo.X() && node[flo.intv].lo <= p.xlo || | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o seatac/heavychains seatac/heavychains-driver.o seatac/heavychains.o -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/filter-nop.o -c seatac/filter-nop.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from seatac/filter-nop.C:9: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from seatac/filter-nop.C:10: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seatac/filter-nop.C:67:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:78: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:90: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C:67:102: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | "M x . . %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s "uint32FMT"\n", | ^ seatac/filter-nop.C: In function ‘void* construct(char*)’: seatac/filter-nop.C:116:16: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 116 | char *seq1 = "UNK"; | ^~~~~ seatac/filter-nop.C:117:16: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 117 | char *seq2 = "UNK"; | ^~~~~ rm -f seatac/filter-nop.so && g++ -Wl,-z,relro -Wl,-z,now -shared -o seatac/filter-nop.so seatac/filter-nop.o -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seatac/filter-heavychains.o -c seatac/filter-heavychains.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from seatac/filter-heavychains.C:24: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seatac/filter-heavychains.C:25: seatac/heavychains.H: In member function ‘double DPTree::matchScore(kd_node, Match&)’: seatac/heavychains.H:374:19: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 374 | if ( (flo.X() && node[flo.intv].lo <= p.xlo || | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seatac/heavychains.H: In function ‘void addHit(void*, char, uint32, uint32, uint32, uint32, uint32, uint32, uint32)’: seatac/heavychains.H:53:12: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 53 | strncpy(assemblyId1, assemblyid1, 31); | ^ seatac/heavychains.H:54:12: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 54 | strncpy(assemblyId2, assemblyid2, 31); | ^ seatac/heavychains.H:53:12: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 53 | strncpy(assemblyId1, assemblyid1, 31); | ^ seatac/heavychains.H:54:12: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 54 | strncpy(assemblyId2, assemblyid2, 31); | ^ seatac/heavychains.H:53:12: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 53 | strncpy(assemblyId1, assemblyid1, 31); | ^ seatac/heavychains.H:54:12: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation] 54 | strncpy(assemblyId2, assemblyid2, 31); | ^ rm -f seatac/filter-heavychains.so && g++ -Wl,-z,relro -Wl,-z,now -shared -o seatac/filter-heavychains.so seatac/filter-heavychains.o seatac/heavychains.o -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/leaff.o -c leaff/leaff.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/leaff.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/leaff.C:311:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 311 | fprintf(stderr, "WARNING: Didn't find sequence with iid '"uint32FMT"'\n", sid); | ^ leaff/leaff.C:400:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 400 | fprintf(stdout, "G\tseq\t%s:"uint32FMT"\t"uint32FMT"\t%s\n", | ^ leaff/leaff.C:400:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 400 | fprintf(stdout, "G\tseq\t%s:"uint32FMT"\t"uint32FMT"\t%s\n", | ^ leaff/leaff.C:469:22: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 469 | sprintf(def, "random"uint32FMTW(06), i); | ^ leaff/leaff.C:727:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 727 | fprintf(stderr, "Couldn't read "uint64FMT" bytes from '%s': %s\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/blocks.o -c leaff/blocks.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/blocks.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/blocks.C:32:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:32:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:32:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:32:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:40:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 40 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:40:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 40 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:40:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 40 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:40:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 40 | fprintf(stdout, "%c "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ leaff/blocks.C:42:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | fprintf(stdout, ". "uint32FMT" "uint32FMT" "uint32FMT"\n", s, pos, uint32ZERO); | ^ leaff/blocks.C:42:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | fprintf(stdout, ". "uint32FMT" "uint32FMT" "uint32FMT"\n", s, pos, uint32ZERO); | ^ leaff/blocks.C:42:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 42 | fprintf(stdout, ". "uint32FMT" "uint32FMT" "uint32FMT"\n", s, pos, uint32ZERO); | ^ leaff/blocks.C: In function ‘void dumpBlocks(char*)’: leaff/blocks.C:7:16: warning: unused variable ‘S’ [-Wunused-variable] 7 | seqInCore *S = 0L; | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/dups.o -c leaff/dups.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/dups.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/dups.C:26:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 26 | fprintf(stdout, uint32FMT" <-> "uint32FMT"\n", sa->getIID(), sb->getIID()); | ^ leaff/dups.C:28:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 28 | fprintf(stderr, "COLLISION DETECTED BETWEEN %s:"uint32FMT" AND %s:"uint32FMT"!\nPLEASE REPORT THIS TO bri@walenz.org!\n", | ^ leaff/dups.C:28:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 28 | fprintf(stderr, "COLLISION DETECTED BETWEEN %s:"uint32FMT" AND %s:"uint32FMT"!\nPLEASE REPORT THIS TO bri@walenz.org!\n", | ^ leaff/dups.C:52:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 52 | fprintf(stderr, "Internal error: found two copies of the same sequence iid ("uint32FMT")!\n", result[idx].i); | ^ leaff/dups.C:60:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 60 | fprintf(stdout, uint32FMT":%s\n"uint32FMT":%s\n\n", | ^ leaff/dups.C:64:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(stderr, "COLLISION DETECTED BETWEEN IID "uint32FMT" AND "uint32FMT"!\nPLEASE REPORT THIS TO bri@walenz.org!\n", | ^ leaff/dups.C:64:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 64 | fprintf(stderr, "COLLISION DETECTED BETWEEN IID "uint32FMT" AND "uint32FMT"!\nPLEASE REPORT THIS TO bri@walenz.org!\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/gc.o -c leaff/gc.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/gc.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/gc.C:68:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/partition.o -c leaff/partition.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/partition.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/partition.C:55:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | fprintf(stderr, "ERROR: Failed to partition "uint32FMT"\n", i); | ^ leaff/partition.C:62:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | sprintf(filename, "%s-"uint32FMTW(03)".fasta", prefix, o); | ^ leaff/partition.C:77:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 77 | fprintf(stderr, "Huh? '%s' "uint32FMT" != "uint32FMT"\n", S->header(), S->sequenceLength(), p[i].length); | ^ leaff/partition.C:77:51: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 77 | fprintf(stderr, "Huh? '%s' "uint32FMT" != "uint32FMT"\n", S->header(), S->sequenceLength(), p[i].length); | ^ leaff/partition.C:96:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stdout, uint32FMT"]("uint32FMT")", o, sizeP); | ^ leaff/partition.C:99:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 99 | fprintf(stdout, " "uint32FMT"("uint32FMT")", p[i].index, p[i].length); | ^ leaff/partition.C:99:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 99 | fprintf(stdout, " "uint32FMT"("uint32FMT")", p[i].index, p[i].length); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/simseq.o -c leaff/simseq.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from leaff/simseq.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o leaff/stats.o -c leaff/stats.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from leaff/stats.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ leaff/stats.C:110:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "numSeqs "uint32FMT"\n", numSeq); | ^ leaff/stats.C:112:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 112 | fprintf(stdout, "SPAN (smallest "uint32FMT" largest "uint32FMT")\n", Ls[numSeq-1], Ls[0]); | ^ leaff/stats.C:112:45: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 112 | fprintf(stdout, "SPAN (smallest "uint32FMT" largest "uint32FMT")\n", Ls[numSeq-1], Ls[0]); | ^ leaff/stats.C:114:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 114 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50s[i], l50s[i]); | ^ leaff/stats.C:114:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 114 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50s[i], l50s[i]); | ^ leaff/stats.C:114:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 114 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50s[i], l50s[i]); | ^ leaff/stats.C:115:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 115 | fprintf(stdout, "totLen "uint64FMTW(10)"\n", Ss); | ^ leaff/stats.C:116:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 116 | fprintf(stdout, "refLen "uint64FMTW(10)"\n", Rs); | ^ leaff/stats.C:118:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 118 | fprintf(stdout, "BASES (smallest "uint32FMT" largest "uint32FMT")\n", Lb[numSeq-1], Lb[0]); | ^ leaff/stats.C:118:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 118 | fprintf(stdout, "BASES (smallest "uint32FMT" largest "uint32FMT")\n", Lb[numSeq-1], Lb[0]); | ^ leaff/stats.C:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50b[i], l50b[i]); | ^ leaff/stats.C:120:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50b[i], l50b[i]); | ^ leaff/stats.C:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stdout, "n"uint32FMT" "uint32FMT" at index "uint32FMT"\n", 10 * i, n50b[i], l50b[i]); | ^ leaff/stats.C:121:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 121 | fprintf(stdout, "totLen "uint64FMTW(10)"\n", Sb); | ^ leaff/stats.C:122:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 122 | fprintf(stdout, "refLen "uint64FMTW(10)"\n", Rb); | ^ g++ -Wl,-z,relro -Wl,-z,now -o leaff/leaff leaff/leaff.o leaff/blocks.o leaff/dups.o leaff/gc.o leaff/partition.o leaff/simseq.o leaff/stats.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/meryl.o -c meryl/meryl.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/meryl.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/args.o -c meryl/args.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/args.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/args.C:26:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 26 | fprintf(stderr, "writeString()-- Failed to write string of length "uint32FMT": %s\n", len, strerror(errno)); | ^ meryl/args.C: In function ‘char* readString(FILE*)’: meryl/args.C:40:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 40 | fread(&len, sizeof(uint32), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ meryl/args.C:50:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 50 | fread(str, sizeof(char), len, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ meryl/args.C: In constructor ‘merylArgs::merylArgs(const char*)’: meryl/args.C:513:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 513 | fread(magic, sizeof(char), 16, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ meryl/args.C:521:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 521 | fread(this, sizeof(merylArgs), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/binaryOp.o -c meryl/binaryOp.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/meryl.H:4, from meryl/binaryOp.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/binaryOp.C:43:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stderr, "ERROR - mersize of '%s' is "uint32FMT"\n", args->mergeFiles[0], A->merSize()); | ^ meryl/binaryOp.C:44:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 44 | fprintf(stderr, "ERROR - mersize of '%s' is "uint32FMT"\n", args->mergeFiles[1], B->merSize()); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/build.o -c meryl/build.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/build.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/build.C:153:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 153 | sprintf(cmd, "qsub -t 1-"uint64FMT" -cwd -b n -j y -o %s-count-\\$TASK_ID.err %s -N mc%s %s-count.sh", | ^ meryl/build.C:156:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 156 | sprintf(cmd, "qsub -t 1-"uint64FMT" -cwd -b n -j y -o %s-count-\\$TASK_ID.err -N mc%s %s-count.sh", | ^ meryl/build.C:238:2: warning: #warning not submitting prepareBatch to grid [-Wcpp] 238 | #warning not submitting prepareBatch to grid | ^~~~~~~ meryl/build.C:293:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 293 | fprintf(stderr, " numMersActual = "uint64FMT"\n", args->numMersActual); | ^ meryl/build.C:294:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 294 | fprintf(stderr, " mersPerBatch = "uint64FMT"\n", args->mersPerBatch); | ^ meryl/build.C:295:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 295 | fprintf(stderr, " basesPerBatch = "uint64FMT"\n", args->basesPerBatch); | ^ meryl/build.C:296:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 296 | fprintf(stderr, " numBuckets = "uint64FMT" ("uint32FMT" bits)\n", args->numBuckets, args->numBuckets_log2); | ^ meryl/build.C:296:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 296 | fprintf(stderr, " numBuckets = "uint64FMT" ("uint32FMT" bits)\n", args->numBuckets, args->numBuckets_log2); | ^ meryl/build.C:297:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 297 | fprintf(stderr, " bucketPointerWidth = "uint32FMT"\n", args->bucketPointerWidth); | ^ meryl/build.C:298:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 298 | fprintf(stderr, " merDataWidth = "uint32FMT"\n", args->merDataWidth); | ^ meryl/build.C:305:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 305 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:305:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 305 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:305:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 305 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:305:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 305 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:310:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 310 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:310:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 310 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:310:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 310 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:310:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 310 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^ meryl/build.C:314:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 314 | fprintf(stderr, " numMersActual = "uint64FMT"\n", args->numMersActual); | ^ meryl/build.C:315:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 315 | fprintf(stderr, " mersPerBatch = "uint64FMT"\n", args->mersPerBatch); | ^ meryl/build.C:316:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 316 | fprintf(stderr, " basesPerBatch = "uint64FMT"\n", args->basesPerBatch); | ^ meryl/build.C:317:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 317 | fprintf(stderr, " numBuckets = "uint64FMT" ("uint32FMT" bits)\n", args->numBuckets, args->numBuckets_log2); | ^ meryl/build.C:317:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 317 | fprintf(stderr, " numBuckets = "uint64FMT" ("uint32FMT" bits)\n", args->numBuckets, args->numBuckets_log2); | ^ meryl/build.C:318:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 318 | fprintf(stderr, " bucketPointerWidth = "uint32FMT"\n", args->bucketPointerWidth); | ^ meryl/build.C:319:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 319 | fprintf(stderr, " merDataWidth = "uint32FMT"\n", args->merDataWidth); | ^ meryl/build.C:342:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 342 | sprintf(filename, "%s.batch"uint64FMT".mcdat", args->outputFile, segment); | ^ meryl/build.C:346:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 346 | fprintf(stderr, "Found result for batch "uint64FMT" in %s.\n", segment, filename); | ^ meryl/build.C:352:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 352 | fprintf(stderr, "Computing segment "uint64FMT" of "uint64FMT".\n", segment+1, args->segmentLimit); | ^ meryl/build.C:352:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 352 | fprintf(stderr, "Computing segment "uint64FMT" of "uint64FMT".\n", segment+1, args->segmentLimit); | ^ meryl/build.C:365:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 365 | fprintf(stderr, " Allocating "uint64FMT"MB for mer storage ("uint32FMT" bits wide).\n", | ^ meryl/build.C:365:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 365 | fprintf(stderr, " Allocating "uint64FMT"MB for mer storage ("uint32FMT" bits wide).\n", | ^ meryl/build.C:384:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 384 | fprintf(stderr, " Allocating "uint64FMT"MB for mer position storage.\n", | ^ meryl/build.C:390:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " Allocating "uint64FMT"MB for bucket pointer table ("uint32FMT" bits wide).\n", | ^ meryl/build.C:390:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 390 | fprintf(stderr, " Allocating "uint64FMT"MB for bucket pointer table ("uint32FMT" bits wide).\n", | ^ meryl/build.C:396:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 396 | fprintf(stderr, " Allocating "uint64FMT"MB for counting the size of each bucket.\n", args->numBuckets >> 18); | ^ meryl/build.C:477:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 477 | fprintf(stderr, " Releasing "uint64FMT"MB from counting the size of each bucket.\n", args->numBuckets >> 18); | ^ meryl/build.C:532:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 532 | sprintf(batchOutputFile, "%s.batch"uint64FMT, args->outputFile, segment); | ^ meryl/build.C:552:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 552 | fprintf(stderr, "ERROR: In segment "uint64FMT"\n", segment); | ^ meryl/build.C:553:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 553 | fprintf(stderr, "ERROR: Bucket "uint64FMT" (out of "uint64FMT") ends before it starts!\n", | ^ meryl/build.C:553:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 553 | fprintf(stderr, "ERROR: Bucket "uint64FMT" (out of "uint64FMT") ends before it starts!\n", | ^ meryl/build.C:555:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 555 | fprintf(stderr, "ERROR: start="uint64FMT"\n", st); | ^ meryl/build.C:556:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 556 | fprintf(stderr, "ERROR: end ="uint64FMT"\n", ed); | ^ meryl/build.C:561:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 561 | fprintf(stderr, "ERROR: In segment "uint64FMT"\n", segment); | ^ meryl/build.C:562:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 562 | fprintf(stderr, "ERROR: Bucket "uint64FMT" (out of "uint64FMT") is HUGE!\n", | ^ meryl/build.C:562:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 562 | fprintf(stderr, "ERROR: Bucket "uint64FMT" (out of "uint64FMT") is HUGE!\n", | ^ meryl/build.C:564:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 564 | fprintf(stderr, "ERROR: start="uint64FMT"\n", st); | ^ meryl/build.C:565:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 565 | fprintf(stderr, "ERROR: end ="uint64FMT"\n", ed); | ^ meryl/build.C:667:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 667 | fprintf(stderr, "Segment "uint64FMT" finished.\n", segment); | ^ meryl/build.C:705:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 705 | fprintf(stdout, "%s -countbatch "uint64FMT" -o %s\n", args->execName, s, args->outputFile); | ^ meryl/build.C:783:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 783 | sprintf(argv[argc], "%s.batch"uint32FMT, args->outputFile, i); | ^ meryl/build.C:807:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 807 | sprintf(filename, "%s.batch"uint32FMT".mcidx", args->outputFile, i); | ^ meryl/build.C:809:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 809 | sprintf(filename, "%s.batch"uint32FMT".mcdat", args->outputFile, i); | ^ meryl/build.C:811:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 811 | sprintf(filename, "%s.batch"uint32FMT".mcpos", args->outputFile, i); | ^ meryl/build.C: In function ‘void prepareBatch(merylArgs*)’: meryl/build.C:310:23: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘uint64’ {aka ‘long unsigned int’} [-Wformat=] 310 | fprintf(stderr, "Computing "uint64FMT" segments using "uint32FMT" threads and "uint64FMT"MB memory ("uint64FMT"MB if in one batch).\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 311 | estimateMemory(args->merSize, args->mersPerBatch, args->positionsEnabled) * args->numThreads, 312 | estimateMemory(args->merSize, args->numMersActual, args->positionsEnabled)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | uint64 {aka long unsigned int} meryl/build.C:310:23: warning: format ‘%lu’ expects a matching ‘long unsigned int’ argument [-Wformat=] meryl/build.C:310:23: warning: format ‘%lu’ expects a matching ‘long unsigned int’ argument [-Wformat=] meryl/build.C: In function ‘void runSegment(merylArgs*, uint64)’: meryl/build.C:412:8: warning: unused variable ‘mstring’ [-Wunused-variable] 412 | char mstring[256]; | ^~~~~~~ meryl/build.C: In function ‘void build(merylArgs*)’: meryl/build.C:769:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 769 | arga[argc] = false; argv[argc++] = "meryl-build-merge"; | ^~~~~~~~~~~~~~~~~~~ meryl/build.C:770:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 770 | arga[argc] = false; argv[argc++] = "-M"; | ^~~~ meryl/build.C:771:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 771 | arga[argc] = false; argv[argc++] = "merge"; | ^~~~~~~ meryl/build.C:775:22: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 775 | argv[argc++] = "-v"; | ^~~~ meryl/build.C:780:22: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 780 | argv[argc++] = "-s"; | ^~~~ meryl/build.C:787:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 787 | arga[argc] = false; argv[argc++] = "-o"; | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/build-threads.o -c meryl/build-threads.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/build-threads.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/dump.o -c meryl/dump.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/meryl.H:4, from meryl/dump.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/dump.C:17:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | fprintf(stdout, ">"uint64FMT"\n%s\n", | ^ meryl/dump.C:35:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(stdout, ">"uint64FMT, M->theCount()); | ^ meryl/dump.C:37:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 37 | fprintf(stdout, " "uint32FMT, M->getPosition(i)); | ^ meryl/dump.C:50:2: warning: #warning make this a test [-Wcpp] 50 | #warning make this a test | ^~~~~~~ meryl/dump.C:72:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 72 | fprintf(stdout, "Found "uint64FMT" mers.\n", M->numberOfTotalMers()); | ^ meryl/dump.C:73:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 73 | fprintf(stdout, "Found "uint64FMT" distinct mers.\n", M->numberOfDistinctMers()); | ^ meryl/dump.C:74:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 74 | fprintf(stdout, "Found "uint64FMT" unique mers.\n", M->numberOfUniqueMers()); | ^ meryl/dump.C:87:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Found "uint64FMT" mers.\n", M->numberOfTotalMers()); | ^ meryl/dump.C:88:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 88 | fprintf(stderr, "Found "uint64FMT" distinct mers.\n", M->numberOfDistinctMers()); | ^ meryl/dump.C:89:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 89 | fprintf(stderr, "Found "uint64FMT" unique mers.\n", M->numberOfUniqueMers()); | ^ meryl/dump.C:91:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(stderr, "Largest mercount is "uint64FMT"; "uint64FMT" mers are too big for histogram.\n", | ^ meryl/dump.C:91:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 91 | fprintf(stderr, "Largest mercount is "uint64FMT"; "uint64FMT" mers are too big for histogram.\n", | ^ meryl/dump.C:101:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 101 | fprintf(stdout, uint32FMT"\t"uint64FMT"\t%.4f\t%.4f\n", | ^ meryl/dump.C:148:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, uint32FMT"\t"uint64FMT"\n", d, hist[d]); | ^ meryl/dump.C:151:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 151 | fprintf(stderr, "huge\t"uint64FMT"\n", histHuge); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/estimate.o -c meryl/estimate.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/estimate.C:4: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/estimate.C:54:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "Can fit "uint64FMT" mers into table with prefix of "uint64FMT" bits, using %.3fMB (%.3fMB for positions)\n", | ^ meryl/estimate.C:54:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "Can fit "uint64FMT" mers into table with prefix of "uint64FMT" bits, using %.3fMB (%.3fMB for positions)\n", | ^ meryl/estimate.C:162:28: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 162 | fprintf(stderr, uint64FMT" "uint32FMT"-mers can be computed using "uint64FMT"MB memory.\n", | ^ meryl/estimate.C:162:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 162 | fprintf(stderr, uint64FMT" "uint32FMT"-mers can be computed using "uint64FMT"MB memory.\n", | ^ meryl/estimate.C: In function ‘uint64 estimateMemory(uint32, uint64, bool)’: meryl/estimate.C:77:13: warning: unused variable ‘N’ [-Wunused-variable] 77 | uint64 N = logBaseTwo64(numMers); // Width of the bucket pointer table | ^ meryl/estimate.C:73:11: warning: variable ‘tMin’ set but not used [-Wunused-but-set-variable] 73 | uint64 tMin = tMax; | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/merge.o -c meryl/merge.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/meryl.H:4, from meryl/merge.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/merge.C:14:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 14 | fprintf(stderr, "ERROR - must have at least two databases (you gave "uint32FMT")!\n", args->mergeFilesLen); | ^ meryl/merge.C: In function ‘void multipleOperations(merylArgs*)’: meryl/merge.C:237:10: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 237 | delete R; | ^ meryl/merge.C:37:71: note: returned from ‘void* operator new [](std::size_t)’ 37 | merylStreamReader **R = new merylStreamReader* [args->mergeFilesLen]; | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/unaryOp.o -c meryl/unaryOp.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/meryl.H:4, from meryl/unaryOp.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ rm -f meryl/libmerylguts.a && ar ruvs meryl/libmerylguts.a meryl/args.o meryl/binaryOp.o meryl/build.o meryl/build-threads.o meryl/dump.o meryl/estimate.o meryl/merge.o meryl/unaryOp.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating meryl/libmerylguts.a a - meryl/args.o a - meryl/binaryOp.o a - meryl/build.o a - meryl/build-threads.o a - meryl/dump.o a - meryl/estimate.o a - meryl/merge.o a - meryl/unaryOp.o g++ -Wl,-z,relro -Wl,-z,now -o meryl/meryl meryl/meryl.o meryl/libmerylguts.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/simple.o -c meryl/simple.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/simple.C:8: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/simple.C:98:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 98 | fprintf(stderr, "Guessing "uint64FMT" mers in input '%s'\n", numMers, inName); | ^ meryl/simple.C:99:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 99 | fprintf(stderr, "Allocating "uint64FMT"MB for mer storage.\n", numMers * 8 >> 20); | ^ meryl/simple.C:129:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "Found "uint64FMT" mers in input '%s'\n", theMersLen, inName); | ^ g++ -Wl,-z,relro -Wl,-z,now -o meryl/simple meryl/simple.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/mapMers.o -c meryl/mapMers.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/mapMers.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/mapMers.C:135:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 135 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:135:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 135 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:76: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:136:102: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 136 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t" | ^ meryl/mapMers.C:137:24: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:76: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:137:102: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 137 | uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:165:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 165 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:165:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 165 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:165:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 165 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:171:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stdout, "%s\t"uint64FMT"\tuncovered\n", S->header(), MS->thePositionInSequence()); | ^ meryl/mapMers.C:176:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 176 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:176:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 176 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:176:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 176 | fprintf(stdout, "%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", S->header(), beg, end+merSize, end+merSize - beg); | ^ meryl/mapMers.C:178:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stderr, "numCovReg: "uint64FMT"\n", numCovReg); | ^ meryl/mapMers.C:179:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 179 | fprintf(stderr, "lenCovReg: "uint64FMT"\n", lenCovReg); | ^ meryl/mapMers.C:193:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "%s\t%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:193:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "%s\t%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:193:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "%s\t%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:193:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "%s\t%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C:193:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 193 | fprintf(stdout, "%s\t%s\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\t"uint64FMT"\n", | ^ meryl/mapMers.C: In function ‘int main(int, char**)’: meryl/mapMers.C:21:13: warning: variable ‘beVerbose’ set but not used [-Wunused-but-set-variable] 21 | bool beVerbose = false; | ^~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o meryl/mapMers meryl/mapMers.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/mapMers-depth.o -c meryl/mapMers-depth.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from meryl/mapMers-depth.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o meryl/mapMers-depth meryl/mapMers-depth.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/kmer-mask.o -c meryl/kmer-mask.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from meryl/kmer-mask.C:4: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ meryl/kmer-mask.C:754:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 754 | fprintf(stderr, "aClean "FW"\n", g->thresholdCounts[0][0]); | ^ meryl/kmer-mask.C:755:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 755 | fprintf(stderr, "aMurky "FW"\n", g->thresholdCounts[1][0]); | ^ meryl/kmer-mask.C:756:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 756 | fprintf(stderr, "aMatch "FW"\n", g->thresholdCounts[2][0]); | ^ meryl/kmer-mask.C:757:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 757 | fprintf(stderr, "aMixed "FW"\n", g->thresholdCounts[3][0]); | ^ meryl/kmer-mask.C:760:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 760 | fprintf(stderr, "aClean "FW" "FW" "FW" "FW"\n", g->thresholdCounts[0][0], g->thresholdCounts[0][1], g->thresholdCounts[0][2], g->thresholdCounts[0][3]); | ^ meryl/kmer-mask.C:760:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 760 | fprintf(stderr, "aClean "FW" "FW" "FW" "FW"\n", g->thresholdCounts[0][0], g->thresholdCounts[0][1], g->thresholdCounts[0][2], g->thresholdCounts[0][3]); | ^ meryl/kmer-mask.C:760:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 760 | fprintf(stderr, "aClean "FW" "FW" "FW" "FW"\n", g->thresholdCounts[0][0], g->thresholdCounts[0][1], g->thresholdCounts[0][2], g->thresholdCounts[0][3]); | ^ meryl/kmer-mask.C:760:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 760 | fprintf(stderr, "aClean "FW" "FW" "FW" "FW"\n", g->thresholdCounts[0][0], g->thresholdCounts[0][1], g->thresholdCounts[0][2], g->thresholdCounts[0][3]); | ^ meryl/kmer-mask.C:761:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 761 | fprintf(stderr, "aMurky "FW" "FW" "FW" "FW"\n", g->thresholdCounts[1][0], g->thresholdCounts[1][1], g->thresholdCounts[1][2], g->thresholdCounts[1][3]); | ^ meryl/kmer-mask.C:761:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 761 | fprintf(stderr, "aMurky "FW" "FW" "FW" "FW"\n", g->thresholdCounts[1][0], g->thresholdCounts[1][1], g->thresholdCounts[1][2], g->thresholdCounts[1][3]); | ^ meryl/kmer-mask.C:761:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 761 | fprintf(stderr, "aMurky "FW" "FW" "FW" "FW"\n", g->thresholdCounts[1][0], g->thresholdCounts[1][1], g->thresholdCounts[1][2], g->thresholdCounts[1][3]); | ^ meryl/kmer-mask.C:761:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 761 | fprintf(stderr, "aMurky "FW" "FW" "FW" "FW"\n", g->thresholdCounts[1][0], g->thresholdCounts[1][1], g->thresholdCounts[1][2], g->thresholdCounts[1][3]); | ^ meryl/kmer-mask.C:762:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "aMatch "FW" "FW" "FW" "FW"\n", g->thresholdCounts[2][0], g->thresholdCounts[2][1], g->thresholdCounts[2][2], g->thresholdCounts[2][3]); | ^ meryl/kmer-mask.C:762:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "aMatch "FW" "FW" "FW" "FW"\n", g->thresholdCounts[2][0], g->thresholdCounts[2][1], g->thresholdCounts[2][2], g->thresholdCounts[2][3]); | ^ meryl/kmer-mask.C:762:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "aMatch "FW" "FW" "FW" "FW"\n", g->thresholdCounts[2][0], g->thresholdCounts[2][1], g->thresholdCounts[2][2], g->thresholdCounts[2][3]); | ^ meryl/kmer-mask.C:762:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 762 | fprintf(stderr, "aMatch "FW" "FW" "FW" "FW"\n", g->thresholdCounts[2][0], g->thresholdCounts[2][1], g->thresholdCounts[2][2], g->thresholdCounts[2][3]); | ^ meryl/kmer-mask.C:763:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 763 | fprintf(stderr, "aMixed "FW" "FW" "FW" "FW"\n", g->thresholdCounts[3][0], g->thresholdCounts[3][1], g->thresholdCounts[3][2], g->thresholdCounts[3][3]); | ^ meryl/kmer-mask.C:763:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 763 | fprintf(stderr, "aMixed "FW" "FW" "FW" "FW"\n", g->thresholdCounts[3][0], g->thresholdCounts[3][1], g->thresholdCounts[3][2], g->thresholdCounts[3][3]); | ^ meryl/kmer-mask.C:763:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 763 | fprintf(stderr, "aMixed "FW" "FW" "FW" "FW"\n", g->thresholdCounts[3][0], g->thresholdCounts[3][1], g->thresholdCounts[3][2], g->thresholdCounts[3][3]); | ^ meryl/kmer-mask.C:763:46: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 763 | fprintf(stderr, "aMixed "FW" "FW" "FW" "FW"\n", g->thresholdCounts[3][0], g->thresholdCounts[3][1], g->thresholdCounts[3][2], g->thresholdCounts[3][3]); | ^ meryl/kmer-mask.C: In member function ‘bool fastqRecord::load(FILE*, FILE*)’: meryl/kmer-mask.C:69:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | fgets(a1, 1024, FASTQ1); chomp(a1); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:70:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | fgets(a2, maxLength, FASTQ1); chomp(a2); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:71:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 71 | fgets(a3, 1024, FASTQ1); chomp(a3); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:72:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | fgets(a4, maxLength, FASTQ1); chomp(a4); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:83:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 83 | fgets(b1, 1024, FASTQ2); chomp(b1); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:84:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 84 | fgets(b2, maxLength, FASTQ2); chomp(b2); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:85:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85 | fgets(b3, 1024, FASTQ2); chomp(b3); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ meryl/kmer-mask.C:86:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 86 | fgets(b4, maxLength, FASTQ2); chomp(b4); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o meryl/kmer-mask meryl/kmer-mask.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/hitMatrix.o -c seagen/hitMatrix.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/hitMatrix.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.C:642:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:80: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.C:642:107: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 642 | sprintf(line, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seagen/hitMatrix.H:126:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/searchGENOME.o -c seagen/searchGENOME.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/searchGENOME.C:4: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seagen/hitMatrix.H:126:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/configuration.o -c seagen/configuration.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/configuration.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/configuration.C:84:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 84 | fprintf(stderr, "\n"uint32FMTW(7)" sequences in %5.2f seconds, %8.3f per second.\n", nq, tm, nq/tm); | ^ seagen/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seagen/hitMatrix.H:126:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/encodedQuery.o -c seagen/encodedQuery.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from seagen/encodedQuery.H:6, from seagen/encodedQuery.C:3: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seagen/encodedQuery.C:142:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 142 | fprintf(stderr, "encodedQuery::test()-- mersAvail incorrect: Recomputed:"uint32FMT" Real:"uint32FMT"\n", _mersAvail, _r_mersAvail); | ^ seagen/encodedQuery.C:142:88: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 142 | fprintf(stderr, "encodedQuery::test()-- mersAvail incorrect: Recomputed:"uint32FMT" Real:"uint32FMT"\n", _mersAvail, _r_mersAvail); | ^ seagen/encodedQuery.C:152:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 152 | fprintf(stderr, "encodedQuery::test()-- skip["uint32FMTW(4)"] incorrect: Acc:%d Real:%d\n", i, getSkip(i, true), _r_skip[i]); | ^ seagen/encodedQuery.C:160:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | fprintf(stderr, "encodedQuery::test()-- mers["uint32FMTW(4)"] incorrect: Acc:"uint64HEX" %s Real:"uint64HEX" %s\n", | ^ seagen/encodedQuery.C:160:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | fprintf(stderr, "encodedQuery::test()-- mers["uint32FMTW(4)"] incorrect: Acc:"uint64HEX" %s Real:"uint64HEX" %s\n", | ^ seagen/encodedQuery.C:160:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | fprintf(stderr, "encodedQuery::test()-- mers["uint32FMTW(4)"] incorrect: Acc:"uint64HEX" %s Real:"uint64HEX" %s\n", | ^ seagen/encodedQuery.C:209:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 209 | fprintf(stderr, "encodedQuery::addOutput()-- from "uint32FMT" to "uint32FMT" bytes.\n", | ^ seagen/encodedQuery.C:209:67: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 209 | fprintf(stderr, "encodedQuery::addOutput()-- from "uint32FMT" to "uint32FMT" bytes.\n", | ^ seagen/encodedQuery.C: In member function ‘void encodedQuery::addOutput(void*, uint32)’: seagen/encodedQuery.C:207:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 207 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/thr-deadlock.o -c seagen/thr-deadlock.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/thr-deadlock.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seagen/hitMatrix.H:126:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/thr-loader.o -c seagen/thr-loader.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/thr-loader.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seagen/hitMatrix.H:126:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ seagen/thr-loader.C: In function ‘void* loaderThread(void*)’: seagen/thr-loader.C:14:17: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 14 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/thr-search.o -c seagen/thr-search.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/thr-search.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seagen/hitMatrix.H:126:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/thr-output.o -c seagen/thr-output.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from seagen/searchGENOME.H:20, from seagen/thr-output.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/searchGENOME.H:22: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ In file included from seagen/searchGENOME.H:25: seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seagen/hitMatrix.H:126:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ seagen/thr-output.C: In function ‘void* writerThread(void*, void*)’: seagen/thr-output.C:48:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 48 | write(config._outputFile, query->theOutput(), query->theOutputLength()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seagen/thr-output.C:62:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 62 | write(config._matchCountsFile, str, strlen(str)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/hitMatrix-sort.o -c seagen/hitMatrix-sort.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from seagen/hitMatrix.H:8, from seagen/hitMatrix-sort.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/hitMatrix.H:9: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ seagen/hitMatrix.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H:128:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ seagen/hitMatrix.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64)’: seagen/hitMatrix.H:126:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 126 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/aHit.o -c seagen/aHit.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/aHit.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seagen/aHit.C:20:14: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C:20:98: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 20 | fprintf(F, "-%c -e "uint32FMT" -D "uint32FMT" "uint32FMT" "uint32FMT" -M "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/aHit.C: In function ‘void ahit_readBinary(aHit*, FILE*)’: seagen/aHit.C:12:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 12 | fread(a, sizeof(aHit), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o seagen/seagen seagen/hitMatrix.o seagen/searchGENOME.o seagen/configuration.o seagen/encodedQuery.o seagen/thr-deadlock.o seagen/thr-loader.o seagen/thr-search.o seagen/thr-output.o seagen/hitMatrix-sort.o seagen/aHit.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/hitConverter.o -c seagen/hitConverter.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/hitConverter.C:3: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seagen/hitConverter.C: In function ‘void asc2bin(FILE*, FILE*)’: seagen/hitConverter.C:39:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | fgets(b, 1024, I); | ~~~~~^~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o seagen/hitConverter seagen/hitConverter.o seagen/aHit.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filterEST.o -c seagen/filterEST.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/filterEST.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/filterEST.C:7: seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/filterEST.C:76:11: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 76 | " hits saved:"uint32FMTW(8)"/"uint32FMTW(8)" = %6.3f%%\r", | ^ seagen/filterEST.C:76:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 76 | " hits saved:"uint32FMTW(8)"/"uint32FMTW(8)" = %6.3f%%\r", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filterEST-complicated.o -c seagen/filterEST-complicated.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/filterEST-complicated.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/filterEST-complicated.C:7: seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/filterEST-complicated.C:67:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | fprintf(logFile, uint32FMT"] unique: aggressively filtered to "uint32FMT" hits out of "uint32FMT" hits.\n", | ^ seagen/filterEST-complicated.C:67:79: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 67 | fprintf(logFile, uint32FMT"] unique: aggressively filtered to "uint32FMT" hits out of "uint32FMT" hits.\n", | ^ seagen/filterEST-complicated.C:115:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 115 | fprintf(logFile, uint32FMT"] knee: filtered "uint32FMT" hits down to "uint32FMT" hits using threshold %f\n", | ^ seagen/filterEST-complicated.C:115:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 115 | fprintf(logFile, uint32FMT"] knee: filtered "uint32FMT" hits down to "uint32FMT" hits using threshold %f\n", | ^ seagen/filterEST-complicated.C:139:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(logFile, uint32FMT"] uniform: uniform signal strength, saving the first "uint32FMT" hits out of "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:139:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 139 | fprintf(logFile, uint32FMT"] uniform: uniform signal strength, saving the first "uint32FMT" hits out of "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:174:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 174 | fprintf(logFile, uint32FMT"] diff: has no clear signal knee, saving the first "uint32FMT" hits out of "uint32FMT" hits, best=%f, worst=%f, largestdiff=%f\n", | ^ seagen/filterEST-complicated.C:174:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 174 | fprintf(logFile, uint32FMT"] diff: has no clear signal knee, saving the first "uint32FMT" hits out of "uint32FMT" hits, best=%f, worst=%f, largestdiff=%f\n", | ^ seagen/filterEST-complicated.C:228:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 228 | fprintf(logFile, uint32FMT"] spike: at "uint32FMT", "uint32FMT" hits saved: thresh=%f, "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:228:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 228 | fprintf(logFile, uint32FMT"] spike: at "uint32FMT", "uint32FMT" hits saved: thresh=%f, "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:228:69: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 228 | fprintf(logFile, uint32FMT"] spike: at "uint32FMT", "uint32FMT" hits saved: thresh=%f, "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:277:31: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 277 | fprintf(logFile, uint32FMT"] is an unclassified signal, "uint32FMT" hits saved out of "uint32FMT" hits, best=%f, worst=%f\n", | ^ seagen/filterEST-complicated.C:277:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 277 | fprintf(logFile, uint32FMT"] is an unclassified signal, "uint32FMT" hits saved out of "uint32FMT" hits, best=%f, worst=%f\n", | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/hitReader.o -c seagen/hitReader.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/hitReader.H:7, from seagen/hitReader.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5, from seagen/hitReader.H:8: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ g++ -Wl,-z,relro -Wl,-z,now -o seagen/filterEST seagen/filterEST.o seagen/filterEST-complicated.o seagen/hitReader.o seagen/aHit.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filterMRNA.o -c seagen/filterMRNA.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/filterMRNA.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/filterMRNA.C:7: seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/filterMRNA.C:53:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 53 | fprintf(stderr, " scores at least %4.2f AND at least "uint32FMT" bases covered are always output\n", MC, ML); | ^ g++ -Wl,-z,relro -Wl,-z,now -o seagen/filterMRNA seagen/filterMRNA.o seagen/hitReader.o seagen/aHit.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filterNULL.o -c seagen/filterNULL.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/filterNULL.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/filterNULL.C:2: seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ g++ -Wl,-z,relro -Wl,-z,now -o seagen/filterNULL seagen/filterNULL.o seagen/hitReader.o seagen/aHit.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filtertest.o -c seagen/filtertest.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/filtertest.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ seagen/filtertest.C:180:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 180 | fprintf(stderr, "reading hits "uint32FMT"\r", hitsLen); | ^ seagen/filtertest.C:186:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 186 | fprintf(stderr, "reading hits "uint32FMT"\n", hitsLen); | ^ seagen/filtertest.C:308:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, "%f %f %f %6.4f %6.4f "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/filtertest.C:308:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, "%f %f %f %6.4f %6.4f "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/filtertest.C:308:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, "%f %f %f %6.4f %6.4f "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/filtertest.C:308:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, "%f %f %f %6.4f %6.4f "uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"\n", | ^ seagen/filtertest.C: In function ‘void ahit_readBinary(aHit*, FILE*)’: seagen/filtertest.C:39:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | fread(a, sizeof(aHit), 1, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ seagen/filtertest.C: In function ‘int main(int, char**)’: seagen/filtertest.C:162:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 162 | fgets(hitLine, 1024, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o seagen/filtertest seagen/filtertest.o -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/sortHits.o -c seagen/sortHits.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/sortHits.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ seagen/sortHits.C: In member function ‘bool aHitReader::readHit(aHit&)’: seagen/sortHits.C:52:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 52 | fgets(buffer, 1024, theFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ seagen/sortHits.C: In member function ‘void aHitTemporary::nextHit()’: seagen/sortHits.C:119:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 119 | fread(&hit, sizeof(aHit), 1, theFile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o seagen/sortHits seagen/sortHits.o seagen/aHit.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o seagen/filterESTsimple.o -c seagen/filterESTsimple.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from seagen/aHit.H:4, from seagen/filterESTsimple.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from seagen/aHit.H:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from seagen/filterESTsimple.C:12: seagen/hitReader.H:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ seagen/hitReader.H:62:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "hitReader::operator[]()-- ERROR: asked for hit "uint32FMT" out of "uint32FMT".\n", x, _listLen); | ^ g++ -Wl,-z,relro -Wl,-z,now -o seagen/filterESTsimple seagen/filterESTsimple.o seagen/hitReader.o seagen/aHit.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/cleanPolishes.o -c sim4dbutils/cleanPolishes.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/cleanPolishes.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/cleanPolishes.C:178:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stderr, "A big intron is one that is at least "uint32FMT"bp long.\n", intronLimit); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/cleanPolishes sim4dbutils/cleanPolishes.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/fixPolishesIID.o -c sim4dbutils/fixPolishesIID.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/fixPolishesIID.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/fixPolishesIID.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/fixPolishesIID sim4dbutils/fixPolishesIID.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/comparePolishes.o -c sim4dbutils/comparePolishes.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/comparePolishes.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/comparePolishes.C:308:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:118: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:145: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:308:158: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 308 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"OLAPTFMT"\t%f\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%8.3f\t%8.3f\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/comparePolishes.C:452:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 452 | fprintf(stderr, "ERROR! inA="uint32FMT" inB="uint32FMT"\n", inA, inB); | ^ sim4dbutils/comparePolishes.C:452:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 452 | fprintf(stderr, "ERROR! inA="uint32FMT" inB="uint32FMT"\n", inA, inB); | ^ sim4dbutils/comparePolishes.C:484:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:484:156: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 484 | fprintf(stderr, "IID:"uint32FMTW(8)" good:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\r", | ^ sim4dbutils/comparePolishes.C:520:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C:520:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C:520:64: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C:520:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C:520:110: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C:520:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 520 | fprintf(stderr, "\ngood:"uint32FMTW(4)" Anovel:"uint32FMTW(4)" Amulti:"uint32FMTW(4)" Bnovel:"uint32FMTW(4)" Bmulti:"uint32FMTW(4)" hairy:"uint32FMTW(4)"\n", | ^ sim4dbutils/comparePolishes.C: In function ‘int main(int, char**)’: sim4dbutils/comparePolishes.C:74:20: warning: variable ‘doGFF3’ set but not used [-Wunused-but-set-variable] 74 | bool doGFF3; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/s4p_overlap.o -c sim4dbutils/s4p_overlap.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from sim4dbutils/s4p_overlap.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/comparePolishes sim4dbutils/comparePolishes.o sim4dbutils/s4p_overlap.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/convertToAtac.o -c sim4dbutils/convertToAtac.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/convertToAtac.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/convertToAtac.C:279:31: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:122: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:279:134: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:31: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:122: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:286:134: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 286 | fprintf(stdout, "M u dupr"uint32FMT" dupp"uint32FMT" %s:"uint32FMT" "uint32FMT" "uint32FMT" 1 %s:"uint32FMT" "uint32FMT" "uint32FMT" %s\n", | ^ sim4dbutils/convertToAtac.C:330:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 330 | fprintf(stderr, "Fixed "uint32FMT" indel/mismatches.\n", totalFixed); | ^ sim4dbutils/convertToAtac.C: In function ‘int main(int, char**)’: sim4dbutils/convertToAtac.C:241:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 241 | if (e->_estAlignment[aPos] != '-') | ^ sim4dbutils/convertToAtac.C:310:16: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 310 | if (e->_estAlignment[aPos] != '-') | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/convertToAtac sim4dbutils/convertToAtac.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/convertToExtent.o -c sim4dbutils/convertToExtent.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/convertToExtent.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/convertToExtent.C:43:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:88: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:43:118: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 43 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C:50:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 50 | fprintf(stdout, "%s\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t%s\t"uint32FMT"\t"uint32FMT"\t%6.3f\t%6.3f\n", | ^ sim4dbutils/convertToExtent.C: In function ‘int main(int, char**)’: sim4dbutils/convertToExtent.C:59:8: warning: variable ‘beVerbose’ set but not used [-Wunused-but-set-variable] 59 | bool beVerbose = false; | ^~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/convertToExtent sim4dbutils/convertToExtent.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/convertPolishes.o -c sim4dbutils/convertPolishes.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/convertPolishes.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/convertPolishes.C:8: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/convertPolishes sim4dbutils/convertPolishes.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/detectChimera.o -c sim4dbutils/detectChimera.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/detectChimera.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/detectChimera.C:129:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stdout, uint32FMTW(3)"-"uint32FMTW(3)" %s%s ("uint32FMT","uint32FMT")\n", | ^ sim4dbutils/detectChimera.C:129:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stdout, uint32FMTW(3)"-"uint32FMTW(3)" %s%s ("uint32FMT","uint32FMT")\n", | ^ sim4dbutils/detectChimera.C:129:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stdout, uint32FMTW(3)"-"uint32FMTW(3)" %s%s ("uint32FMT","uint32FMT")\n", | ^ sim4dbutils/detectChimera.C:153:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 153 | fprintf(stdout, "first "uint32FMT" alignments.\n", maxPts); | ^ sim4dbutils/detectChimera.C: In function ‘int main(int, char**)’: sim4dbutils/detectChimera.C:19:10: warning: variable ‘beVerbose’ set but not used [-Wunused-but-set-variable] 19 | bool beVerbose = false; | ^~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/detectChimera sim4dbutils/detectChimera.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/depthOfPolishes.o -c sim4dbutils/depthOfPolishes.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/depthOfPolishes.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/depthOfPolishes.C:103:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 103 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/depthOfPolishes sim4dbutils/depthOfPolishes.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/filterPolishes.o -c sim4dbutils/filterPolishes.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/filterPolishes.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/filterPolishes.C:8: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/filterPolishes.C:178:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stderr, "Filtering at "uint32FMT"%% coverage and "uint32FMT"%% identity and "uint32FMT"bp.\n", minC, minI, minL); | ^ sim4dbutils/filterPolishes.C:178:45: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stderr, "Filtering at "uint32FMT"%% coverage and "uint32FMT"%% identity and "uint32FMT"bp.\n", minC, minI, minL); | ^ sim4dbutils/filterPolishes.C:178:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 178 | fprintf(stderr, "Filtering at "uint32FMT"%% coverage and "uint32FMT"%% identity and "uint32FMT"bp.\n", minC, minI, minL); | ^ sim4dbutils/filterPolishes.C:181:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | fprintf(stderr, "Filtering for cDNA idx "uint32FMT" and genomic idx "uint32FMT"\n", cdna, geno); | ^ sim4dbutils/filterPolishes.C:181:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 181 | fprintf(stderr, "Filtering for cDNA idx "uint32FMT" and genomic idx "uint32FMT"\n", cdna, geno); | ^ sim4dbutils/filterPolishes.C:183:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 183 | fprintf(stderr, "Filtering for cDNA idx "uint32FMT".\n", cdna); | ^ sim4dbutils/filterPolishes.C:185:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 185 | fprintf(stderr, "Filtering for genomic idx "uint32FMT".\n", geno); | ^ sim4dbutils/filterPolishes.C:259:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 259 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed) ("uint64FMT" failed/intractable)\r", | ^ sim4dbutils/filterPolishes.C:259:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 259 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed) ("uint64FMT" failed/intractable)\r", | ^ sim4dbutils/filterPolishes.C:264:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 264 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed)\r", | ^ sim4dbutils/filterPolishes.C:274:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 274 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed) ("uint64FMT" failed/intractable)\n", | ^ sim4dbutils/filterPolishes.C:274:52: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 274 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed) ("uint64FMT" failed/intractable)\n", | ^ sim4dbutils/filterPolishes.C:279:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 279 | fprintf(stderr, " Filter: %6.2f%% ("uint64FMT" matches processed)\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/filterPolishes sim4dbutils/filterPolishes.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/headPolishes.o -c sim4dbutils/headPolishes.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/headPolishes.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/headPolishes sim4dbutils/headPolishes.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/mappedCoverage.o -c sim4dbutils/mappedCoverage.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/mappedCoverage.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/mappedCoverage.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/mappedCoverage.C:94:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 94 | fprintf(stderr, "Found "uint32FMT" sequences in the input file.\n", covMax); | ^ sim4dbutils/mappedCoverage.C:130:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "ERROR: Found iid "uint32FMT", but only allocated "uint32FMT" places!\n", | ^ sim4dbutils/mappedCoverage.C:130:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "ERROR: Found iid "uint32FMT", but only allocated "uint32FMT" places!\n", | ^ sim4dbutils/mappedCoverage.C:153:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 153 | fprintf(stderr, "ERROR: Found iid "uint32FMT", but only allocated "uint32FMT" places!\n", | ^ sim4dbutils/mappedCoverage.C:153:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 153 | fprintf(stderr, "ERROR: Found iid "uint32FMT", but only allocated "uint32FMT" places!\n", | ^ sim4dbutils/mappedCoverage.C:219:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 219 | fprintf(stderr, "ERROR: range "uint32FMT"-"uint32FMT" out of bounds (seqLen = "uint32FMT")\n", | ^ sim4dbutils/mappedCoverage.C:219:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 219 | fprintf(stderr, "ERROR: range "uint32FMT"-"uint32FMT" out of bounds (seqLen = "uint32FMT")\n", | ^ sim4dbutils/mappedCoverage.C:219:66: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 219 | fprintf(stderr, "ERROR: range "uint32FMT"-"uint32FMT" out of bounds (seqLen = "uint32FMT")\n", | ^ sim4dbutils/mappedCoverage.C:242:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 242 | fprintf(C, uint32FMT"\t"uint32FMT"\t%5.3f\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/mappedCoverage.C:242:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 242 | fprintf(C, uint32FMT"\t"uint32FMT"\t%5.3f\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/mappedCoverage.C:242:60: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 242 | fprintf(C, uint32FMT"\t"uint32FMT"\t%5.3f\t"uint32FMT"\t"uint32FMT"\n", | ^ sim4dbutils/mappedCoverage.C: In function ‘int main(int, char**)’: sim4dbutils/mappedCoverage.C:106:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 106 | fgets(inLine, 1024, stdin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/mappedCoverage sim4dbutils/mappedCoverage.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/mergePolishes.o -c sim4dbutils/mergePolishes.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/mergePolishes.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/mergePolishes.C: In function ‘int main(int, char**)’: sim4dbutils/mergePolishes.C:139:10: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 139 | delete inMatch; | ^~~~~~~ sim4dbutils/mergePolishes.C:28:62: note: returned from ‘void* operator new [](std::size_t)’ 28 | sim4polishReader **inMatch = new sim4polishReader * [argc]; | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/mergePolishes sim4dbutils/mergePolishes.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/parseSNP.o -c sim4dbutils/parseSNP.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/parseSNP.C:9: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/parseSNP.C:10: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/parseSNP.C:229:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:63: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:75: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:229:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 229 | fprintf(F, "%s %s "uint32FMT" %c/%c %s global["uint32FMT" "uint32FMT"] exon["uint32FMT" "uint32FMT" "uint32FMT" "uint32FMT"]\n", | ^ sim4dbutils/parseSNP.C:269:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:98: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:113: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:269:143: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 269 | fprintf(F, "%s %s "uint32FMT" sa=%c ga=%c mo=%c pi="uint32FMT" pc="uint32FMT" nb="uint32FMT" bl="uint32FMT" bp="uint32FMT" bi="uint32FMT" bc="uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:538:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 538 | fprintf(stderr, "ERROR: Polishes not sorted by SNP idx! this="uint32FMT", looking for "uint32FMT"\n", | ^ sim4dbutils/parseSNP.C:538:80: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 538 | fprintf(stderr, "ERROR: Polishes not sorted by SNP idx! this="uint32FMT", looking for "uint32FMT"\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/parseSNP sim4dbutils/parseSNP.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/pickBestPolish.o -c sim4dbutils/pickBestPolish.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/pickBestPolish.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/pickBestPolish.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/pickBestPolish.C:35:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(O, uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(4)" "uint32FMTW(4), | ^ sim4dbutils/pickBestPolish.C:35:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(O, uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(4)" "uint32FMTW(4), | ^ sim4dbutils/pickBestPolish.C:35:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 35 | fprintf(O, uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(4)" "uint32FMTW(4), | ^ sim4dbutils/pickBestPolish.C:39:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(O, " ("uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(3)")", | ^ sim4dbutils/pickBestPolish.C:39:33: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(O, " ("uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(3)")", | ^ sim4dbutils/pickBestPolish.C:39:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(O, " ("uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(3)")", | ^ sim4dbutils/pickBestPolish.C:39:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(O, " ("uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(3)")", | ^ sim4dbutils/pickBestPolish.C:39:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 39 | fprintf(O, " ("uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(6)"/"uint32FMTW(6)" "uint32FMTW(3)")", | ^ sim4dbutils/pickBestPolish.C:69:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 69 | fprintf(stderr, "Picking Best for estID="uint32FMT" with %5d choices.\r", p[0]->_estID, pNum); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/pickBestPolish sim4dbutils/pickBestPolish.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/pickBestPair.o -c sim4dbutils/pickBestPair.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/pickBestPair.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/pickBestPair.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/pickBestPair.C:546:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:52: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:80: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:546:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 546 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:52: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:80: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:569:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 569 | fprintf(LOG, "%c "uint32FMT" "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s ("uint32FMT","uint32FMT") "uint32FMT" %s\n", | ^ sim4dbutils/pickBestPair.C:584:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 584 | fprintf(STA, "alignments: "uint32FMT" "uint32FMT"\n", mr1END, mr2END); | ^ sim4dbutils/pickBestPair.C:584:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 584 | fprintf(STA, "alignments: "uint32FMT" "uint32FMT"\n", mr1END, mr2END); | ^ sim4dbutils/pickBestPair.C: In function ‘int main(int, char**)’: sim4dbutils/pickBestPair.C:266:19: warning: variable ‘minIdent’ set but not used [-Wunused-but-set-variable] 266 | double minIdent = 0; | ^~~~~~~~ sim4dbutils/pickBestPair.C:267:19: warning: variable ‘minLength’ set but not used [-Wunused-but-set-variable] 267 | double minLength = 0; | ^~~~~~~~~ sim4dbutils/pickBestPair.C:268:19: warning: variable ‘minCoverage’ set but not used [-Wunused-but-set-variable] 268 | double minCoverage = 0; | ^~~~~~~~~~~ sim4dbutils/pickBestPair.C: In function ‘bool readMR(FILE*, mapResult&)’: sim4dbutils/pickBestPair.C:54:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 54 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:57:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C: In function ‘bool readMRcoords(FILE*, mapResult&)’: sim4dbutils/pickBestPair.C:123:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 123 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:124:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 124 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:125:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 125 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:126:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 126 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:129:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 129 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C: In function ‘bool readMRcoords(FILE*, mapResult&, bool&)’: sim4dbutils/pickBestPair.C:189:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 189 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:190:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 190 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:191:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 191 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:192:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 192 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:195:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 195 | fgets(line, 1024, in); | ~~~~~^~~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C: In function ‘int main(int, char**)’: sim4dbutils/pickBestPair.C:354:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 354 | fgets(LL, 10240, IN); | ~~~~~^~~~~~~~~~~~~~~ sim4dbutils/pickBestPair.C:365:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 365 | fgets(LL, 10240, IN); | ~~~~~^~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/pickBestPair sim4dbutils/pickBestPair.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/pickUniquePolish.o -c sim4dbutils/pickUniquePolish.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from sim4dbutils/pickUniquePolish.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/pickUniquePolish.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/pickUniquePolish sim4dbutils/pickUniquePolish.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/plotCoverageVsIdentity.o -c sim4dbutils/plotCoverageVsIdentity.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/plotCoverageVsIdentity.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/plotCoverageVsIdentity.C:32:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(S, uint32FMT" "uint32FMT"\n", p->_percentIdentity, p->_querySeqIdentity); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/plotCoverageVsIdentity sim4dbutils/plotCoverageVsIdentity.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/removeDuplicate.o -c sim4dbutils/removeDuplicate.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/removeDuplicate.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/removeDuplicate sim4dbutils/removeDuplicate.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/sortPolishes.o -c sim4dbutils/sortPolishes.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/sortPolishes.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/sortPolishes.C:87:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Read: "uint32FMTW(8)" polishes -- "uint32FMTW(5)" temporary files -- "uint64FMTW(5)"MB / "uint64FMTW(5)"MB -- "uint64FMTW(5)" bytes/polish\r", | ^ sim4dbutils/sortPolishes.C:87:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Read: "uint32FMTW(8)" polishes -- "uint32FMTW(5)" temporary files -- "uint64FMTW(5)"MB / "uint64FMTW(5)"MB -- "uint64FMTW(5)" bytes/polish\r", | ^ sim4dbutils/sortPolishes.C:87:70: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Read: "uint32FMTW(8)" polishes -- "uint32FMTW(5)" temporary files -- "uint64FMTW(5)"MB / "uint64FMTW(5)"MB -- "uint64FMTW(5)" bytes/polish\r", | ^ sim4dbutils/sortPolishes.C:87:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Read: "uint32FMTW(8)" polishes -- "uint32FMTW(5)" temporary files -- "uint64FMTW(5)"MB / "uint64FMTW(5)"MB -- "uint64FMTW(5)" bytes/polish\r", | ^ sim4dbutils/sortPolishes.C:87:125: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 87 | fprintf(stderr, "Read: "uint32FMTW(8)" polishes -- "uint32FMTW(5)" temporary files -- "uint64FMTW(5)"MB / "uint64FMTW(5)"MB -- "uint64FMTW(5)" bytes/polish\r", | ^ sim4dbutils/sortPolishes.C: In function ‘sim4polish* savePolish(sim4polish*, uint64*)’: sim4dbutils/sortPolishes.C:39:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class sim4polish’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 39 | memcpy(r, q, sizeof(sim4polish)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:99:7: note: ‘class sim4polish’ declared here 99 | class sim4polish { | ^~~~~~~~~~ sim4dbutils/sortPolishes.C:59:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class sim4polishExon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 59 | memcpy(r->_exons, q->_exons, sizeof(sim4polishExon) * q->_numExons); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:49:7: note: ‘class sim4polishExon’ declared here 49 | class sim4polishExon { | ^~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/sortPolishes sim4dbutils/sortPolishes.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/summarizePolishes.o -c sim4dbutils/summarizePolishes.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/summarizePolishes.C:4: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/summarizePolishes.C:167:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 167 | fprintf(stderr, "numSeqs: "uint32FMT"\n", numSeqs); | ^ sim4dbutils/summarizePolishes.C:169:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 169 | fprintf(stderr, "ids: "uint32FMT" -- ", idLen); | ^ sim4dbutils/summarizePolishes.C:171:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 171 | fprintf(stderr, " "uint32FMT"", id[i]); | ^ sim4dbutils/summarizePolishes.C:173:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 173 | fprintf(stderr, "cvs: "uint32FMT" -- ", cvLen); | ^ sim4dbutils/summarizePolishes.C:175:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 175 | fprintf(stderr, " "uint32FMT"", cv[i]); | ^ sim4dbutils/summarizePolishes.C:244:34: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 244 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:244:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 244 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:244:60: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 244 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:244:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 244 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:244:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 244 | fprintf(stdout, uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:247:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 247 | fprintf(stdout, uint32FMTW(3)" "uint32FMTW(3)": mapped="uint32FMTW(8)" notmapped="uint32FMTW(8)" est="uint32FMTW(8)" gen="uint32FMTW(8)"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:247:54: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 247 | fprintf(stdout, uint32FMTW(3)" "uint32FMTW(3)": mapped="uint32FMTW(8)" notmapped="uint32FMTW(8)" est="uint32FMTW(8)" gen="uint32FMTW(8)"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:247:78: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 247 | fprintf(stdout, uint32FMTW(3)" "uint32FMTW(3)": mapped="uint32FMTW(8)" notmapped="uint32FMTW(8)" est="uint32FMTW(8)" gen="uint32FMTW(8)"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:247:104: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 247 | fprintf(stdout, uint32FMTW(3)" "uint32FMTW(3)": mapped="uint32FMTW(8)" notmapped="uint32FMTW(8)" est="uint32FMTW(8)" gen="uint32FMTW(8)"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ sim4dbutils/summarizePolishes.C:247:125: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 247 | fprintf(stdout, uint32FMTW(3)" "uint32FMTW(3)": mapped="uint32FMTW(8)" notmapped="uint32FMTW(8)" est="uint32FMTW(8)" gen="uint32FMTW(8)"\n", id[i], cv[c], mapped, notmapped, uniqest, uniqgen); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/summarizePolishes sim4dbutils/summarizePolishes.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/uniqPolishes.o -c sim4dbutils/uniqPolishes.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/uniqPolishes.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/uniqPolishes sim4dbutils/uniqPolishes.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/vennPolishes.o -c sim4dbutils/vennPolishes.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/vennPolishes.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/vennPolishes.C:115:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 115 | fprintf(stderr, "WARNING: You gave me "uint32FMT" files! That's pretty big. I don't know\n", numFiles); | ^ sim4dbutils/vennPolishes.C:175:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 175 | fprintf(stdout, " "uint32FMTW(8)" ", counts[index]); | ^ sim4dbutils/vennPolishes.C:183:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 183 | fprintf(stdout, "%c = ("uint32FMTW(8)" total) %s\n", 'A' + (char)i, sizes[i], argv[i+numArgs]); | ^ sim4dbutils/vennPolishes.C:189:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 189 | fprintf(stdout, "] "uint32FMT"\n", counts[index]); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/vennPolishes sim4dbutils/vennPolishes.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/realignPolishes.o -c sim4dbutils/realignPolishes.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/realignPolishes.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/realignPolishes.C:160:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | "MERGE: "uint32FMTW(4)"-"uint32FMTW(4)" (%6.2f,%6.2f) "uint32FMTW(4)"-"uint32FMTW(4) | ^ sim4dbutils/realignPolishes.C:160:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | "MERGE: "uint32FMTW(4)"-"uint32FMTW(4)" (%6.2f,%6.2f) "uint32FMTW(4)"-"uint32FMTW(4) | ^ sim4dbutils/realignPolishes.C:160:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | "MERGE: "uint32FMTW(4)"-"uint32FMTW(4)" (%6.2f,%6.2f) "uint32FMTW(4)"-"uint32FMTW(4) | ^ sim4dbutils/realignPolishes.C:160:89: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 160 | "MERGE: "uint32FMTW(4)"-"uint32FMTW(4)" (%6.2f,%6.2f) "uint32FMTW(4)"-"uint32FMTW(4) | ^ sim4dbutils/realignPolishes.C:161:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 161 | " and "uint32FMTW(8)"-"uint32FMTW(8)" (%6.2f,%6.2f) "uint32FMTW(8)"-"uint32FMTW(8)"\n", | ^ sim4dbutils/realignPolishes.C:161:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 161 | " and "uint32FMTW(8)"-"uint32FMTW(8)" (%6.2f,%6.2f) "uint32FMTW(8)"-"uint32FMTW(8)"\n", | ^ sim4dbutils/realignPolishes.C:161:57: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 161 | " and "uint32FMTW(8)"-"uint32FMTW(8)" (%6.2f,%6.2f) "uint32FMTW(8)"-"uint32FMTW(8)"\n", | ^ sim4dbutils/realignPolishes.C:161:87: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 161 | " and "uint32FMTW(8)"-"uint32FMTW(8)" (%6.2f,%6.2f) "uint32FMTW(8)"-"uint32FMTW(8)"\n", | ^ sim4dbutils/realignPolishes.C:243:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | fprintf(stdout, "WARNING: CHANGED! "uint32FMT" -> "uint32FMT"\n", nm, p->_numMatches); | ^ sim4dbutils/realignPolishes.C:243:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 243 | fprintf(stdout, "WARNING: CHANGED! "uint32FMT" -> "uint32FMT"\n", nm, p->_numMatches); | ^ sim4dbutils/realignPolishes.C:248:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(mergeLog, "MERGED\tEST\t"uint32FMT"\tfrom\t%8.3f\t%8.3f\tto\t%8.3f\t%8.3f\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/realignPolishes sim4dbutils/realignPolishes.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/removeRedundant.o -c sim4dbutils/removeRedundant.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4dbutils/removeRedundant.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/removeRedundant.C:107:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "IID="uint32FMTW(8)" -- overlap:"uint32FMT" noOverlap:"uint32FMT"\r", | ^ sim4dbutils/removeRedundant.C:107:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "IID="uint32FMTW(8)" -- overlap:"uint32FMT" noOverlap:"uint32FMT"\r", | ^ sim4dbutils/removeRedundant.C:107:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 107 | fprintf(stderr, "IID="uint32FMTW(8)" -- overlap:"uint32FMT" noOverlap:"uint32FMT"\r", | ^ sim4dbutils/removeRedundant.C:212:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "\nNOT A PERFECT CLIQUE! Found "uint32FMT" overlaps, wanted "uint32FMT" in the clique.\n", | ^ sim4dbutils/removeRedundant.C:212:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 212 | fprintf(stderr, "\nNOT A PERFECT CLIQUE! Found "uint32FMT" overlaps, wanted "uint32FMT" in the clique.\n", | ^ sim4dbutils/removeRedundant.C:260:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 260 | fprintf(stderr, "\nmatches withOvl:"uint32FMT" withoutOvl:"uint32FMT"\n", | ^ sim4dbutils/removeRedundant.C:260:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 260 | fprintf(stderr, "\nmatches withOvl:"uint32FMT" withoutOvl:"uint32FMT"\n", | ^ sim4dbutils/removeRedundant.C:262:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 262 | fprintf(stderr, "not perfect clique:"uint32FMT"\n", notPerfectClique); | ^ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/removeRedundant sim4dbutils/removeRedundant.o sim4dbutils/s4p_overlap.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4dbutils/reportAlignmentDifferences.o -c sim4dbutils/reportAlignmentDifferences.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4polish/sim4polish.H:11, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/sim4.H:1, from sim4dbutils/reportAlignmentDifferences.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4dbutils/reportAlignmentDifferences.C: In function ‘int main(int, char**)’: sim4dbutils/reportAlignmentDifferences.C:155:12: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 155 | if (e->_estAlignment[aPos] != '-') | ^ sim4dbutils/reportAlignmentDifferences.C:201:9: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 201 | system(gnuCmd); | ~~~~~~^~~~~~~~ sim4dbutils/reportAlignmentDifferences.C:200:30: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 4086 [-Wformat-overflow=] 200 | sprintf(gnuCmd, "gnuplot < %s", gnuName); | ^~ ~~~~~~~ In file included from /usr/include/stdio.h:970, from sim4dbutils/reportAlignmentDifferences.C:1: In function ‘int sprintf(char*, const char*, ...)’, inlined from ‘int main(int, char**)’ at sim4dbutils/reportAlignmentDifferences.C:200:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 11 and 4106 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4dbutils/reportAlignmentDifferences sim4dbutils/reportAlignmentDifferences.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o sim4db/sim4th.o -c sim4db/sim4th.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from sim4db/sim4th.C:34: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ sim4db/sim4th.C:327:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 327 | sprintf(str, "%s -Y "uint32FMT" "uint32FMT"\n", | ^ sim4db/sim4th.C:327:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 327 | sprintf(str, "%s -Y "uint32FMT" "uint32FMT"\n", | ^ sim4db/sim4th.C: In function ‘void writer(void*, void*)’: sim4db/sim4th.C:316:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 316 | write(fOutput, o, strlen(o) * sizeof(char)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sim4db/sim4th.C:332:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 332 | write(fYesNo, str, strlen(str) * sizeof(char)); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o sim4db/sim4db sim4db/sim4th.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/snapper2.o -c snapper/snapper2.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/snapper2.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.C:59:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 59 | fprintf(F, "%6.4f %6.4f %6.4f %6.4f %6.4f "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)"\n", | ^ snapper/snapper2.C:59:65: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 59 | fprintf(F, "%6.4f %6.4f %6.4f %6.4f %6.4f "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)"\n", | ^ snapper/snapper2.C:59:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 59 | fprintf(F, "%6.4f %6.4f %6.4f %6.4f %6.4f "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)"\n", | ^ snapper/snapper2.C:59:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 59 | fprintf(F, "%6.4f %6.4f %6.4f %6.4f %6.4f "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)" "uint32FMTW(8)"\n", | ^ snapper/snapper2.C:248:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stderr, "WARNING: Found "uint32FMT" queries shorter than minimum reportable size (-discardexonlength = "uint32FMT")\n", | ^ snapper/snapper2.C:248:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 248 | fprintf(stderr, "WARNING: Found "uint32FMT" queries shorter than minimum reportable size (-discardexonlength = "uint32FMT")\n", | ^ snapper/snapper2.C:254:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 254 | fprintf(stderr, "WARNING: Found "uint32FMT" queries longer than maximum size ("uint32FMT")\n", | ^ snapper/snapper2.C:254:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 254 | fprintf(stderr, "WARNING: Found "uint32FMT" queries longer than maximum size ("uint32FMT")\n", | ^ snapper/snapper2.C:295:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 295 | fprintf(stderr, "Created "uint32FMT" filters (out of "uint32FMT" available) to test/validate.\n", | ^ snapper/snapper2.C:295:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 295 | fprintf(stderr, "Created "uint32FMT" filters (out of "uint32FMT" available) to test/validate.\n", | ^ snapper/snapper2.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64, uint64)’: snapper/snapper2.H:419:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ snapper/snapper2.C: In function ‘void writerThread(void*, void*)’: snapper/snapper2.C:155:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | write(resultFILE, qry->theOutput, sizeof(char) * qry->theOutputLen); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H: In member function ‘void logMsg::write(int, const char*)’: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:85:12: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85 | ::write(file, _log, sizeof(char) * _logLen); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/configuration.o -c snapper/configuration.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/configuration.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/configuration.C:205:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 205 | fprintf(stderr, "ERROR: Invalid afLength "uint32FMT", should be < 64.\n", _afLength), err++; | ^ snapper/snapper2.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64, uint64)’: snapper/snapper2.H:419:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/thr-search.o -c snapper/thr-search.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/thr-search.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64, uint64)’: snapper/snapper2.H:419:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/thr-filter.o -c snapper/thr-filter.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/thr-filter.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64, uint64)’: snapper/snapper2.H:419:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/thr-polish.o -c snapper/thr-polish.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/thr-polish.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/thr-polish.C:311:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 311 | fprintf(stderr, "doPolish()-- Can't reallocate space for the output string ("uint32FMT" bytes) in thread "uint64FMT"\n", qry->theOutputMax, state->threadID); | ^ snapper/thr-polish.C:311:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 311 | fprintf(stderr, "doPolish()-- Can't reallocate space for the output string ("uint32FMT" bytes) in thread "uint64FMT"\n", qry->theOutputMax, state->threadID); | ^ snapper/snapper2.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64, uint64)’: snapper/snapper2.H:419:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/thr-polish-dp.o -c snapper/thr-polish-dp.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/thr-polish-dp.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/thr-polish-dp.C:89:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 89 | fprintf(stderr, "dpMatrix-- reallocate to "uint32FMT" x "uint32FMT"\n", aMax, bMax); | ^ snapper/thr-polish-dp.C:89:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 89 | fprintf(stderr, "dpMatrix-- reallocate to "uint32FMT" x "uint32FMT"\n", aMax, bMax); | ^ snapper/thr-polish-dp.C:441:29: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 441 | fprintf(stderr, "doPolish()-- Can't reallocate space for the output string ("uint32FMT" bytes) in thread "uint64FMT"\n", qry->theOutputMax, state->threadID); | ^ snapper/thr-polish-dp.C:441:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 441 | fprintf(stderr, "doPolish()-- Can't reallocate space for the output string ("uint32FMT" bytes) in thread "uint64FMT"\n", qry->theOutputMax, state->threadID); | ^ snapper/snapper2.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64, uint64)’: snapper/snapper2.H:419:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/hitMatrix.o -c snapper/hitMatrix.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/hitMatrix.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/hitMatrix.C:385:27: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 385 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT".\n", theHitsPos, theHitsMax); | ^ snapper/hitMatrix.C:385:95: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 385 | fprintf(stderr, "hitMatrix::filter()-- tried to extend output string from "uint32FMT" to "uint32FMT".\n", theHitsPos, theHitsMax); | ^ snapper/snapper2.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64, uint64)’: snapper/snapper2.H:419:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ snapper/hitMatrix.C: In member function ‘void hitMatrix::filter(char, double, uint32, aHit*&, uint32&, uint32&)’: snapper/hitMatrix.C:383:23: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 383 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o snapper/hitMatrix-sort.o -c snapper/hitMatrix-sort.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from snapper/snapper2.H:18, from snapper/hitMatrix-sort.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from snapper/snapper2.H:20: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ snapper/snapper2.H:421:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H:421:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 421 | fprintf(stderr, "hitMatrix::addHits()-- have "uint32FMT" hits, tried to add "uint64FMT" more\n", _hitsLen, cn); | ^ snapper/snapper2.H: In member function ‘void hitMatrix::addHits(uint32, uint64*, uint64, uint64)’: snapper/snapper2.H:419:19: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=] 419 | } catch (std::bad_alloc) { | ^~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o snapper/snapper2 snapper/snapper2.o snapper/configuration.o snapper/thr-search.o snapper/thr-filter.o snapper/thr-polish.o snapper/thr-polish-dp.o snapper/hitMatrix.o snapper/hitMatrix-sort.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tagger.o -c tapper/tagger.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from tapper/tapperTag.H:1, from tapper/tagger.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tagger.C:2: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tagger.C:4: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tagger.C:151:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 151 | fprintf(stdout, "%s\tlength\t"uint32FMT"\n", tagfile, TF->metaData()->tagSize()); | ^ tapper/tagger.C:152:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 152 | fprintf(stdout, "%s\tnumMates\t"uint64FMT"\n", tagfile, TF->numberOfMatePairs()); | ^ tapper/tagger.C:153:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 153 | fprintf(stdout, "%s\tmean\t"uint32FMT"\n", tagfile, TF->metaData()->mean()); | ^ tapper/tagger.C:154:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 154 | fprintf(stdout, "%s\tstddev\t"uint32FMT"\n", tagfile, TF->metaData()->stddev()); | ^ tapper/tagger.C:157:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 157 | fprintf(stdout, "%s\tlength\t"uint32FMT"\n", tagfile, TF->metaData()->tagSize()); | ^ tapper/tagger.C:158:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 158 | fprintf(stdout, "%s\tnumTags\t"uint64FMT"\n", tagfile, TF->numberOfFragmentTags()); | ^ tapper/tagger.C:182:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:92: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:104: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:182:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 182 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\t>"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:191:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 191 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:191:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 191 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:191:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 191 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:191:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 191 | fprintf(stdout, ">"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t%s/%s\n", | ^ tapper/tagger.C:362:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 362 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t0\t"uint32FMT"\t%c\t%s%s\t%s\n", | ^ tapper/tagger.C:362:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 362 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t0\t"uint32FMT"\t%c\t%s%s\t%s\n", | ^ tapper/tagger.C:362:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 362 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t0\t"uint32FMT"\t%c\t%s%s\t%s\n", | ^ tapper/tagger.C:362:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 362 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t0\t"uint32FMT"\t%c\t%s%s\t%s\n", | ^ tapper/tagger.C:362:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 362 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t0\t"uint32FMT"\t%c\t%s%s\t%s\n", | ^ tapper/tapperResult.H: In member function ‘void tapperResultIndex::print(FILE*)’: tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 11 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 12 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 13 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 14 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 15 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 16 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 17 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 18 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 19 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function ‘char* tapperHit::printHit(char*, uint64)’: tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 9 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int tapper/tagger.C: In function ‘bool readTag(uint32, FILE*, FILE*, tapperTag*)’: tapper/tagger.C:52:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 52 | fgets(seqhdr, 1024, seq); | ~~~~~^~~~~~~~~~~~~~~~~~~ tapper/tagger.C:54:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 54 | fgets(seqhdr, 1024, seq); | ~~~~~^~~~~~~~~~~~~~~~~~~ tapper/tagger.C:55:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 55 | fgets(seqseq, 1024, seq); | ~~~~~^~~~~~~~~~~~~~~~~~~ tapper/tagger.C:57:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | fgets(qlthdr, 1024, qlt); | ~~~~~^~~~~~~~~~~~~~~~~~~ tapper/tagger.C:59:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 59 | fgets(qlthdr, 1024, qlt); | ~~~~~^~~~~~~~~~~~~~~~~~~ tapper/tagger.C:60:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | fgets(qltseq, 1024, qlt); | ~~~~~^~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o tapper/tagger tapper/tagger.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tapper.o -c tapper/tapper.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from tapper/tapperTag.H:1, from tapper/tapper.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tapper.C:2: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tapper.C:4: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ In file included from tapper/tapperGlobalData.H:1, from tapper/tapper.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ tapper/tapperGlobalData.H:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:109:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:144:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperGlobalData.H:144:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapper.C:633:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 633 | fprintf(stderr, "Reallocate t->numHappiesMax to "uint32FMT"\n", t->numHappiesMax); | ^ tapper/tapper.C:1048:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1048 | fprintf(stderr, "sizeof(tapperResultIndex) -- "sizetFMT"\n", sizeof(tapperResultIndex)); | ^ tapper/tapper.C:1049:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1049 | fprintf(stderr, "sizeof(tapperResultQV) -- "sizetFMT"\n", sizeof(tapperResultQV)); | ^ tapper/tapper.C:1050:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1050 | fprintf(stderr, "sizeof(tapperResultFragment) -- "sizetFMT"\n", sizeof(tapperResultFragment)); | ^ tapper/tapper.C:1051:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1051 | fprintf(stderr, "sizeof(tapperResultMated) -- "sizetFMT"\n", sizeof(tapperResultMated)); | ^ tapper/tapper.C:1052:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1052 | fprintf(stderr, "sizeof(tapperResultTangled) -- "sizetFMT"\n", sizeof(tapperResultTangled)); | ^ tapper/tapper.C:1053:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1053 | fprintf(stderr, "sizeof(tapperHit) -- "sizetFMT"\n", sizeof(tapperHit)); | ^ tapper/tapper.C:1054:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1054 | fprintf(stderr, "sizeof(tapperTag) -- "sizetFMT"\n", sizeof(tapperTag)); | ^ tapper/tapper.C:1124:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 1124 | fprintf(stderr, " all alignments. The default is "uint32FMT".\n", g->repeatThreshold); | ^ tapper/tapperResult.H: In member function ‘void tapperResultIndex::print(FILE*)’: tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 11 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 12 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 13 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 14 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 15 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 16 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 17 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 18 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 19 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function ‘char* tapperHit::printHit(char*, uint64)’: tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 9 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int tapper/tapper.C: In member function ‘bool tapperHit::alignToReference(tapperGlobalData*, uint32, uint32, char*, uint32)’: tapper/tapper.C:399:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32’ {aka ‘unsigned int’} [-Wsign-compare] 399 | if (_colorMismatch + _colorInconsistent > g->maxColorError) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ tapper/tapper.C:415:23: warning: comparison of integer expressions of different signedness: ‘uint32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 415 | for (uint32 ti=0; ti<_len-1; ti++) { | ~~^~~~~~~ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/recordFile.H:6, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:39: tapper/tapper.C:468:13: warning: comparison of integer expressions of different signedness: ‘uint32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 468 | assert(nn == _colorMismatch + _colorInconsistent); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tapper/tapper.C:7: tapper/tapperComputation.H: In constructor ‘tapperComputation::tapperComputation(tapperTag*, tapperTag*)’: tapper/tapperComputation.H:51:28: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 51 | tag1rseq[tag1size-1] = complementSymbol[tag1rseq[tag1size-1]]; | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tapper/tapperComputation.H:186:38: note: at offset 4294967295 into destination object ‘tapperComputation::tag1rseq’ of size 32 186 | char tag1fseq[TAG_LEN_MAX], tag1rseq[TAG_LEN_MAX]; | ^~~~~~~~ tapper/tapperComputation.H:75:28: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 75 | tag2rseq[tag2size-1] = complementSymbol[tag2rseq[tag2size-1]]; | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tapper/tapperComputation.H:187:38: note: at offset 4294967295 into destination object ‘tapperComputation::tag2rseq’ of size 32 187 | char tag2fseq[TAG_LEN_MAX], tag2rseq[TAG_LEN_MAX]; | ^~~~~~~~ In constructor ‘tapperComputation::tapperComputation(tapperTag*, tapperTag*)’, inlined from ‘void* tapperReader(void*)’ at tapper/tapper.C:28:39: tapper/tapperComputation.H:51:28: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 51 | tag1rseq[tag1size-1] = complementSymbol[tag1rseq[tag1size-1]]; | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tapper/tapperComputation.H: In function ‘void* tapperReader(void*)’: tapper/tapperComputation.H:186:38: note: at offset 4294967295 into destination object ‘tapperComputation::tag1rseq’ of size 32 186 | char tag1fseq[TAG_LEN_MAX], tag1rseq[TAG_LEN_MAX]; | ^~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o tapper/tapper tapper/tapper.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tapperconvert.o -c tapper/tapperconvert.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from tapper/tapperTag.H:1, from tapper/tapperconvert.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tapperconvert.C:2: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tapperconvert.C:4: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ In file included from tapper/tapperGlobalData.H:1, from tapper/tapperconvert.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ tapper/tapperGlobalData.H:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:109:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:144:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperGlobalData.H:144:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperResult.H: In member function ‘void tapperResultIndex::print(FILE*)’: tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 11 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 12 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 13 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 14 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 15 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 16 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 17 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 18 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 19 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function ‘char* tapperHit::printHit(char*, uint64)’: tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 9 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int g++ -Wl,-z,relro -Wl,-z,now -o tapper/tapperconvert tapper/tapperconvert.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tappermerge.o -c tapper/tappermerge.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from tapper/tapperTag.H:1, from tapper/tappermerge.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tappermerge.C:2: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tappermerge.C:4: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ In file included from tapper/tapperGlobalData.H:1, from tapper/tappermerge.C:5: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ tapper/tapperGlobalData.H:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:109:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:144:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperGlobalData.H:144:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperResult.H: In member function ‘void tapperResultIndex::print(FILE*)’: tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 11 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 12 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 13 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 14 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 15 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 16 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 17 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 18 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 19 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function ‘char* tapperHit::printHit(char*, uint64)’: tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 9 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int g++ -Wl,-z,relro -Wl,-z,now -o tapper/tappermerge tapper/tappermerge.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tappersort.o -c tapper/tappersort.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from tapper/tappersort.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from tapper/tappersort.C:3: tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tappersort.C:4: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tappersort.C:6: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ In file included from tapper/tapperGlobalData.H:1, from tapper/tappersort.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ tapper/tapperGlobalData.H:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:109:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:144:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperGlobalData.H:144:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tappersort.C:148:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | sprintf(filename, "%s."uint32FMTW(03)".tapperAlignment", outputName, outputIndex); | ^ tapper/tappersort.C:150:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 150 | fprintf(stderr, "Writing "uint32FMT" sorted alignments to '%s'\n", aliLen, filename); | ^ tapper/tappersort.C:202:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 202 | fprintf(stderr, "Can fit "uint32FMT" alignments into "uint64FMT" bytes memory; "uint32FMT" bytes each.\n", | ^ tapper/tappersort.C:202:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 202 | fprintf(stderr, "Can fit "uint32FMT" alignments into "uint64FMT" bytes memory; "uint32FMT" bytes each.\n", | ^ tapper/tappersort.C:202:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 202 | fprintf(stderr, "Can fit "uint32FMT" alignments into "uint64FMT" bytes memory; "uint32FMT" bytes each.\n", | ^ tapper/tappersort.C:257:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 257 | sprintf(filename, "%s."uint32FMTW(03)".tapperAlignment", outputName, x); | ^ tapper/tappersort.C:299:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 299 | sprintf(filename, "%s."uint32FMTW(03)".tapperAlignment", outputName, x); | ^ tapper/tapperResult.H: In member function ‘void tapperResultIndex::print(FILE*)’: tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 11 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 12 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 13 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 14 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 15 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 16 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 17 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 18 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 19 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function ‘char* tapperHit::printHit(char*, uint64)’: tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 9 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int g++ -Wl,-z,relro -Wl,-z,now -o tapper/tappersort tapper/tappersort.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o tapper/tappererrorcorrect.o -c tapper/tappererrorcorrect.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:4, from tapper/tappererrorcorrect.C:1: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from tapper/tappererrorcorrect.C:3: tapper/tapperTag.H:204:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 204 | fprintf(stderr, "tapperTagFile()-- ERROR! Tag file was built with TAPPER_TAG_WORDS="uint32FMT", but code has %d.\n", | ^ In file included from tapper/tappererrorcorrect.C:4: tapper/tapperResult.H:41:18: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:32: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:44: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:56: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:68: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:81: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:93: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:105: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:117: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:130: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:142: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:155: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:168: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:183: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:198: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:41:228: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^ tapper/tapperResult.H:116:2: warning: #warning do not know real tag length [-Wcpp] 116 | #warning do not know real tag length | ^~~~~~~ tapper/tapperResult.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:132:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:37: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:73: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:86: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:99: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:116: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:155:128: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 155 | fprintf(stdout, "F\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t'%s'\n", | ^ tapper/tapperResult.H:187:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:114: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:126: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:138: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:151: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:163: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:175: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:187: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:200: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:213: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:230: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:187:242: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 187 | fprintf(stdout, "M\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t%c\t"uint32FMT"/"uint32FMT"/"uint32FMT"\n", | ^ tapper/tapperResult.H:224:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:47: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:59: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:84: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:109: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:121: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:133: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:146: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:159: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ tapper/tapperResult.H:224:172: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 224 | fprintf(stdout, "T\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\t"uint32FMT"\n", | ^ In file included from tapper/tappererrorcorrect.C:6: tapper/tapperHit.H:17:17: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:30: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:43: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:55: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ tapper/tapperHit.H:17:83: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, | ^ In file included from tapper/tapperGlobalData.H:1, from tapper/tappererrorcorrect.C:7: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ tapper/tapperGlobalData.H:109:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:109:61: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 109 | fprintf(stderr, "ERROR: invalid partition n="uint32FMT" m="uint32FMT".\n", thisPartition, numPartitions); | ^ tapper/tapperGlobalData.H:120:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:50: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:71: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:120:97: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 120 | fprintf(stderr, "Set partition for "uint64FMT" frags or "uint64FMT" mates: -begin "uint32FMT" -end "uint32FMT"\n", | ^ tapper/tapperGlobalData.H:144:20: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tapperGlobalData.H:144:36: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 144 | sprintf(colName, "%s.ms"uint32FMT".ce"uint32FMT".posDB", genName, tagSize, maxColorError); | ^ tapper/tappererrorcorrect.C:25:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 25 | fprintf(stderr, "block "uint32FMT" has "uint32FMT" things.\n", i, alignsLen[i]); | ^ tapper/tappererrorcorrect.C:25:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 25 | fprintf(stderr, "block "uint32FMT" has "uint32FMT" things.\n", i, alignsLen[i]); | ^ tapper/tappererrorcorrect.C:49:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 49 | fprintf(stderr, "block[0] - seq "uint32FMT" pos "uint32FMT"\n", | ^ tapper/tappererrorcorrect.C:49:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 49 | fprintf(stderr, "block[0] - seq "uint32FMT" pos "uint32FMT"\n", | ^ tapper/tappererrorcorrect.C:62:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "block "uint32FMT" has "uint32FMT" things.\n", alignsMax-1, alignsLen[alignsMax-1]); | ^ tapper/tappererrorcorrect.C:62:40: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 62 | fprintf(stderr, "block "uint32FMT" has "uint32FMT" things.\n", alignsMax-1, alignsLen[alignsMax-1]); | ^ tapper/tappererrorcorrect.C:160:2: warning: #warning need the real read size here [-Wcpp] 160 | #warning need the real read size here | ^~~~~~~ tapper/tappererrorcorrect.C:213:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 213 | fprintf(stdout, "\nALIGN "uint32FMT"-"uint32FMT"\n", winLo, winHi); | ^ tapper/tappererrorcorrect.C:213:42: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 213 | fprintf(stdout, "\nALIGN "uint32FMT"-"uint32FMT"\n", winLo, winHi); | ^ tapper/tapperResult.H: In member function ‘void tapperResultIndex::print(FILE*)’: tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 11 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 12 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 44 | _maxColrMismatchMapped, _maxBaseMismatchMapped, | ~~~~~~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 13 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 14 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 45 | _mean, _stddev, | ~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 15 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 16 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 17 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 18 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~ | | | int tapper/tapperResult.H:41:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 19 has type ‘int’ [-Wformat=] 41 | fprintf(out, "R\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint16FMT"_"uint16FMT"_"uint16FMT"_"uint16FMT"\t"uint64FMT"/"uint64FMT"\t"uint64FMT"+-"uint64FMT"\tf:"uint64FMT"\td:"uint64FMT"\ts:"uint64FMT"\tm:"uint64FMT"\tt:"uint64FMT"\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 46 | _numFrag, _numFragDiscarded, _numFragSingleton, _numMated, _numTangled); | ~~~~~~~~~~~ | | | int tapper/tapperHit.H: In member function ‘char* tapperHit::printHit(char*, uint64)’: tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~ | | | int tapper/tapperHit.H:17:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 9 has type ‘int’ [-Wformat=] 17 | sprintf(OS, "0x"uint64FMT"\t"uint32FMT":"uint32FMT":%c\t"uint64FMT","uint64FMT","uint64FMT, ...... 20 | _basesMismatch, _colorMismatch, _colorInconsistent); | ~~~~~~~~~~~~~~~~~~ | | | int tapper/tappererrorcorrect.C: In function ‘int main(int, char**)’: tapper/tappererrorcorrect.C:102:13: warning: variable ‘memoryLimit’ set but not used [-Wunused-but-set-variable] 102 | uint64 memoryLimit = 1024 * 1024 * 1024; | ^~~~~~~~~~~ tapper/tappererrorcorrect.C:141:21: warning: unused variable ‘id’ [-Wunused-variable] 141 | uint16 id[4]; | ^~ g++ -Wl,-z,relro -Wl,-z,now -o tapper/tappererrorcorrect tapper/tappererrorcorrect.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libsim4/libsim4.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-existDB.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-existDB.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-existDB.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-existDB.C:53:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 53 | fprintf(stderr, "mer "uint64HEX" not found : e=%d f=%d g=%d\n", m, ee, ef, eg); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-existDB.C:56:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | fprintf(stderr, "mer "uint64HEX" count differs : e=%u f=%u g=%u (exists=%d)\n", m, ce, cf, cg, ee); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-existDB.C:65:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | fprintf(stderr, "mer "uint64HEX" : e=%u f=%u g=%u (exists=%d)\n", m, ce, cf, cg, ee); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-existDB.C:96:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stderr, "Tried "uint64FMT", didn't find "uint64FMT" merStream mers in the existDB.\n", tried, lost); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-existDB.C:96:38: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 96 | fprintf(stderr, "Tried "uint64FMT", didn't find "uint64FMT" merStream mers in the existDB.\n", tried, lost); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-existDB.C:128:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "Found "uint64FMT" mers in the meryl database.\n", expected); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-existDB.C:148:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "Expected to find "uint64FMT" mers, but found "uint64FMT" instead.\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-existDB.C:148:49: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 148 | fprintf(stderr, "Expected to find "uint64FMT" mers, but found "uint64FMT" instead.\n", | ^ g++ -Wl,-z,relro -Wl,-z,now -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/existDB /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-existDB.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++03 -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/ -I/build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/ -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio.h:4, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:14, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:6: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:55:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 55 | #define uint64FMT "%"PRIu64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:56:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 56 | #define uint64HEX "0x%016"PRIx64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:58:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 58 | #define int64FMT "%"PRId64 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:65:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 65 | #define uint32FMT "%"PRIu32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:66:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 66 | #define uint32HEX "0x%08"PRIx32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:68:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | #define int32FMT "%"PRId32 | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util.h:75:26: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | #define uint16FMT "%"PRIu16 | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:37, from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/bio++.H:15: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedArray.H:222:39: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 222 | fprintf(stderr, "HEAP["uint32FMT"]="uint64FMT"\n", i, _array->get(i)); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:38: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:16: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/bitPackedFile.H:32:35: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 32 | fprintf(f, "inside: "uint64FMT" outside: "uint64FMT"\n", stat_seekInside, stat_seekOutside); | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/util++.H:43: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/logMsg.H:75:15: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 75 | "logMsg::add()-- HEY! I wrote "uint32FMT" bytes beyond the end of the buffer!\n" | ^ In file included from /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:8: /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:127:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 127 | fprintf(stderr, "shift1 = "uint32FMT"\n", _shift1); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:128:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 128 | fprintf(stderr, "shift2 = "uint32FMT"\n", _shift2); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:129:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 129 | fprintf(stderr, "M = "uint64HEX"\n", m); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:130:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 130 | fprintf(stderr, "H = "uint64HEX"\n", h); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:131:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 131 | fprintf(stderr, "C = "uint64HEX"\n", c); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB.H:132:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 132 | fprintf(stderr, "R = "uint64HEX"\n", r); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:54:25: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "%s @ "uint64FMT"/"uint64FMT": Found "uint64FMT" table entries, and "uint32FMT" matching positions (", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:54:41: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "%s @ "uint64FMT"/"uint64FMT": Found "uint64FMT" table entries, and "uint32FMT" matching positions (", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:54:53: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "%s @ "uint64FMT"/"uint64FMT": Found "uint64FMT" table entries, and "uint32FMT" matching positions (", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:54:72: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 54 | fprintf(stdout, "%s @ "uint64FMT"/"uint64FMT": Found "uint64FMT" table entries, and "uint32FMT" matching positions (", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:68:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 68 | fprintf(stdout, "Found no matches for mer=%s at pos="uint64FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:101:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 101 | fprintf(stdout, "Got a F match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:101:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 101 | fprintf(stdout, "Got a F match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:101:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 101 | fprintf(stdout, "Got a F match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:110:23: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "Got a R match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:110:62: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "Got a R match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:110:74: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 110 | fprintf(stdout, "Got a R match for mer=%s at "uint64FMT"/"uint64FMT" (in mers), numMatches="uint64FMT"\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:255:21: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 255 | fprintf(stderr, "ERROR: merbegin="uint64FMT" and merend="uint64FMT" are incompatible.\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:255:48: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 255 | fprintf(stderr, "ERROR: merbegin="uint64FMT" and merend="uint64FMT" are incompatible.\n", | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:275:19: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 275 | fprintf(stderr, "Building table with merSize "uint32FMT", merSkip "uint32FMT"\n", mersize, merskip); | ^ /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.C:275:58: warning: C++11 requires a space between string literal and macro [-Wc++11-compat] 275 | fprintf(stderr, "Building table with merSize "uint32FMT", merSkip "uint32FMT"\n", mersize, merskip); | ^ g++ -Wl,-z,relro -Wl,-z,now -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/positionDB /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/driver-posDB.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libkmer/libkmer.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libmeryl/libmeryl.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wl,-z,relro -Wl,-z,now -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqCache.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wl,-z,relro -Wl,-z,now -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-seqStream.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm g++ -Wl,-z,relro -Wl,-z,now -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/test-merStream.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libseq/libseq.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libbio/libbio.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/libutil.a -pthread -ldl -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/kmer-8W5TPl/kmer-0~20150903+r2013=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/test.o -c /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/test.c rm -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/libmt19937ar.a && ar ruvs /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/libmt19937ar.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/test.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/libmt19937ar.a a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/mt19937ar.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/mt19937ar/test.o rm -f /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/libkaz.a && ar ruvs /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/libkaz.a /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/dict.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/except.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/hash.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/list.o /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/sfx.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/libkaz.a a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/dict.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/except.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/hash.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/list.o a - /build/kmer-8W5TPl/kmer-0~20150903+r2013/libutil/kazlib/sfx.o make[2]: Leaving directory '/build/kmer-8W5TPl/kmer-0~20150903+r2013' mv installdir/bin/atac.pl installdir/bin/atac mv -v installdir/lib/halignmodule.so installdir/lib/halign.so renamed 'installdir/lib/halignmodule.so' -> 'installdir/lib/halign.so' mv -v installdir/lib/localAlignerInterfacemodule.so installdir/lib/localAlignerInterface.so renamed 'installdir/lib/localAlignerInterfacemodule.so' -> 'installdir/lib/localAlignerInterface.so' make[1]: Leaving directory '/build/kmer-8W5TPl/kmer-0~20150903+r2013' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j2 install DESTDIR=/build/kmer-8W5TPl/kmer-0\~20150903\+r2013/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[1]: Entering directory '/build/kmer-8W5TPl/kmer-0~20150903+r2013' make[1]: Leaving directory '/build/kmer-8W5TPl/kmer-0~20150903+r2013' dh_install debian/rules execute_after_dh_install make[1]: Entering directory '/build/kmer-8W5TPl/kmer-0~20150903+r2013' for perlscript in `grep -l '#!/usr/bin/env \+perl' debian/*/usr/bin/*` `grep -l '#!/usr/bin/env \+perl' debian/*/usr/lib/atac/bin/*` ; do \ sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' ${perlscript} ; \ done make[1]: Leaving directory '/build/kmer-8W5TPl/kmer-0~20150903+r2013' dh_installdocs dh_installchangelogs dh_installman debian/rules override_dh_python3 make[1]: Entering directory '/build/kmer-8W5TPl/kmer-0~20150903+r2013' dh_python3 --no-ext-rename I: dh_python3 tools:128: replacing shebang in debian/atac/usr/lib/atac/lib/AtacDriver.py I: dh_python3 tools:128: replacing shebang in debian/atac/usr/lib/atac/lib/AtacFile.py I: dh_python3 tools:128: replacing shebang in debian/atac/usr/lib/atac/lib/MyFile.py I: dh_python3 tools:128: replacing shebang in debian/atac/usr/lib/atac/lib/PerfectRuns.py I: dh_python3 tools:128: replacing shebang in debian/atac/usr/lib/atac/lib/UniqueFilter.py I: dh_python3 tools:128: replacing shebang in debian/atac/usr/lib/atac/lib/dedashMatches.py I: dh_python3 tools:128: replacing shebang in debian/atac/usr/lib/atac/lib/mkstats.py I: dh_python3 tools:128: replacing shebang in debian/atac/usr/lib/atac/bin/AtacDriver.py make[1]: Leaving directory '/build/kmer-8W5TPl/kmer-0~20150903+r2013' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libkmer-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libmeryl-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'leaff-dbgsym' in '../leaff-dbgsym_0~20150903+r2013-10_amd64.deb'. dpkg-deb: building package 'kmer' in '../kmer_0~20150903+r2013-10_all.deb'. dpkg-deb: building package 'libkmer-dev' in '../libkmer-dev_0~20150903+r2013-10_amd64.deb'. dpkg-deb: building package 'sim4db' in '../sim4db_0~20150903+r2013-10_amd64.deb'. dpkg-deb: building package 'meryl' in '../meryl_0~20150903+r2013-10_amd64.deb'. dpkg-deb: building package 'meryl-dbgsym' in '../meryl-dbgsym_0~20150903+r2013-10_amd64.deb'. dpkg-deb: building package 'sim4db-dbgsym' in '../sim4db-dbgsym_0~20150903+r2013-10_amd64.deb'. dpkg-deb: building package 'libmeryl-dev' in '../libmeryl-dev_0~20150903+r2013-10_amd64.deb'. dpkg-deb: building package 'leaff' in '../leaff_0~20150903+r2013-10_amd64.deb'. dpkg-deb: building package 'atac' in '../atac_0~20150903+r2013-10_amd64.deb'. dpkg-deb: building package 'atac-dbgsym' in '../atac-dbgsym_0~20150903+r2013-10_amd64.deb'. dpkg-deb: building package 'kmer-examples' in '../kmer-examples_0~20150903+r2013-10_all.deb'. dpkg-genbuildinfo -O../kmer_0~20150903+r2013-10_amd64.buildinfo dpkg-genchanges -O../kmer_0~20150903+r2013-10_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2026-04-27T01:39:39Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 27 Apr 2026 01:39:40 +0000 | +------------------------------------------------------------------------------+ kmer_0~20150903+r2013-10_amd64.changes: --------------------------------------- Format: 1.8 Date: Tue, 12 Aug 2025 09:42:29 +0200 Source: kmer Binary: atac atac-dbgsym kmer kmer-examples leaff leaff-dbgsym libkmer-dev libmeryl-dev meryl meryl-dbgsym sim4db sim4db-dbgsym Architecture: source amd64 all Version: 0~20150903+r2013-10 Distribution: perl-5.42-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: atac - genome assembly-to-assembly comparison kmer - suite of tools for DNA sequence analysis kmer-examples - sample data for kmer suite of tools for DNA sequence analysis leaff - biological sequence library utilities and applications libkmer-dev - suite of tools for DNA sequence analysis (development lib) libmeryl-dev - in- and out-of-core kmer counting and utilities (development lib) meryl - in- and out-of-core kmer counting and utilities sim4db - batch spliced alignment of cDNA sequences to a target genome Changes: kmer (0~20150903+r2013-10) unstable; urgency=medium . * Team upload. * d/control: apply Multiarch hints. * Cleanup patch metadata. * d/tests: make the test scripts shellcheck-clean. Also fixes a lintian warning about a bash-ism. * Standards-Version: 4.7.2 (routine-update) * d/patches/fix_wrong_evaluation_order.patch: mark as forwarded * d/atac.lintian-overrides: silence a false positive Checksums-Sha1: cb8a0e884c519597cca95c7961254ca09b9eb922 1492 kmer_0~20150903+r2013-10.dsc f2b1d45b3a88f7311b0af09fbe6575a4af63b140 2381852 kmer_0~20150903+r2013-10.debian.tar.xz 9d5091ecd188a90ca7f11f500920a33742a2d181 2693716 atac-dbgsym_0~20150903+r2013-10_amd64.deb dd454a4e29aa528746a3efdbb61b93c9c2ef893a 389780 atac_0~20150903+r2013-10_amd64.deb abc9109c344649c386a93d9cdaef353b0a756750 2352288 kmer-examples_0~20150903+r2013-10_all.deb 7aad69d93e6936cb493e63cccaea72bd24dfda13 4980 kmer_0~20150903+r2013-10_all.deb 0544a780c6df08f47e7f02041df5ecc3051b69fa 9109 kmer_0~20150903+r2013-10_amd64.buildinfo a4236816f957f37e1f1437114b3e8c659ee7965d 174856 leaff-dbgsym_0~20150903+r2013-10_amd64.deb a5f739d1fe36a1c302929d8e4fdce185fc85a1da 70496 leaff_0~20150903+r2013-10_amd64.deb a25a215b1bfee583aef3750ab70edd90e842085c 201384 libkmer-dev_0~20150903+r2013-10_amd64.deb ffe58646b7967b4b1139520b6e0dbafcc1f601c4 53532 libmeryl-dev_0~20150903+r2013-10_amd64.deb 4aa6a36c85e9368547e07bb343aa3a42713286e8 1482136 meryl-dbgsym_0~20150903+r2013-10_amd64.deb a90da0e87cc22f450a959a8c7981099b2b68f7cc 202760 meryl_0~20150903+r2013-10_amd64.deb 1453e92957718ba818ed3e44c4ade40f64e2ffe7 2098384 sim4db-dbgsym_0~20150903+r2013-10_amd64.deb 23420cd146dc172aa1f8a949d77be5f141c4d23f 453116 sim4db_0~20150903+r2013-10_amd64.deb Checksums-Sha256: 5c3145f359097f011d6585f211283e57002ccd3737f00d9a43f17ca789dd892c 1492 kmer_0~20150903+r2013-10.dsc b222a57be520cb861ac1afb05e2ffce75aaa175bdcf53446285c96213b8f1c44 2381852 kmer_0~20150903+r2013-10.debian.tar.xz a4ba9c9d4b144304ec6e4da0cdaa963524ef1052f54234b5cd5dc6212377e15d 2693716 atac-dbgsym_0~20150903+r2013-10_amd64.deb 622cf63c7a49022852946eed2cd1a22968f5cad8f205a1cb6c0b87d703775d71 389780 atac_0~20150903+r2013-10_amd64.deb 9c373e22b40e91c68501c813f58865f838326978f8ec890488c7453cde067677 2352288 kmer-examples_0~20150903+r2013-10_all.deb 58aca9d95da197a82c07de96ac802c3ca5f845280da7eda407cf3fb9dc6225e5 4980 kmer_0~20150903+r2013-10_all.deb da85fef97c2dc7978591cdf8db4aae0277f6eed75428b15d9c8b3c545b5300f8 9109 kmer_0~20150903+r2013-10_amd64.buildinfo 7f31dcc493d8838ba90147a896bde90ca669a0d450b60101a66db6cfbe9eca3a 174856 leaff-dbgsym_0~20150903+r2013-10_amd64.deb a1d94ff2b798633bd8cbde86e35adb5d5bb7641d73cadf042b32dccd40686312 70496 leaff_0~20150903+r2013-10_amd64.deb c1ef6b9c64b8d3d8a2144b6555e07b0538cc4055937bfe1367d24557e28b2e65 201384 libkmer-dev_0~20150903+r2013-10_amd64.deb cb92455cefc5ea432df3e2e0e6f017733d3f60bc7ebf2fcad2023c097ebd377c 53532 libmeryl-dev_0~20150903+r2013-10_amd64.deb 3a22344c615f40d2c4ec14727b97b9f22a8aab345723c24e62c7707c6c6de873 1482136 meryl-dbgsym_0~20150903+r2013-10_amd64.deb 93827d1c897a72d671e954d931bdec7d46f4dc009fa479e7a06b4072fd239927 202760 meryl_0~20150903+r2013-10_amd64.deb df3006e39441127922b7f68da2609c5f1b3f1253ac107a32c534f29a57998838 2098384 sim4db-dbgsym_0~20150903+r2013-10_amd64.deb ff50fa20a77514b4f3721957d24204574d53082d8ab99e759db584b34ecb3767 453116 sim4db_0~20150903+r2013-10_amd64.deb Files: a2815cd848e5b0453ac10684a260886b 1492 science optional kmer_0~20150903+r2013-10.dsc a04e15bc3d55a1433b30db886cef8efd 2381852 science optional kmer_0~20150903+r2013-10.debian.tar.xz 2d076f8348adb087cad243c2d74c4faa 2693716 debug optional atac-dbgsym_0~20150903+r2013-10_amd64.deb 9132dc53837878eb17b1d08de4980d9b 389780 science optional atac_0~20150903+r2013-10_amd64.deb 4f18eaf161d944398cc9712157d8e927 2352288 science optional kmer-examples_0~20150903+r2013-10_all.deb ac68ec0eeb4c54bd123ab330c2bf6383 4980 science optional kmer_0~20150903+r2013-10_all.deb 4354d0a938fe71d4bbee31b5ca297f96 9109 science optional kmer_0~20150903+r2013-10_amd64.buildinfo f2dabc6acb7239a84b492dceed06d119 174856 debug optional leaff-dbgsym_0~20150903+r2013-10_amd64.deb 44c5f501293e1f39eabc41482e97f885 70496 science optional leaff_0~20150903+r2013-10_amd64.deb d00655075a779c9c96646998f313c264 201384 libdevel optional libkmer-dev_0~20150903+r2013-10_amd64.deb db627c19efe60a5a2158d7c7113daec2 53532 libdevel optional libmeryl-dev_0~20150903+r2013-10_amd64.deb 525eff93a97091dfde5833df6187cf76 1482136 debug optional meryl-dbgsym_0~20150903+r2013-10_amd64.deb d77d9d3690858491d7b1f7da653dd08a 202760 science optional meryl_0~20150903+r2013-10_amd64.deb 65b1709593c04ca4cb07a0b1b81b1a03 2098384 debug optional sim4db-dbgsym_0~20150903+r2013-10_amd64.deb 2283f0136ef9bcf7ef06a1ce0e6ed2a4 453116 science optional sim4db_0~20150903+r2013-10_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Mon, 27 Apr 2026 01:39:40 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: kmer Binary: atac atac-dbgsym kmer kmer-examples leaff leaff-dbgsym libkmer-dev libmeryl-dev meryl meryl-dbgsym sim4db sim4db-dbgsym Architecture: all amd64 source Version: 0~20150903+r2013-10 Checksums-Md5: a2815cd848e5b0453ac10684a260886b 1492 kmer_0~20150903+r2013-10.dsc 2d076f8348adb087cad243c2d74c4faa 2693716 atac-dbgsym_0~20150903+r2013-10_amd64.deb 9132dc53837878eb17b1d08de4980d9b 389780 atac_0~20150903+r2013-10_amd64.deb 4f18eaf161d944398cc9712157d8e927 2352288 kmer-examples_0~20150903+r2013-10_all.deb ac68ec0eeb4c54bd123ab330c2bf6383 4980 kmer_0~20150903+r2013-10_all.deb f2dabc6acb7239a84b492dceed06d119 174856 leaff-dbgsym_0~20150903+r2013-10_amd64.deb 44c5f501293e1f39eabc41482e97f885 70496 leaff_0~20150903+r2013-10_amd64.deb d00655075a779c9c96646998f313c264 201384 libkmer-dev_0~20150903+r2013-10_amd64.deb db627c19efe60a5a2158d7c7113daec2 53532 libmeryl-dev_0~20150903+r2013-10_amd64.deb 525eff93a97091dfde5833df6187cf76 1482136 meryl-dbgsym_0~20150903+r2013-10_amd64.deb d77d9d3690858491d7b1f7da653dd08a 202760 meryl_0~20150903+r2013-10_amd64.deb 65b1709593c04ca4cb07a0b1b81b1a03 2098384 sim4db-dbgsym_0~20150903+r2013-10_amd64.deb 2283f0136ef9bcf7ef06a1ce0e6ed2a4 453116 sim4db_0~20150903+r2013-10_amd64.deb Checksums-Sha1: cb8a0e884c519597cca95c7961254ca09b9eb922 1492 kmer_0~20150903+r2013-10.dsc 9d5091ecd188a90ca7f11f500920a33742a2d181 2693716 atac-dbgsym_0~20150903+r2013-10_amd64.deb dd454a4e29aa528746a3efdbb61b93c9c2ef893a 389780 atac_0~20150903+r2013-10_amd64.deb abc9109c344649c386a93d9cdaef353b0a756750 2352288 kmer-examples_0~20150903+r2013-10_all.deb 7aad69d93e6936cb493e63cccaea72bd24dfda13 4980 kmer_0~20150903+r2013-10_all.deb a4236816f957f37e1f1437114b3e8c659ee7965d 174856 leaff-dbgsym_0~20150903+r2013-10_amd64.deb a5f739d1fe36a1c302929d8e4fdce185fc85a1da 70496 leaff_0~20150903+r2013-10_amd64.deb a25a215b1bfee583aef3750ab70edd90e842085c 201384 libkmer-dev_0~20150903+r2013-10_amd64.deb ffe58646b7967b4b1139520b6e0dbafcc1f601c4 53532 libmeryl-dev_0~20150903+r2013-10_amd64.deb 4aa6a36c85e9368547e07bb343aa3a42713286e8 1482136 meryl-dbgsym_0~20150903+r2013-10_amd64.deb a90da0e87cc22f450a959a8c7981099b2b68f7cc 202760 meryl_0~20150903+r2013-10_amd64.deb 1453e92957718ba818ed3e44c4ade40f64e2ffe7 2098384 sim4db-dbgsym_0~20150903+r2013-10_amd64.deb 23420cd146dc172aa1f8a949d77be5f141c4d23f 453116 sim4db_0~20150903+r2013-10_amd64.deb Checksums-Sha256: 5c3145f359097f011d6585f211283e57002ccd3737f00d9a43f17ca789dd892c 1492 kmer_0~20150903+r2013-10.dsc a4ba9c9d4b144304ec6e4da0cdaa963524ef1052f54234b5cd5dc6212377e15d 2693716 atac-dbgsym_0~20150903+r2013-10_amd64.deb 622cf63c7a49022852946eed2cd1a22968f5cad8f205a1cb6c0b87d703775d71 389780 atac_0~20150903+r2013-10_amd64.deb 9c373e22b40e91c68501c813f58865f838326978f8ec890488c7453cde067677 2352288 kmer-examples_0~20150903+r2013-10_all.deb 58aca9d95da197a82c07de96ac802c3ca5f845280da7eda407cf3fb9dc6225e5 4980 kmer_0~20150903+r2013-10_all.deb 7f31dcc493d8838ba90147a896bde90ca669a0d450b60101a66db6cfbe9eca3a 174856 leaff-dbgsym_0~20150903+r2013-10_amd64.deb a1d94ff2b798633bd8cbde86e35adb5d5bb7641d73cadf042b32dccd40686312 70496 leaff_0~20150903+r2013-10_amd64.deb c1ef6b9c64b8d3d8a2144b6555e07b0538cc4055937bfe1367d24557e28b2e65 201384 libkmer-dev_0~20150903+r2013-10_amd64.deb cb92455cefc5ea432df3e2e0e6f017733d3f60bc7ebf2fcad2023c097ebd377c 53532 libmeryl-dev_0~20150903+r2013-10_amd64.deb 3a22344c615f40d2c4ec14727b97b9f22a8aab345723c24e62c7707c6c6de873 1482136 meryl-dbgsym_0~20150903+r2013-10_amd64.deb 93827d1c897a72d671e954d931bdec7d46f4dc009fa479e7a06b4072fd239927 202760 meryl_0~20150903+r2013-10_amd64.deb df3006e39441127922b7f68da2609c5f1b3f1253ac107a32c534f29a57998838 2098384 sim4db-dbgsym_0~20150903+r2013-10_amd64.deb ff50fa20a77514b4f3721957d24204574d53082d8ab99e759db584b34ecb3767 453116 sim4db_0~20150903+r2013-10_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 27 Apr 2026 01:39:39 +0000 Build-Path: /build/kmer-8W5TPl/kmer-0~20150903+r2013 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-6), automake (= 1:1.18.1-4), autopoint (= 0.23.2-2), autotools-dev (= 20240727.1+nmu1), base-files (= 14), base-passwd (= 3.6.8), bash (= 5.3-2), binutils (= 2.46-3), binutils-common (= 2.46-3), binutils-x86-64-linux-gnu (= 2.46-3), bsdextrautils (= 2.42-5), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-14 (= 14.3.0-14), cpp-14-x86-64-linux-gnu (= 14.3.0-14), cpp-15 (= 15.2.0-17), cpp-15-x86-64-linux-gnu (= 15.2.0-17), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 13.31), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-exec (= 0.31), dh-python (= 7.20260309), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.46-5+b2), findutils (= 4.10.0-3), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.2.0-17), g++-15-x86-64-linux-gnu (= 15.2.0-17), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-14 (= 14.3.0-14), gcc-14-base (= 14.3.0-14), gcc-14-x86-64-linux-gnu (= 14.3.0-14), gcc-15 (= 15.2.0-17), gcc-15-base (= 15.2.0-17), gcc-15-x86-64-linux-gnu (= 15.2.0-17), gcc-16-base (= 16-20260425-1), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gettext (= 0.23.2-2), gettext-base (= 0.23.2-2), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 16-20260425-1), libatomic1 (= 16-20260425-1), libattr1 (= 1:2.5.2-4), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46-3), libblkid1 (= 2.42-5), libbz2-1.0 (= 1.0.8-6+b2), libc-bin (= 2.42-15), libc-dev-bin (= 2.42-15), libc-gconv-modules-extra (= 2.42-15), libc6 (= 2.42-15), libc6-dev (= 2.42-15), libcap-ng0 (= 0.9.3-1), libcc1-0 (= 16-20260425-1), libcrypt1 (= 1:4.5.1-1+b1), libctf-nobfd0 (= 2.46-3), libctf0 (= 2.46-3), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.282+b3), libdebhelper-perl (= 13.31), libdpkg-perl (= 1.23.7), libelf1t64 (= 0.195-1), libexpat1 (= 2.8.0-1), libexpat1-dev (= 2.8.0-1), libffi8 (= 3.5.2-4), libfile-stripnondeterminism-perl (= 1.15.0-1), libgcc-14-dev (= 14.3.0-14), libgcc-15-dev (= 15.2.0-17), libgcc-s1 (= 16-20260425-1), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgomp1 (= 16-20260425-1), libgprofng0 (= 2.46-3), libhwasan0 (= 16-20260425-1), libisl23 (= 0.27-2), libitm1 (= 16-20260425-1), libjansson4 (= 2.14-2+b4), libjs-sphinxdoc (= 8.2.3-12), liblsan0 (= 16-20260425-1), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.46-5+b2), libmagic1t64 (= 1:5.46-5+b2), libmd0 (= 1.1.0-2+b2), libmount1 (= 2.42-5), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libncursesw6 (= 6.6+20251231-1), libpam-modules (= 1.7.0-5+b1), libpam-modules-bin (= 1.7.0-5+b1), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5+b1), libpcre2-8-0 (= 10.46-1+b1), libperl5.42 (= 5.42.2-1), libpipeline1 (= 1.5.8-3), libpython3-dev (= 3.13.9-3), libpython3-stdlib (= 3.13.9-3), libpython3.13 (= 3.13.12-1), libpython3.13-dev (= 3.13.12-1), libpython3.13-minimal (= 3.13.12-1), libpython3.13-stdlib (= 3.13.12-1), libquadmath0 (= 16-20260425-1), libreadline8t64 (= 8.3-4), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.10-1), libsframe3 (= 2.46-3), libsmartcols1 (= 2.42-5), libsqlite3-0 (= 3.46.1-9+b1), libssl3t64 (= 3.6.2-1), libstdc++-15-dev (= 15.2.0-17), libstdc++6 (= 16-20260425-1), libsystemd0 (= 260.1-1), libtinfo6 (= 6.6+20251231-1), libtool (= 2.5.4-11), libtsan2 (= 16-20260425-1), libubsan1 (= 16-20260425-1), libuchardet0 (= 0.0.8-2+b1), libudev1 (= 260.1-1), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42-5), libxml2-16 (= 2.15.2+dfsg-0.1), libzstd1 (= 1.5.7+dfsg-3+b1), linux-libc-dev (= 6.19.14-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), media-types (= 14.0.0), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1), netbase (= 6.5), openssl-provider-legacy (= 3.6.2-1), patch (= 2.8-2), perl (= 5.42.2-1), perl-base (= 5.42.2-1), perl-modules-5.42 (= 5.42.2-1), po-debconf (= 1.0.22), python3 (= 3.13.9-3), python3-dev (= 3.13.9-3), python3-minimal (= 3.13.9-3), python3.13 (= 3.13.12-1), python3.13-dev (= 3.13.12-1), python3.13-minimal (= 3.13.12-1), readline-common (= 8.3-4), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-3), sensible-utils (= 0.0.26), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), tzdata (= 2026b-1), util-linux (= 2.42-5), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1754984549" +------------------------------------------------------------------------------+ | Package contents Mon, 27 Apr 2026 01:39:40 +0000 | +------------------------------------------------------------------------------+ atac-dbgsym_0~20150903+r2013-10_amd64.deb ----------------------------------------- new Debian package, version 2.0. size 2693716 bytes: control archive=1604 bytes. 1244 bytes, 12 lines control 2413 bytes, 23 lines md5sums Package: atac-dbgsym Source: kmer Version: 0~20150903+r2013-10 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 3486 Depends: atac (= 0~20150903+r2013-10) Section: debug Priority: optional Description: debug symbols for atac Build-Ids: 02de1578abc23f5ccf005725c1bfb017d50e1e06 05d57d20a7af36afdc0b7cc605c27460da181021 19311dba8c793d1f634748f89076b740b1071fae 1fedaba401e751270b311241de397cce532b173f 24d26c5180f676ea2dd7e1f8638da0bf792e4ceb 3e3f746cd0c04d05258183068a4c5bcfbe156830 4bd9f54a2d75d63173195c0f0aac7ca4a000d791 577a913631646b87119161b529f2b1bba8515f48 5c631c75704ca07ea292238b42a8065d0fb5884c 7b5f9bf091af5f97911a9053f564cf83de3988b4 7e185e32a5a849eeeb7d67e6ab77524ae8672bff 829dbdcad733acb0a0c3428d8483470f6701c5be 90bc9e3b013496d3f652d047f271e9743ea2e63a 979daaee8b5d0734d318cf5354e4d3ffeef45487 9dc69dbaf8f75fe88deba77e6d22e78984784420 b02e61042af0b59279cf447bd6759b752a6cb78f b19f611e20964da5e3140e55ec7e69aa38336e3d b587c6d53ba7361f89d54ab921b7ab28b5c2c6af bcb55c3cc92bc592f1c1c5eca54485f5ee832bf0 de3e15ccda49f5deaf3d6b37bbf3245405d47385 e6df47cfd8d481db207ea3fe8d81176e32836937 e74d92cedaa0c61ca3652b1a5eb7b0fb85a7b05b drwxr-xr-x root/root 0 2025-08-12 07:42 ./ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/02/ -rw-r--r-- root/root 184320 2025-08-12 07:42 ./usr/lib/debug/.build-id/02/de1578abc23f5ccf005725c1bfb017d50e1e06.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/05/ -rw-r--r-- root/root 208024 2025-08-12 07:42 ./usr/lib/debug/.build-id/05/d57d20a7af36afdc0b7cc605c27460da181021.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/19/ -rw-r--r-- root/root 179056 2025-08-12 07:42 ./usr/lib/debug/.build-id/19/311dba8c793d1f634748f89076b740b1071fae.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/1f/ -rw-r--r-- root/root 15160 2025-08-12 07:42 ./usr/lib/debug/.build-id/1f/edaba401e751270b311241de397cce532b173f.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/24/ -rw-r--r-- root/root 51560 2025-08-12 07:42 ./usr/lib/debug/.build-id/24/d26c5180f676ea2dd7e1f8638da0bf792e4ceb.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/3e/ -rw-r--r-- root/root 11464 2025-08-12 07:42 ./usr/lib/debug/.build-id/3e/3f746cd0c04d05258183068a4c5bcfbe156830.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/4b/ -rw-r--r-- root/root 19248 2025-08-12 07:42 ./usr/lib/debug/.build-id/4b/d9f54a2d75d63173195c0f0aac7ca4a000d791.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/57/ -rw-r--r-- root/root 219096 2025-08-12 07:42 ./usr/lib/debug/.build-id/57/7a913631646b87119161b529f2b1bba8515f48.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/5c/ -rw-r--r-- root/root 196624 2025-08-12 07:42 ./usr/lib/debug/.build-id/5c/631c75704ca07ea292238b42a8065d0fb5884c.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/7b/ -rw-r--r-- root/root 252920 2025-08-12 07:42 ./usr/lib/debug/.build-id/7b/5f9bf091af5f97911a9053f564cf83de3988b4.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/7e/ -rw-r--r-- root/root 54632 2025-08-12 07:42 ./usr/lib/debug/.build-id/7e/185e32a5a849eeeb7d67e6ab77524ae8672bff.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/82/ -rw-r--r-- root/root 186168 2025-08-12 07:42 ./usr/lib/debug/.build-id/82/9dbdcad733acb0a0c3428d8483470f6701c5be.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/90/ -rw-r--r-- root/root 76784 2025-08-12 07:42 ./usr/lib/debug/.build-id/90/bc9e3b013496d3f652d047f271e9743ea2e63a.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/97/ -rw-r--r-- root/root 236176 2025-08-12 07:42 ./usr/lib/debug/.build-id/97/9daaee8b5d0734d318cf5354e4d3ffeef45487.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/9d/ -rw-r--r-- root/root 177952 2025-08-12 07:42 ./usr/lib/debug/.build-id/9d/c69dbaf8f75fe88deba77e6d22e78984784420.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/b0/ -rw-r--r-- root/root 179728 2025-08-12 07:42 ./usr/lib/debug/.build-id/b0/2e61042af0b59279cf447bd6759b752a6cb78f.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/b1/ -rw-r--r-- root/root 374904 2025-08-12 07:42 ./usr/lib/debug/.build-id/b1/9f611e20964da5e3140e55ec7e69aa38336e3d.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/b5/ -rw-r--r-- root/root 186000 2025-08-12 07:42 ./usr/lib/debug/.build-id/b5/87c6d53ba7361f89d54ab921b7ab28b5c2c6af.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/bc/ -rw-r--r-- root/root 181392 2025-08-12 07:42 ./usr/lib/debug/.build-id/bc/b55c3cc92bc592f1c1c5eca54485f5ee832bf0.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/de/ -rw-r--r-- root/root 181656 2025-08-12 07:42 ./usr/lib/debug/.build-id/de/3e15ccda49f5deaf3d6b37bbf3245405d47385.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/e6/ -rw-r--r-- root/root 240704 2025-08-12 07:42 ./usr/lib/debug/.build-id/e6/df47cfd8d481db207ea3fe8d81176e32836937.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/e7/ -rw-r--r-- root/root 52600 2025-08-12 07:42 ./usr/lib/debug/.build-id/e7/4d92cedaa0c61ca3652b1a5eb7b0fb85a7b05b.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 59064 2025-08-12 07:42 ./usr/lib/debug/.dwz/x86_64-linux-gnu/atac.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-08-12 07:42 ./usr/share/doc/atac-dbgsym -> atac atac_0~20150903+r2013-10_amd64.deb ---------------------------------- new Debian package, version 2.0. size 389780 bytes: control archive=2692 bytes. 1348 bytes, 27 lines control 3004 bytes, 46 lines md5sums 305 bytes, 12 lines * postinst #!/bin/sh 401 bytes, 12 lines * prerm #!/bin/sh Package: atac Source: kmer Version: 0~20150903+r2013-10 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2807 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2), python3 (<< 3.14), python3 (>= 3.13~), python3.13, python3:any, perl:any, libfile-which-perl, leaff, meryl, gnuplot Recommends: kmer-examples Section: science Priority: optional Homepage: http://kmer.sourceforge.net Description: genome assembly-to-assembly comparison atac computes a one-to-one pairwise alignment of large DNA sequences. It first finds the unique k-mers in each sequence, chains them to larger blocks, and fills in spaces between blocks. It was written primarily to transfer annotations between different assemblies of the human genome. . The output is a set of ungapped 'matches', and a set of gapped 'runs' formed from the matches. Each match or run associates one sequence with the other sequence. The association is 'unique', in that there is no other (sizeable) associations for either sequence. Thus, large repeats and duplications are not present in the output - they appear as unmapped regions. . Though the output is always pairwise, atac can cache intermediate results to speed a comparisons of multiple sequences. . This package is part of the Kmer suite. drwxr-xr-x root/root 0 2025-08-12 07:42 ./ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/bin/ -rwxr-xr-x root/root 32718 2025-08-12 07:42 ./usr/bin/atac drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/atac/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/atac/bin/ -rwxr-xr-x root/root 22723 2025-08-12 07:42 ./usr/lib/atac/bin/AtacDriver.py -rwxr-xr-x root/root 139600 2025-08-12 07:42 ./usr/lib/atac/bin/cleanAtac -rwxr-xr-x root/root 143696 2025-08-12 07:42 ./usr/lib/atac/bin/clumpMaker -rwxr-xr-x root/root 139600 2025-08-12 07:42 ./usr/lib/atac/bin/coalesceMatches -rwxr-xr-x root/root 143696 2025-08-12 07:42 ./usr/lib/atac/bin/correctGaps -rwxr-xr-x root/root 139600 2025-08-12 07:42 ./usr/lib/atac/bin/extractSequence -rwxr-xr-x root/root 151888 2025-08-12 07:42 ./usr/lib/atac/bin/extractUnmapped -rwxr-xr-x root/root 155984 2025-08-12 07:42 ./usr/lib/atac/bin/gapShifter -rwxr-xr-x root/root 31240 2025-08-12 07:42 ./usr/lib/atac/bin/happy-clones-span-clumps -rwxr-xr-x root/root 35136 2025-08-12 07:42 ./usr/lib/atac/bin/heavychains -rwxr-xr-x root/root 14656 2025-08-12 07:42 ./usr/lib/atac/bin/lengthFilter -rwxr-xr-x root/root 10582 2025-08-12 07:42 ./usr/lib/atac/bin/makeplot.pl -rwxr-xr-x root/root 156016 2025-08-12 07:42 ./usr/lib/atac/bin/matchExtender -rwxr-xr-x root/root 139600 2025-08-12 07:42 ./usr/lib/atac/bin/mismatchCounter -rwxr-xr-x root/root 176464 2025-08-12 07:42 ./usr/lib/atac/bin/overlap -rwxr-xr-x root/root 139600 2025-08-12 07:42 ./usr/lib/atac/bin/projectFeatures -rwxr-xr-x root/root 279696 2025-08-12 07:42 ./usr/lib/atac/bin/seatac -rwxr-xr-x root/root 192848 2025-08-12 07:42 ./usr/lib/atac/bin/statsGenerator -rwxr-xr-x root/root 139600 2025-08-12 07:42 ./usr/lib/atac/bin/testAtac -rwxr-xr-x root/root 164208 2025-08-12 07:42 ./usr/lib/atac/bin/uniqueFilter drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/atac/lib/ -rwxr-xr-x root/root 22723 2025-08-12 07:42 ./usr/lib/atac/lib/AtacDriver.py -rwxr-xr-x root/root 2913 2025-08-12 07:42 ./usr/lib/atac/lib/AtacFile.py -rw-r--r-- root/root 2140 2005-02-28 22:49 ./usr/lib/atac/lib/DNA.py -rw-r--r-- root/root 6434 2025-08-12 07:42 ./usr/lib/atac/lib/IdxStore.py -rw-r--r-- root/root 7832 2025-08-12 07:42 ./usr/lib/atac/lib/MatchRecord.py -rwxr-xr-x root/root 2965 2025-08-12 07:42 ./usr/lib/atac/lib/MyFile.py -rwxr-xr-x root/root 9069 2025-08-12 07:42 ./usr/lib/atac/lib/PerfectRuns.py -rw-r--r-- root/root 11165 2025-08-12 07:42 ./usr/lib/atac/lib/TrimMatchOverlaps.py -rwxr-xr-x root/root 11013 2025-08-12 07:42 ./usr/lib/atac/lib/UniqueFilter.py -rwxr-xr-x root/root 4822 2025-08-12 07:42 ./usr/lib/atac/lib/dedashMatches.py -rw-r--r-- root/root 15642 2025-08-12 07:42 ./usr/lib/atac/lib/fillIntraRunGaps.py -rw-r--r-- root/root 34896 2025-08-12 07:42 ./usr/lib/atac/lib/filter-heavychains.so -rw-r--r-- root/root 14416 2025-08-12 07:42 ./usr/lib/atac/lib/filter-nop.so -rw-r--r-- root/root 22760 2025-08-12 07:42 ./usr/lib/atac/lib/halign.so -rw-r--r-- root/root 72072 2025-08-12 07:42 ./usr/lib/atac/lib/localAlignerInterface.so -rwxr-xr-x root/root 2682 2025-08-12 07:42 ./usr/lib/atac/lib/mkstats.py -rw-r--r-- root/root 21269 2025-08-12 07:42 ./usr/lib/atac/lib/squeezeIntraRunGaps.py drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/atac/ -rw-r--r-- root/root 3178 2025-08-12 07:42 ./usr/share/doc/atac/README.atac -rw-r--r-- root/root 244 2025-08-12 07:42 ./usr/share/doc/atac/README.test -rw-r--r-- root/root 833 2025-08-12 07:42 ./usr/share/doc/atac/atac-unit-test -rw-r--r-- root/root 1016 2025-08-12 07:42 ./usr/share/doc/atac/changelog.Debian.gz -rw-r--r-- root/root 7520 2025-08-12 07:42 ./usr/share/doc/atac/copyright drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/lintian/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 172 2025-08-12 07:42 ./usr/share/lintian/overrides/atac drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/man/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/man/man1/ -rw-r--r-- root/root 704 2025-08-12 07:42 ./usr/share/man/man1/atac.1.gz drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/python3/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/python3/runtime.d/ -rwxr-xr-x root/root 132 2025-08-12 07:42 ./usr/share/python3/runtime.d/atac.rtupdate kmer-examples_0~20150903+r2013-10_all.deb ----------------------------------------- new Debian package, version 2.0. size 2352288 bytes: control archive=828 bytes. 728 bytes, 19 lines control 309 bytes, 4 lines md5sums Package: kmer-examples Source: kmer Version: 0~20150903+r2013-10 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 2307 Enhances: atac, sim4db Section: science Priority: optional Multi-Arch: foreign Homepage: http://kmer.sourceforge.net Description: sample data for kmer suite of tools for DNA sequence analysis The kmer package is a suite of tools for DNA sequence analysis. It provides tools for searching (ESTs, mRNAs, sequencing reads); aligning (ESTs, mRNAs, whole genomes); and a variety of analyses based on kmers. . This package contains a test data set as well as sample scripts running some test suite provided by Debian also as autopkgtest. drwxr-xr-x root/root 0 2025-08-12 07:42 ./ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/kmer-examples/ -rw-r--r-- root/root 275 2025-08-12 07:42 ./usr/share/doc/kmer-examples/README.Debian -rw-r--r-- root/root 1020 2025-08-12 07:42 ./usr/share/doc/kmer-examples/changelog.Debian.gz -rw-r--r-- root/root 7520 2025-08-12 07:42 ./usr/share/doc/kmer-examples/copyright -rw-r--r-- root/root 2345682 2025-08-12 07:42 ./usr/share/doc/kmer-examples/test_data.tar.gz kmer_0~20150903+r2013-10_all.deb -------------------------------- new Debian package, version 2.0. size 4980 bytes: control archive=716 bytes. 627 bytes, 16 lines control 136 bytes, 2 lines md5sums Package: kmer Version: 0~20150903+r2013-10 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 15 Depends: meryl, leaff, sim4db, atac Section: science Priority: optional Homepage: http://kmer.sourceforge.net Description: suite of tools for DNA sequence analysis The kmer package is a suite of tools for DNA sequence analysis. It provides tools for searching (ESTs, mRNAs, sequencing reads); aligning (ESTs, mRNAs, whole genomes); and a variety of analyses based on kmers. . This is a metapackage depending on the executable components of the kmer suite. drwxr-xr-x root/root 0 2025-08-12 07:42 ./ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/kmer/ -rw-r--r-- root/root 1015 2025-08-12 07:42 ./usr/share/doc/kmer/changelog.Debian.gz -rw-r--r-- root/root 7520 2025-08-12 07:42 ./usr/share/doc/kmer/copyright leaff-dbgsym_0~20150903+r2013-10_amd64.deb ------------------------------------------ new Debian package, version 2.0. size 174856 bytes: control archive=544 bytes. 385 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: leaff-dbgsym Source: kmer Version: 0~20150903+r2013-10 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 228 Depends: leaff (= 0~20150903+r2013-10) Section: debug Priority: optional Description: debug symbols for leaff Build-Ids: 9667acc3f1ace83ec121fdff227ba5cccf614b4c drwxr-xr-x root/root 0 2025-08-12 07:42 ./ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/96/ -rw-r--r-- root/root 222456 2025-08-12 07:42 ./usr/lib/debug/.build-id/96/67acc3f1ace83ec121fdff227ba5cccf614b4c.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-08-12 07:42 ./usr/share/doc/leaff-dbgsym -> leaff leaff_0~20150903+r2013-10_amd64.deb ----------------------------------- new Debian package, version 2.0. size 70496 bytes: control archive=872 bytes. 636 bytes, 16 lines control 320 bytes, 5 lines md5sums Package: leaff Source: kmer Version: 0~20150903+r2013-10 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 202 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libstdc++6 (>= 4.1.1) Section: science Priority: optional Homepage: http://kmer.sourceforge.net Description: biological sequence library utilities and applications LEAFF (Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions. . This package is part of the Kmer suite. drwxr-xr-x root/root 0 2025-08-12 07:42 ./ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/bin/ -rwxr-xr-x root/root 180512 2025-08-12 07:42 ./usr/bin/leaff drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/leaff/ -rw-r--r-- root/root 3373 2011-01-20 03:32 ./usr/share/doc/leaff/README.leaff.gz -rw-r--r-- root/root 1019 2025-08-12 07:42 ./usr/share/doc/leaff/changelog.Debian.gz -rw-r--r-- root/root 7520 2025-08-12 07:42 ./usr/share/doc/leaff/copyright drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/man/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/man/man1/ -rw-r--r-- root/root 2732 2025-08-12 07:42 ./usr/share/man/man1/leaff.1.gz libkmer-dev_0~20150903+r2013-10_amd64.deb ----------------------------------------- new Debian package, version 2.0. size 201384 bytes: control archive=2172 bytes. 636 bytes, 17 lines control 3725 bytes, 54 lines md5sums Package: libkmer-dev Source: kmer Version: 0~20150903+r2013-10 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 870 Depends: libmeryl-dev Section: libdevel Priority: optional Homepage: http://kmer.sourceforge.net Description: suite of tools for DNA sequence analysis (development lib) The kmer package is a suite of tools for DNA sequence analysis. It provides tools for searching (ESTs, mRNAs, sequencing reads); aligning (ESTs, mRNAs, whole genomes); and a variety of analyses based on kmers. . This package contains headers and static libraries for kmer. drwxr-xr-x root/root 0 2025-08-12 07:42 ./ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/include/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/include/kmer/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/include/kmer/bio/ -rw-r--r-- root/root 647 2008-07-28 21:43 ./usr/include/kmer/bio/alphabet.h -rw-r--r-- root/root 381 2008-09-09 23:55 ./usr/include/kmer/bio/bio++.H -rw-r--r-- root/root 766 2014-04-11 20:17 ./usr/include/kmer/bio/bio.h -rw-r--r-- root/root 5588 2014-04-11 20:17 ./usr/include/kmer/bio/kmer.H -rw-r--r-- root/root 10979 2014-04-11 20:17 ./usr/include/kmer/bio/kmerhuge.H -rw-r--r-- root/root 2715 2014-04-11 20:17 ./usr/include/kmer/bio/kmeriface.H -rw-r--r-- root/root 3402 2014-04-11 20:17 ./usr/include/kmer/bio/kmertiny.H -rw-r--r-- root/root 7314 2014-04-11 20:17 ./usr/include/kmer/bio/merCovering.H -rw-r--r-- root/root 2024 2014-04-11 20:17 ./usr/include/kmer/bio/merList.H -rw-r--r-- root/root 1395 2014-04-11 20:17 ./usr/include/kmer/bio/mers.h drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/include/kmer/kmer/ -rw-r--r-- root/root 4358 2014-04-11 20:17 ./usr/include/kmer/kmer/existDB.H -rw-r--r-- root/root 2098 2014-04-11 20:17 ./usr/include/kmer/kmer/merTable.H -rw-r--r-- root/root 6987 2014-04-11 20:17 ./usr/include/kmer/kmer/positionDB.H drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/include/kmer/seq/ -rw-r--r-- root/root 1797 2014-04-11 20:17 ./usr/include/kmer/seq/fastaFile.H -rw-r--r-- root/root 1323 2014-08-23 02:01 ./usr/include/kmer/seq/fastaStdin.H -rw-r--r-- root/root 1797 2014-04-11 20:17 ./usr/include/kmer/seq/fastqFile.H -rw-r--r-- root/root 1423 2014-08-23 02:01 ./usr/include/kmer/seq/fastqStdin.H -rw-r--r-- root/root 3129 2014-04-11 20:17 ./usr/include/kmer/seq/merStream.H -rw-r--r-- root/root 2941 2014-08-23 02:01 ./usr/include/kmer/seq/seqCache.H -rw-r--r-- root/root 563 2014-04-11 20:17 ./usr/include/kmer/seq/seqFactory.H -rw-r--r-- root/root 1516 2014-08-23 02:01 ./usr/include/kmer/seq/seqFile.H -rw-r--r-- root/root 3046 2014-04-11 20:17 ./usr/include/kmer/seq/seqStore.H -rw-r--r-- root/root 3705 2014-04-11 20:17 ./usr/include/kmer/seq/seqStream.H -rw-r--r-- root/root 2591 2014-04-11 20:17 ./usr/include/kmer/seq/sffFile.H -rw-r--r-- root/root 3714 2014-04-11 20:17 ./usr/include/kmer/seq/test-correctSequence.H drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/include/kmer/util/ -rw-r--r-- root/root 4720 2014-04-11 20:17 ./usr/include/kmer/util/bigQueue.H -rw-r--r-- root/root 4475 2014-04-11 20:17 ./usr/include/kmer/util/bitOperations.h -rw-r--r-- root/root 7072 2014-04-11 20:17 ./usr/include/kmer/util/bitPackedArray.H -rw-r--r-- root/root 2734 2014-04-11 20:17 ./usr/include/kmer/util/bitPackedFile.H -rw-r--r-- root/root 13015 2014-04-11 20:17 ./usr/include/kmer/util/bitPacking.h -rw-r--r-- root/root 1395 2014-04-11 20:17 ./usr/include/kmer/util/bzipBuffer.H -rw-r--r-- root/root 737 2014-04-11 20:17 ./usr/include/kmer/util/eliasDeltaEncoding.h -rw-r--r-- root/root 702 2014-04-11 20:17 ./usr/include/kmer/util/eliasGammaEncoding.h -rw-r--r-- root/root 1365 2014-04-11 20:17 ./usr/include/kmer/util/endianess.H -rw-r--r-- root/root 3558 2014-04-11 20:17 ./usr/include/kmer/util/fibonacciEncoding.h -rw-r--r-- root/root 3234 2014-04-11 20:17 ./usr/include/kmer/util/generalizedUnaryEncoding.h -rw-r--r-- root/root 16331 2015-04-22 22:49 ./usr/include/kmer/util/intervalList.H -rw-r--r-- root/root 2599 2014-04-11 20:17 ./usr/include/kmer/util/logMsg.H -rw-r--r-- root/root 1829 2014-04-11 20:17 ./usr/include/kmer/util/readBuffer.H -rw-r--r-- root/root 1614 2014-04-11 20:17 ./usr/include/kmer/util/recordFile.H -rw-r--r-- root/root 2012 2014-04-11 20:17 ./usr/include/kmer/util/speedCounter.H -rw-r--r-- root/root 2758 2014-04-11 20:17 ./usr/include/kmer/util/splitToWords.H -rw-r--r-- root/root 2654 2014-04-11 20:17 ./usr/include/kmer/util/sweatShop.H -rw-r--r-- root/root 1004 2014-04-11 20:17 ./usr/include/kmer/util/uint32List.H -rw-r--r-- root/root 1489 2014-04-11 20:17 ./usr/include/kmer/util/unaryEncoding.h -rw-r--r-- root/root 1024 2014-04-11 20:17 ./usr/include/kmer/util/util++.H -rw-r--r-- root/root 9288 2014-04-11 20:17 ./usr/include/kmer/util/util.h drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/x86_64-linux-gnu/kmer/ -rw-r--r-- root/root 4632 2025-08-12 07:42 ./usr/lib/x86_64-linux-gnu/kmer/libmt19937ar.a -rw-r--r-- root/root 224114 2025-08-12 07:42 ./usr/lib/x86_64-linux-gnu/kmer/libutil.a -rw-r--r-- root/root 71410 2025-08-12 07:42 ./usr/lib/x86_64-linux-gnu/libbio.a -rw-r--r-- root/root 153714 2025-08-12 07:42 ./usr/lib/x86_64-linux-gnu/libkmer.a -rw-r--r-- root/root 227730 2025-08-12 07:42 ./usr/lib/x86_64-linux-gnu/libseq.a drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/libkmer-dev/ -rw-r--r-- root/root 1021 2025-08-12 07:42 ./usr/share/doc/libkmer-dev/changelog.Debian.gz -rw-r--r-- root/root 7520 2025-08-12 07:42 ./usr/share/doc/libkmer-dev/copyright libmeryl-dev_0~20150903+r2013-10_amd64.deb ------------------------------------------ new Debian package, version 2.0. size 53532 bytes: control archive=1008 bytes. 928 bytes, 22 lines control 413 bytes, 6 lines md5sums Package: libmeryl-dev Source: kmer Version: 0~20150903+r2013-10 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 204 Section: libdevel Priority: optional Multi-Arch: same Homepage: http://kmer.sourceforge.net Description: in- and out-of-core kmer counting and utilities (development lib) meryl computes the kmer content of genomic sequences. Kmer content is represented as a list of kmers and the number of times each occurs in the input sequences. The kmer can be restricted to only the forward kmer, only the reverse kmer, or the canonical kmer (lexicographically smaller of the forward and reverse kmer at each location). Meryl can report the histogram of counts, the list of kmers and their counts, or can perform mathematical and set operations on the processed data files. . This package contains the static libraries and header files. drwxr-xr-x root/root 0 2025-08-12 07:42 ./ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/include/ -rw-r--r-- root/root 5822 2014-04-11 20:17 ./usr/include/libmeryl.H -rw-r--r-- root/root 3420 2015-05-29 12:35 ./usr/include/meryl.H drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 46388 2025-08-12 07:42 ./usr/lib/x86_64-linux-gnu/libmeryl.a drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/x86_64-linux-gnu/meryl/ -rw-r--r-- root/root 131900 2025-08-12 07:42 ./usr/lib/x86_64-linux-gnu/meryl/libmerylguts.a drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/libmeryl-dev/ -rw-r--r-- root/root 1022 2025-08-12 07:42 ./usr/share/doc/libmeryl-dev/changelog.Debian.gz -rw-r--r-- root/root 7520 2025-08-12 07:42 ./usr/share/doc/libmeryl-dev/copyright meryl-dbgsym_0~20150903+r2013-10_amd64.deb ------------------------------------------ new Debian package, version 2.0. size 1482136 bytes: control archive=912 bytes. 632 bytes, 12 lines control 824 bytes, 8 lines md5sums Package: meryl-dbgsym Source: kmer Version: 0~20150903+r2013-10 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1845 Depends: meryl (= 0~20150903+r2013-10) Section: debug Priority: optional Description: debug symbols for meryl Build-Ids: 31f01cff689e2950475d269001f620a01180dc3e 7747956749c84c69e38e2652adbb5a4ae228c0d1 791ff2d9c7101452d94b8680988f1fac1487cb9f aef5d2ed95c6364dc31bbae9d7c652f5585e5a54 bbb6e642cadb65dd4f04b84c0c1bc4ea03b21695 dac1c08d2eb67cc23aeacdac9929f938c672a5b9 f201ef69aa40cfb65d821b20959f386f25d5a275 drwxr-xr-x root/root 0 2025-08-12 07:42 ./ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/31/ -rw-r--r-- root/root 269736 2025-08-12 07:42 ./usr/lib/debug/.build-id/31/f01cff689e2950475d269001f620a01180dc3e.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/77/ -rw-r--r-- root/root 241664 2025-08-12 07:42 ./usr/lib/debug/.build-id/77/47956749c84c69e38e2652adbb5a4ae228c0d1.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/79/ -rw-r--r-- root/root 243312 2025-08-12 07:42 ./usr/lib/debug/.build-id/79/1ff2d9c7101452d94b8680988f1fac1487cb9f.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/ae/ -rw-r--r-- root/root 292720 2025-08-12 07:42 ./usr/lib/debug/.build-id/ae/f5d2ed95c6364dc31bbae9d7c652f5585e5a54.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/bb/ -rw-r--r-- root/root 244408 2025-08-12 07:42 ./usr/lib/debug/.build-id/bb/b6e642cadb65dd4f04b84c0c1bc4ea03b21695.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/da/ -rw-r--r-- root/root 333096 2025-08-12 07:42 ./usr/lib/debug/.build-id/da/c1c08d2eb67cc23aeacdac9929f938c672a5b9.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/f2/ -rw-r--r-- root/root 209736 2025-08-12 07:42 ./usr/lib/debug/.build-id/f2/01ef69aa40cfb65d821b20959f386f25d5a275.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 33584 2025-08-12 07:42 ./usr/lib/debug/.dwz/x86_64-linux-gnu/meryl.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-08-12 07:42 ./usr/share/doc/meryl-dbgsym -> meryl meryl_0~20150903+r2013-10_amd64.deb ----------------------------------- new Debian package, version 2.0. size 202760 bytes: control archive=1324 bytes. 961 bytes, 23 lines control 1036 bytes, 17 lines md5sums Package: meryl Source: kmer Version: 0~20150903+r2013-10 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1473 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libstdc++6 (>= 4.1.1) Suggests: gridengine-client Section: science Priority: optional Homepage: http://kmer.sourceforge.net Description: in- and out-of-core kmer counting and utilities meryl computes the kmer content of genomic sequences. Kmer content is represented as a list of kmers and the number of times each occurs in the input sequences. The kmer can be restricted to only the forward kmer, only the reverse kmer, or the canonical kmer (lexicographically smaller of the forward and reverse kmer at each location). Meryl can report the histogram of counts, the list of kmers and their counts, or can perform mathematical and set operations on the processed data files. . This package is part of the Kmer suite. drwxr-xr-x root/root 0 2025-08-12 07:42 ./ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/bin/ -rwxr-xr-x root/root 201816 2025-08-12 07:42 ./usr/bin/existDB -rwxr-xr-x root/root 218200 2025-08-12 07:42 ./usr/bin/kmer-mask -rwxr-xr-x root/root 197720 2025-08-12 07:42 ./usr/bin/mapMers -rwxr-xr-x root/root 201816 2025-08-12 07:42 ./usr/bin/mapMers-depth -rwxr-xr-x root/root 222296 2025-08-12 07:42 ./usr/bin/meryl -rwxr-xr-x root/root 259224 2025-08-12 07:42 ./usr/bin/positionDB -rwxr-xr-x root/root 169048 2025-08-12 07:42 ./usr/bin/simple drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/meryl/ -rw-r--r-- root/root 2684 2015-05-20 07:56 ./usr/share/doc/meryl/README.meryl.gz -rw-r--r-- root/root 1017 2025-08-12 07:42 ./usr/share/doc/meryl/changelog.Debian.gz -rw-r--r-- root/root 7520 2025-08-12 07:42 ./usr/share/doc/meryl/copyright drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/man/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/man/man1/ -rw-r--r-- root/root 634 2025-08-12 07:42 ./usr/share/man/man1/existDB.1.gz -rw-r--r-- root/root 1069 2025-08-12 07:42 ./usr/share/man/man1/kmer-mask.1.gz -rw-r--r-- root/root 484 2025-08-12 07:42 ./usr/share/man/man1/mapMers-depth.1.gz -rw-r--r-- root/root 388 2025-08-12 07:42 ./usr/share/man/man1/mapMers.1.gz -rw-r--r-- root/root 2669 2025-08-12 07:42 ./usr/share/man/man1/meryl.1.gz -rw-r--r-- root/root 672 2025-08-12 07:42 ./usr/share/man/man1/positionDB.1.gz -rw-r--r-- root/root 511 2025-08-12 07:42 ./usr/share/man/man1/simple.1.gz sim4db-dbgsym_0~20150903+r2013-10_amd64.deb ------------------------------------------- new Debian package, version 2.0. size 2098384 bytes: control archive=1712 bytes. 1332 bytes, 12 lines control 2627 bytes, 25 lines md5sums Package: sim4db-dbgsym Source: kmer Version: 0~20150903+r2013-10 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2894 Depends: sim4db (= 0~20150903+r2013-10) Section: debug Priority: optional Description: debug symbols for sim4db Build-Ids: 0388b07968f4c78477afec5280c4ed91d9ab6b36 11ae389e70a6e3f4d580a06cc35d678580447d33 1a9f22f804c993dd5f232b922467d42fde00f2b7 26c95ae73fff1491a9bb2dd3111bb21ab0e3efa6 28e714c00b67bc1d10b3dcbf8200c381f2626fbb 2a68087e79442efff996df9a17be8832f93ce029 382f2960d125394b5adfe4e70b6e56ea372beda5 3cfbe5e6eca2ef7b0f8b3bd20d22d02c1059cd21 459413451feb48bac7825954bc9dd6444897efab 4cfdae339766ff7feb8f4f29bbda184d440b077c 4e1ecfded1d42eacd48c8c0f122e13473ec914c3 4fb883d149741a4e206f988f1d771ee41c10b8d4 54fd96032cb385a1e3551e939a00bffca0b892be 71bc7096bf5da9b09818dbc55ffc2f25999f750f 860efb275e300f7424099dc410bcf27281121a19 9a2751aa050eadeee52b0705bee963a33087eafe a069bb0fc90a3b6882f0fcd627ca003ee4dede4f a40425aecd96d28543736f63ae4563e73ba6e255 b7df3262f08e5dae606427eca64355a056d1d796 ba0952f9e95187af649963c9ae683d202548aa11 c59fc937d01b1cf30bb5db1783be261ec6e299f9 e4c84e6b91302791ccd0cfb6c05bcfbe19b45899 e974f3ec979ec6190f81cd28c0abc4482d921d04 f791b0687b6bf4fc1183e7cdbfb5f5329a305ef6 drwxr-xr-x root/root 0 2025-08-12 07:42 ./ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/03/ -rw-r--r-- root/root 133464 2025-08-12 07:42 ./usr/lib/debug/.build-id/03/88b07968f4c78477afec5280c4ed91d9ab6b36.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/11/ -rw-r--r-- root/root 189112 2025-08-12 07:42 ./usr/lib/debug/.build-id/11/ae389e70a6e3f4d580a06cc35d678580447d33.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/1a/ -rw-r--r-- root/root 470176 2025-08-12 07:42 ./usr/lib/debug/.build-id/1a/9f22f804c993dd5f232b922467d42fde00f2b7.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/26/ -rw-r--r-- root/root 84192 2025-08-12 07:42 ./usr/lib/debug/.build-id/26/c95ae73fff1491a9bb2dd3111bb21ab0e3efa6.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/28/ -rw-r--r-- root/root 74896 2025-08-12 07:42 ./usr/lib/debug/.build-id/28/e714c00b67bc1d10b3dcbf8200c381f2626fbb.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/2a/ -rw-r--r-- root/root 91536 2025-08-12 07:42 ./usr/lib/debug/.build-id/2a/68087e79442efff996df9a17be8832f93ce029.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/38/ -rw-r--r-- root/root 75288 2025-08-12 07:42 ./usr/lib/debug/.build-id/38/2f2960d125394b5adfe4e70b6e56ea372beda5.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/3c/ -rw-r--r-- root/root 218032 2025-08-12 07:42 ./usr/lib/debug/.build-id/3c/fbe5e6eca2ef7b0f8b3bd20d22d02c1059cd21.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/45/ -rw-r--r-- root/root 187024 2025-08-12 07:42 ./usr/lib/debug/.build-id/45/9413451feb48bac7825954bc9dd6444897efab.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/4c/ -rw-r--r-- root/root 82104 2025-08-12 07:42 ./usr/lib/debug/.build-id/4c/fdae339766ff7feb8f4f29bbda184d440b077c.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/4e/ -rw-r--r-- root/root 78920 2025-08-12 07:42 ./usr/lib/debug/.build-id/4e/1ecfded1d42eacd48c8c0f122e13473ec914c3.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/4f/ -rw-r--r-- root/root 91912 2025-08-12 07:42 ./usr/lib/debug/.build-id/4f/b883d149741a4e206f988f1d771ee41c10b8d4.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/54/ -rw-r--r-- root/root 77440 2025-08-12 07:42 ./usr/lib/debug/.build-id/54/fd96032cb385a1e3551e939a00bffca0b892be.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/71/ -rw-r--r-- root/root 76992 2025-08-12 07:42 ./usr/lib/debug/.build-id/71/bc7096bf5da9b09818dbc55ffc2f25999f750f.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/86/ -rw-r--r-- root/root 79496 2025-08-12 07:42 ./usr/lib/debug/.build-id/86/0efb275e300f7424099dc410bcf27281121a19.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/9a/ -rw-r--r-- root/root 90176 2025-08-12 07:42 ./usr/lib/debug/.build-id/9a/2751aa050eadeee52b0705bee963a33087eafe.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/a0/ -rw-r--r-- root/root 174248 2025-08-12 07:42 ./usr/lib/debug/.build-id/a0/69bb0fc90a3b6882f0fcd627ca003ee4dede4f.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/a4/ -rw-r--r-- root/root 74704 2025-08-12 07:42 ./usr/lib/debug/.build-id/a4/0425aecd96d28543736f63ae4563e73ba6e255.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/b7/ -rw-r--r-- root/root 80568 2025-08-12 07:42 ./usr/lib/debug/.build-id/b7/df3262f08e5dae606427eca64355a056d1d796.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/ba/ -rw-r--r-- root/root 83856 2025-08-12 07:42 ./usr/lib/debug/.build-id/ba/0952f9e95187af649963c9ae683d202548aa11.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/c5/ -rw-r--r-- root/root 90032 2025-08-12 07:42 ./usr/lib/debug/.build-id/c5/9fc937d01b1cf30bb5db1783be261ec6e299f9.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/e4/ -rw-r--r-- root/root 89232 2025-08-12 07:42 ./usr/lib/debug/.build-id/e4/c84e6b91302791ccd0cfb6c05bcfbe19b45899.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/e9/ -rw-r--r-- root/root 91088 2025-08-12 07:42 ./usr/lib/debug/.build-id/e9/74f3ec979ec6190f81cd28c0abc4482d921d04.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.build-id/f7/ -rw-r--r-- root/root 95480 2025-08-12 07:42 ./usr/lib/debug/.build-id/f7/91b0687b6bf4fc1183e7cdbfb5f5329a305ef6.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 34184 2025-08-12 07:42 ./usr/lib/debug/.dwz/x86_64-linux-gnu/sim4db.debug drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-08-12 07:42 ./usr/share/doc/sim4db-dbgsym -> sim4db sim4db_0~20150903+r2013-10_amd64.deb ------------------------------------ new Debian package, version 2.0. size 453116 bytes: control archive=2128 bytes. 1552 bytes, 30 lines control 3551 bytes, 54 lines md5sums Package: sim4db Source: kmer Version: 0~20150903+r2013-10 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 3376 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2) Recommends: leaff, kmer-examples Section: science Priority: optional Homepage: http://kmer.sourceforge.net Description: batch spliced alignment of cDNA sequences to a target genome Sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc algorithms to determine the alignments, but incorporates a fast sequence indexing and retrieval mechanism, implemented in the sister package 'leaff', to speedily process large volumes of sequences. . While sim4db produces alignments in the same way as sim4 or sim4cc, it has additional features to make it more amenable for use with whole-genome annotation pipelines. A script file can be used to group pairings between cDNAs and their corresponding genomic regions, to be aligned as one run and using the same set of parameters. Sim4db also optionally reports more than one alignment for the same cDNA within a genomic region, as long as they meet user-defined criteria such as minimum length, percentage sequence identity or coverage. This feature is instrumental in finding all alignments of a gene family at one locus. Lastly, the output is presented either as custom sim4db alignments or as GFF3 gene features. . This package is part of the Kmer suite. drwxr-xr-x root/root 0 2025-08-12 07:42 ./ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/bin/ -rwxr-xr-x root/root 102600 2025-08-12 07:42 ./usr/bin/cleanPolishes -rwxr-xr-x root/root 123080 2025-08-12 07:42 ./usr/bin/comparePolishes -rwxr-xr-x root/root 90312 2025-08-12 07:42 ./usr/bin/convertPolishes -rwxr-xr-x root/root 94408 2025-08-12 07:42 ./usr/bin/convertToAtac -rwxr-xr-x root/root 94408 2025-08-12 07:42 ./usr/bin/convertToExtent -rwxr-xr-x root/root 98504 2025-08-12 07:42 ./usr/bin/depthOfPolishes -rwxr-xr-x root/root 98504 2025-08-12 07:42 ./usr/bin/detectChimera -rwxr-xr-x root/root 98504 2025-08-12 07:42 ./usr/bin/filterPolishes -rwxr-xr-x root/root 156120 2025-08-12 07:42 ./usr/bin/fixPolishesIID -rwxr-xr-x root/root 90312 2025-08-12 07:42 ./usr/bin/headPolishes -rwxr-xr-x root/root 156120 2025-08-12 07:42 ./usr/bin/mappedCoverage -rwxr-xr-x root/root 156120 2025-08-12 07:42 ./usr/bin/mergePolishes -rwxr-xr-x root/root 102632 2025-08-12 07:42 ./usr/bin/parseSNP -rwxr-xr-x root/root 110824 2025-08-12 07:42 ./usr/bin/pickBestPolish -rwxr-xr-x root/root 98536 2025-08-12 07:42 ./usr/bin/pickUniquePolish -rwxr-xr-x root/root 90312 2025-08-12 07:42 ./usr/bin/plotCoverageVsIdentity -rwxr-xr-x root/root 168440 2025-08-12 07:42 ./usr/bin/realignPolishes -rwxr-xr-x root/root 90312 2025-08-12 07:42 ./usr/bin/removeDuplicate -rwxr-xr-x root/root 94408 2025-08-12 07:42 ./usr/bin/reportAlignmentDifferences -rwxr-xr-x root/root 855768 2025-08-12 07:42 ./usr/bin/sim4db -rwxr-xr-x root/root 106728 2025-08-12 07:42 ./usr/bin/sortPolishes -rwxr-xr-x root/root 98504 2025-08-12 07:42 ./usr/bin/summarizePolishes -rwxr-xr-x root/root 90312 2025-08-12 07:42 ./usr/bin/uniqPolishes -rwxr-xr-x root/root 94440 2025-08-12 07:42 ./usr/bin/vennPolishes drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/doc/sim4db/ -rw-r--r-- root/root 4962 2011-01-20 03:32 ./usr/share/doc/sim4db/README.sim4db.gz -rw-r--r-- root/root 244 2025-08-12 07:42 ./usr/share/doc/sim4db/README.test -rw-r--r-- root/root 1018 2025-08-12 07:42 ./usr/share/doc/sim4db/changelog.Debian.gz -rw-r--r-- root/root 7520 2025-08-12 07:42 ./usr/share/doc/sim4db/copyright -rw-r--r-- root/root 1053 2025-08-12 07:42 ./usr/share/doc/sim4db/sim4db-unit-test drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/man/ drwxr-xr-x root/root 0 2025-08-12 07:42 ./usr/share/man/man1/ -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/cleanPolishes.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/comparePolishes.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/convertPolishes.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/convertToAtac.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/convertToExtent.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/depthOfPolishes.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/detectChimera.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/filterPolishes.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/fixPolishesIID.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/headPolishes.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/mappedCoverage.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/mergePolishes.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/parseSNP.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/pickBestPolish.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/pickUniquePolish.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/plotCoverageVsIdentity.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/realignPolishes.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/removeDuplicate.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/reportAlignmentDifferences.1.gz -rw-r--r-- root/root 2206 2025-08-12 07:42 ./usr/share/man/man1/sim4db.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/sim4dbutils.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/sortPolishes.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/summarizePolishes.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/uniqPolishes.1.gz -rw-r--r-- root/root 1058 2025-08-12 07:42 ./usr/share/man/man1/vennPolishes.1.gz +------------------------------------------------------------------------------+ | Post Build Mon, 27 Apr 2026 01:39:41 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 27 Apr 2026 01:39:41 +0000 | +------------------------------------------------------------------------------+ Purging /build/kmer-8W5TPl Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 27 Apr 2026 01:39:43 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 173576 Build-Time: 118 Distribution: perl-5.42-throwaway Host Architecture: amd64 Install-Time: 9 Job: /srv/debomatic/incoming/kmer_0~20150903+r2013-10.dsc Machine Architecture: amd64 Package: kmer Package-Time: 131 Source-Version: 0~20150903+r2013-10 Space: 173576 Status: successful Version: 0~20150903+r2013-10 -------------------------------------------------------------------------------- Finished at 2026-04-27T01:39:39Z Build needed 00:02:11, 173576k disk space