sbuild (Debian sbuild) 0.89.1 (28 April 2025) on carme.larted.org.uk +==============================================================================+ | mecat2 0.0+git20200428.f54c542+ds-4 (amd64) Mon, 18 Aug 2025 12:23:29 +0000 | +==============================================================================+ Package: mecat2 Version: 0.0+git20200428.f54c542+ds-4 Source Version: 0.0+git20200428.f54c542+ds-4 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, 18 Aug 2025 12:23:30 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup mecat2_0.0+git20200428.f54c542+ds-4 perl-5.42-throwaway amd64 ------------------------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup mecat2_0.0+git20200428.f54c542+ds-4 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Mon, 18 Aug 2025 12:23:30 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.42 InRelease [3024 B] Get:1 file:/srv/reprepro perl-5.42 InRelease [3024 B] Get:2 file:/srv/reprepro perl-5.42/main amd64 Packages [547 kB] Get:3 http://deb.debian.org/debian unstable InRelease [216 kB] Get:4 http://deb.debian.org/debian sid InRelease [216 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:6 http://deb.debian.org/debian sid/main Sources.diff/Index [63.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-08-18-0810.54-F-2025-08-16-2015.43.pdiff [176 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-08-18-0810.54-F-2025-08-16-2015.43.pdiff [176 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2025-08-18-0810.54-F-2025-08-16-2015.43.pdiff [126 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2025-08-18-0810.54-F-2025-08-16-2015.43.pdiff [126 kB] Fetched 861 kB in 8s (105 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: binutils binutils-common binutils-x86-64-linux-gnu init-system-helpers libbinutils libctf-nobfd0 libctf0 libgprofng0 libidn2-0 libldap2 libsframe2 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5687 kB/5881 kB of archives. After this operation, 7168 B of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.42/main amd64 libldap2 amd64 2.6.10+dfsg-1+b1 [194 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 init-system-helpers all 1.69 [39.3 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libgprofng0 amd64 2.45-4 [810 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libctf0 amd64 2.45-4 [89.7 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libctf-nobfd0 amd64 2.45-4 [157 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 binutils-x86-64-linux-gnu amd64 2.45-4 [1042 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 binutils amd64 2.45-4 [266 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libbinutils amd64 2.45-4 [539 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 binutils-common amd64 2.45-4 [2556 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libsframe2 amd64 2.45-4 [79.5 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-3 [109 kB] Fetched 5687 kB in 0s (67.4 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14970 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.69_all.deb ... Unpacking init-system-helpers (1.69) over (1.68) ... Setting up init-system-helpers (1.69) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14971 files and directories currently installed.) Preparing to unpack .../0-libgprofng0_2.45-4_amd64.deb ... Unpacking libgprofng0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../1-libctf0_2.45-4_amd64.deb ... Unpacking libctf0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../2-libctf-nobfd0_2.45-4_amd64.deb ... Unpacking libctf-nobfd0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../3-binutils-x86-64-linux-gnu_2.45-4_amd64.deb ... Unpacking binutils-x86-64-linux-gnu (2.45-4) over (2.45-3) ... Preparing to unpack .../4-binutils_2.45-4_amd64.deb ... Unpacking binutils (2.45-4) over (2.45-3) ... Preparing to unpack .../5-libbinutils_2.45-4_amd64.deb ... Unpacking libbinutils:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../6-binutils-common_2.45-4_amd64.deb ... Unpacking binutils-common:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../7-libsframe2_2.45-4_amd64.deb ... Unpacking libsframe2:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../8-libidn2-0_2.3.8-3_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-3) over (2.3.8-2) ... Preparing to unpack .../9-libldap2_2.6.10+dfsg-1+b1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1+b1) over (2.6.10+dfsg-1) ... Setting up libsframe2:amd64 (2.45-4) ... Setting up binutils-common:amd64 (2.45-4) ... Setting up libctf-nobfd0:amd64 (2.45-4) ... Setting up libidn2-0:amd64 (2.3.8-3) ... Setting up libbinutils:amd64 (2.45-4) ... Setting up libldap2:amd64 (2.6.10+dfsg-1+b1) ... Setting up libctf0:amd64 (2.45-4) ... Setting up libgprofng0:amd64 (2.45-4) ... Setting up binutils-x86-64-linux-gnu (2.45-4) ... Setting up binutils (2.45-4) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Fetch source files Mon, 18 Aug 2025 12:23:44 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/mecat2_0.0+git20200428.f54c542+ds-4.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 18 Aug 2025 12:23:45 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, perl, build-essential Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, perl, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/mecat2-jpSdtR/resolver-Py8JKd/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/mecat2-jpSdtR/resolver-Py8JKd/apt_archive ./ InRelease Get:2 copy:/build/mecat2-jpSdtR/resolver-Py8JKd/apt_archive ./ Release [609 B] Ign:3 copy:/build/mecat2-jpSdtR/resolver-Py8JKd/apt_archive ./ Release.gpg Get:4 copy:/build/mecat2-jpSdtR/resolver-Py8JKd/apt_archive ./ Sources [618 B] Get:5 copy:/build/mecat2-jpSdtR/resolver-Py8JKd/apt_archive ./ Packages [657 B] Fetched 1884 B in 0s (94.6 kB/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... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libfile-stripnondeterminism-perl libmagic-mgc libmagic1t64 libpipeline1 libtool libuchardet0 libxml2-16 m4 man-db po-debconf sensible-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libfile-stripnondeterminism-perl libmagic-mgc libmagic1t64 libpipeline1 libtool libuchardet0 libxml2-16 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 11.6 MB of archives. After this operation, 41.6 MB of additional disk space will be used. Get:1 copy:/build/mecat2-jpSdtR/resolver-Py8JKd/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [868 B] Get:2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-1 [94.7 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.25 [91.6 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.1 [640 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.25 [937 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Preconfiguring packages ... Fetched 11.6 MB in 0s (86.3 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 14972 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-1_amd64.deb ... Unpacking bsdextrautils (2.41.1-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... 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Preparing to unpack .../18-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 .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../23-libxml2-16_2.14.5+dfsg-0.1_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../24-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../25-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 .../26-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../27-debhelper_13.25_all.deb ... Unpacking debhelper (13.25) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../28-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../29-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41.1-1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.1) ... Setting up libdebhelper-perl (13.25) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.25) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Check architectures Mon, 18 Aug 2025 12:23:52 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any-amd64) +------------------------------------------------------------------------------+ | Build environment Mon, 18 Aug 2025 12:23:52 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.25-1 (2025-04-25) amd64 (x86_64) Toolchain package versions: binutils_2.45-4 dpkg-dev_1.22.21 g++-14_14.3.0-5 gcc-14_14.3.0-5 libc6-dev_2.41-12 libstdc++-14-dev_14.3.0-5 libstdc++6_15.2.0-1 linux-libc-dev_6.12.38-1 Package versions: adduser_3.152 apt_3.1.4 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.7 bash_5.2.37-2+b5 binutils_2.45-4 binutils-common_2.45-4 binutils-gold_2.44-2 binutils-gold-x86-64-linux-gnu_2.44-2 binutils-x86-64-linux-gnu_2.45-4 bsdextrautils_2.41.1-1 bsdutils_1:2.41.1-1 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.7-3 cpp_4:14.2.0-1 cpp-14_14.3.0-5 cpp-14-x86-64-linux-gnu_14.3.0-5 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.25 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-4 dirmngr_2.4.8-2 dpkg_1.22.21 dpkg-dev_1.22.21 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.3.0-5 g++-14-x86-64-linux-gnu_14.3.0-5 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.3.0-5 gcc-14-base_14.3.0-5 gcc-14-x86-64-linux-gnu_14.3.0-5 gcc-15-base_15.2.0-1 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2+b1 gettext-base_0.23.1-2+b1 gnupg_2.4.8-2 gnupg-l10n_2.4.8-2 gpg_2.4.8-2 gpg-agent_2.4.8-2 gpgconf_2.4.8-2 gpgsm_2.4.8-2 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg7.0_3.1.4 libarchive-zip-perl_1.68-1 libasan8_15.2.0-1 libassuan9_3.0.2-2 libatomic1_15.2.0-1 libattr1_1:2.5.2-3 libaudit-common_1:4.0.5-1 libaudit1_1:4.0.5-1 libbinutils_2.45-4 libblkid1_2.41.1-1 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.41-12 libc-dev-bin_2.41-12 libc6_2.41-12 libc6-dev_2.41-12 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-10+b1 libcc1-0_15.2.0-1 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.45-4 libctf0_2.45-4 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.280 libdebhelper-perl_13.25 libdpkg-perl_1.22.21 libeatmydata1_131-2+b1 libelf1t64_0.192-4 libffi8_3.4.8-2 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-14-dev_14.3.0-5 libgcc-s1_15.2.0-1 libgcrypt20_1.11.2-2 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp10_2:6.3.0+dfsg-3 libgnutls30t64_3.8.10-2 libgomp1_15.2.0-1 libgpg-error0_1.55-2 libgprofng0_2.45-4 libhogweed6t64_3.10.1-1 libhwasan0_15.2.0-1 libidn2-0_2.3.8-3 libisl23_0.27-1 libitm1_15.2.0-1 libjansson4_2.14-2+b3 libksba8_1.6.7-2+b1 liblastlog2-2_2.41.1-1 libldap2_2.6.10+dfsg-1+b1 liblsan0_15.2.0-1 liblz4-1_1.10.0-4 liblzma5_5.8.1-1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41.1-1 libmpc3_1.3.1-1+b3 libmpfr6_4.2.2-1 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.1-1 libnpth0t64_1.8-3 libp11-kit0_0.25.5-3 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-8-0_10.45-1 libperl5.40_5.40.1-6 libperl5.42_5.42.0-1 libpipeline1_1.5.8-1 libquadmath0_15.2.0-1 libreadline8t64_8.2-6 libsasl2-2_2.1.28+dfsg1-9 libsasl2-modules-db_2.1.28+dfsg1-9 libseccomp2_2.6.0-2 libselinux1_3.8.1-1 libsemanage-common_3.8.1-1 libsemanage2_3.8.1-1 libsepol2_3.8.1-1 libsframe2_2.45-4 libsmartcols1_2.41.1-1 libsqlite3-0_3.46.1-7 libssl3t64_3.5.2-1 libstdc++-14-dev_14.3.0-5 libstdc++6_15.2.0-1 libsystemd0_258~rc2-2 libtasn1-6_4.20.0-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_15.2.0-1 libubsan1_15.2.0-1 libuchardet0_0.0.8-1+b2 libudev1_258~rc2-2 libunistring5_1.3-2 libuuid1_2.41.1-1 libxml2-16_2.14.5+dfsg-0.1 libxxhash0_0.8.3-2 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.38-1 login.defs_1:4.17.4-2 m4_1.4.19-8 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 openssl-provider-legacy_3.5.2-1 passwd_1:4.17.4-2 patch_2.8-2 perl_5.42.0-1 perl-base_5.42.0-1 perl-modules-5.40_5.40.1-6 perl-modules-5.42_5.42.0-1 pinentry-curses_1.3.2-3 po-debconf_1.0.21+nmu1 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.25 sqv_1.3.0-3 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 util-linux_2.41.1-1 xz-utils_5.8.1-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Mon, 18 Aug 2025 12:23:52 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: mecat2 Binary: mecat2 Architecture: any-amd64 Version: 0.0+git20200428.f54c542+ds-4 Maintainer: Debian Med Packaging Team Uploaders: Shayan Doust Homepage: https://github.com/xiaochuanle/MECAT2 Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/mecat2 Vcs-Git: https://salsa.debian.org/med-team/mecat2.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev, perl Package-List: mecat2 deb science optional arch=any-amd64,x32 Checksums-Sha1: 3422fa4cc700ac60aaec8050b8a98612b444b678 381084 mecat2_0.0+git20200428.f54c542+ds.orig.tar.xz 8b283121f74d8922811d74c432b6ec2fecc24e86 338661480 mecat2_0.0+git20200428.f54c542+ds-4.debian.tar.xz Checksums-Sha256: 32f66c44306f1ebffed4ef3b5ba26041387d16561627ff93aa69bf6ee1107e31 381084 mecat2_0.0+git20200428.f54c542+ds.orig.tar.xz e00dea2e6659c6dee053a91d67c5dce92a8ff59fc023d029443b7998ec083ab0 338661480 mecat2_0.0+git20200428.f54c542+ds-4.debian.tar.xz Files: 1e944b07acb5474e4da65cb10b829ec0 381084 mecat2_0.0+git20200428.f54c542+ds.orig.tar.xz 449343e86843c0b8f229b939ba98b1b5 338661480 mecat2_0.0+git20200428.f54c542+ds-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmVJ7fgRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFy0w/+PQiqPpvomriZT2Cf02AW4rmh5bEoDr4g Fwc2Vmw1DYtPazf3JODz/mC8mDKaCfYP88TjoeiOHubH3BroBsIcyXeO4tnmMc8O luDH+9nsaYWGZxjvg9Z2GtF6Cvft9UoeS11yZOkPdK+O232BCeoOc9y0I5EbFFAU eEFAxe4YNvTmOXGiUrBQTqMZSwxEA0c9g7ifDQxKTPM261i4+b0ARGLoK+bnonq/ AmSDEjC5JfAeEkmF2xpCrdbFWmsJvNtMcCAOSgL1qB23O8fskOB9936lYSKY1xvF MGVblCwFoQ638NQiRyhq2P58z1eXl9pLFGhaiagYIuOes0tobTGfIDWaVKjab3hB 48OWCRvC/nl6aD/RH9prrvZS6VCromvKgPSsN8QVYmvnnffmZ5REXSzm/Af62tVn 5BH9wP1MVH1V4aH8DjzD88oLJKzZhtZgs/Fy/29GDdEsYbEq209jlxdwyn5QcH6o 4M9d6ZLEjvvr8TkWcpDYAUisCWeFD4B6vsNhfi6GoSLltKG38AJYVQBRSW/mkHqQ 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+------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network mecat2_0.0+git20200428.f54c542+ds-4 perl-5.42-throwaway amd64 ------------------------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network mecat2_0.0+git20200428.f54c542+ds-4 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent 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/mecat2-jpSdtR/mecat2-0.0+git20200428.f54c542+ds 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-0473d06d-62e5-42cf-9e83-0512dce26ea7 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 mecat2 dpkg-buildpackage: info: source version 0.0+git20200428.f54c542+ds-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j2 clean make[1]: Entering directory '/build/mecat2-jpSdtR/mecat2-0.0+git20200428.f54c542+ds' cd src && make clean make[2]: Entering directory '/build/mecat2-jpSdtR/mecat2-0.0+git20200428.f54c542+ds/src' Building for 'Linux' '6.12.25-amd64' as 'amd64' Makefile:401: warning: overriding recipe for target '../Linux-amd64/bin/mecat2cns' Makefile:401: warning: ignoring old recipe for target '../Linux-amd64/bin/mecat2cns' Makefile:418: warning: overriding recipe for target 'clean_mecat2cns' Makefile:418: warning: ignoring old recipe for target 'clean_mecat2cns' rm -f ../Linux-amd64/bin/libhbn.a ../Linux-amd64/obj/libhbn.a/corelib/build_db.[doP] ../Linux-amd64/obj/libhbn.a/corelib/cmd_arg.[doP] ../Linux-amd64/obj/libhbn.a/corelib/cstr_util.[doP] ../Linux-amd64/obj/libhbn.a/corelib/db_format.[doP] ../Linux-amd64/obj/libhbn.a/corelib/fasta.[doP] ../Linux-amd64/obj/libhbn.a/corelib/gapped_candidate.[doP] ../Linux-amd64/obj/libhbn.a/corelib/hbn_aux.[doP] ../Linux-amd64/obj/libhbn.a/corelib/hbn_format.[doP] ../Linux-amd64/obj/libhbn.a/corelib/hbn_hit.[doP] ../Linux-amd64/obj/libhbn.a/corelib/hbn_package_version.[doP] ../Linux-amd64/obj/libhbn.a/corelib/kstring.[doP] ../Linux-amd64/obj/libhbn.a/corelib/line_reader.[doP] ../Linux-amd64/obj/libhbn.a/corelib/m4_record.[doP] ../Linux-amd64/obj/libhbn.a/corelib/name2id_map.[doP] ../Linux-amd64/obj/libhbn.a/corelib/partition_aux.[doP] ../Linux-amd64/obj/libhbn.a/corelib/raw_reads.[doP] ../Linux-amd64/obj/libhbn.a/corelib/seqdb_summary.[doP] ../Linux-amd64/obj/libhbn.a/corelib/seqdb.[doP] ../Linux-amd64/obj/libhbn.a/corelib/seq_tag.[doP] ../Linux-amd64/obj/libhbn.a/corelib/seq_tag_report.[doP] ../Linux-amd64/obj/libhbn.a/corelib/small_object_alloc.[doP] ../Linux-amd64/obj/libhbn.a/corelib/string2hsp.[doP] ../Linux-amd64/obj/libhbn.a/algo/chain_dp.[doP] ../Linux-amd64/obj/libhbn.a/algo/diff_gapalign.[doP] ../Linux-amd64/obj/libhbn.a/algo/hash_list_bucket_sort.[doP] ../Linux-amd64/obj/libhbn.a/algo/kalloc.[doP] ../Linux-amd64/obj/libhbn.a/algo/ksw2_extd2_sse.[doP] ../Linux-amd64/obj/libhbn.a/algo/ksw2_extz2_sse.[doP] ../Linux-amd64/obj/libhbn.a/algo/ksw2_wrapper.[doP] ../Linux-amd64/obj/libhbn.a/algo/hbn_lookup_table.[doP] ../Linux-amd64/obj/libhbn.a/algo/hbn_traceback_aux.[doP] ../Linux-amd64/obj/libhbn.a/algo/word_finder.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/c_ncbi_blast_aux.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/ncbi_blast_aux.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/blast_args.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/cmdline_flags.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/format_flags.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_allow.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_desc.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_types.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr_util.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_cmp.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/numeric_str_interconv.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_util.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_encoding.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_hits.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_message.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_options.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_stat.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_parameters.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_program.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_types.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/boost_erf.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/hsp2string.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/ncbi_math.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_query_info.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_sequence_blk.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/gapinfo.[doP] rm -f ../Linux-amd64/bin/mecat2pcan ../Linux-amd64/obj/mecat2pcan/app/mecat2pcan/pcan.[doP] rm -f ../Linux-amd64/bin/mecat2map ../Linux-amd64/obj/mecat2map/app/map/cmdline_args.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_align_one_volume.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_build_seqdb.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_extend_subseq_hit.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_find_subseq_hit.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_job_control.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_options.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_subseq_hit.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_task_struct.[doP] ../Linux-amd64/obj/mecat2map/app/map/main.[doP] ../Linux-amd64/obj/mecat2map/app/map/mecat_results.[doP] rm -f ../Linux-amd64/bin/mecat2cns ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cmdline_args.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_aux.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_part.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_read.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_options.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_align_tag.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_aux.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/hbn_task_struct.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/main.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/raw_reads_reader.[doP] rm -f ../Linux-amd64/bin/mecat2viewdb ../Linux-amd64/obj/mecat2viewdb/app/hbndb/viewhbndb.[doP] rm -f ../Linux-amd64/bin/mecat2lcr ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/cmdline_args.[doP] ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/largest_cover_range.[doP] ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/main.[doP] ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/range_list.[doP] ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/m4_aux.[doP] rm -f ../Linux-amd64/bin/mecat2splitreads ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/cmdline_args.[doP] ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/main.[doP] ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/split_reads.[doP] ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/range_list.[doP] ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/m4_aux.[doP] rm -f ../Linux-amd64/bin/mecat2trimbases ../Linux-amd64/obj/mecat2trimbases/app/mecat2trim/3_trim_bases/main.[doP] rm -f ../Linux-amd64/bin/mecat2pm4 ../Linux-amd64/obj/mecat2pm4/app/mecat2pm4/main.[doP] rm -f ../Linux-amd64/bin/mecat2extseqs ../Linux-amd64/obj/mecat2extseqs/app/mecat2extseqs/main.[doP] rm -f ../Linux-amd64/bin/libfsa.a ../Linux-amd64/obj/libfsa.a/app/fsa/argument_parser.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/getopt.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/logger.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/overlap.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/read_store.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/sequence.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/utility.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/fasta_reader.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/fastq_reader.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_store.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/simple_align.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_filter.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_stat.[doP] rm -f ../Linux-amd64/bin/fsa_ol_filter ../Linux-amd64/obj/fsa_ol_filter/app/fsa/fsa_ol_filter.[doP] rm -f ../Linux-amd64/bin/fsa_assemble ../Linux-amd64/obj/fsa_assemble/app/fsa/fsa_assemble.[doP] ../Linux-amd64/obj/fsa_assemble/app/fsa/assembly.[doP] ../Linux-amd64/obj/fsa_assemble/app/fsa/graph.[doP] ../Linux-amd64/obj/fsa_assemble/app/fsa/string_graph.[doP] ../Linux-amd64/obj/fsa_assemble/app/fsa/path_graph.[doP] rm -f ../Linux-amd64/bin/fsa_ctg_bridge ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/fsa_ctg_bridge.[doP] ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_bridge.[doP] ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_graph.[doP] ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link.[doP] ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link_store.[doP] rm -f ../Linux-amd64/bin/fsa_rd_stat ../Linux-amd64/obj/fsa_rd_stat/app/fsa/fsa_rd_stat.[doP] ../Linux-amd64/obj/fsa_rd_stat/app/fsa/read_stat.[doP] rm -f ../Linux-amd64/bin/mecat.pl rm -f ../Linux-amd64/bin/mecat.sh rm -f rm -f ../Linux-amd64/bin/Plgd/Grid.pm ../Linux-amd64/bin/Plgd/GridLsf.pm ../Linux-amd64/bin/Plgd/GridPbs.pm ../Linux-amd64/bin/Plgd/GridSge.pm ../Linux-amd64/bin/Plgd/GridSlurm.pm ../Linux-amd64/bin/Plgd/Project.pm ../Linux-amd64/bin/Plgd/Script.pm ../Linux-amd64/bin/Plgd/Utils.pm rm -rf ../Linux-amd64/bin/Plgd make[2]: Leaving directory '/build/mecat2-jpSdtR/mecat2-0.0+git20200428.f54c542+ds/src' make[1]: Leaving directory '/build/mecat2-jpSdtR/mecat2-0.0+git20200428.f54c542+ds' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building mecat2 using existing ./mecat2_0.0+git20200428.f54c542+ds.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building mecat2 in mecat2_0.0+git20200428.f54c542+ds-4.debian.tar.xz dpkg-source: info: building mecat2 in mecat2_0.0+git20200428.f54c542+ds-4.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j2 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/mecat2-jpSdtR/mecat2-0.0+git20200428.f54c542+ds' cd src && make make[2]: Entering directory '/build/mecat2-jpSdtR/mecat2-0.0+git20200428.f54c542+ds/src' Building for 'Linux' '6.12.25-amd64' as 'amd64' Makefile:401: warning: overriding recipe for target '../Linux-amd64/bin/mecat2cns' Makefile:401: warning: ignoring old recipe for target '../Linux-amd64/bin/mecat2cns' Makefile:418: warning: overriding recipe for target 'clean_mecat2cns' Makefile:418: warning: ignoring old recipe for target 'clean_mecat2cns' cp -pf pipeline/mecat.pl ../Linux-amd64/bin/mecat.pl cp -pf pipeline/mecat.sh ../Linux-amd64/bin/mecat.sh chmod +x ../Linux-amd64/bin/mecat.pl chmod +x ../Linux-amd64/bin/mecat.sh cp -pf pipeline/Plgd/Grid.pm ../Linux-amd64/bin/Plgd/Grid.pm cp -pf pipeline/Plgd/GridLsf.pm ../Linux-amd64/bin/Plgd/GridLsf.pm cp -pf pipeline/Plgd/GridPbs.pm ../Linux-amd64/bin/Plgd/GridPbs.pm cp -pf pipeline/Plgd/GridSge.pm ../Linux-amd64/bin/Plgd/GridSge.pm cp -pf pipeline/Plgd/GridSlurm.pm ../Linux-amd64/bin/Plgd/GridSlurm.pm cp -pf pipeline/Plgd/Project.pm ../Linux-amd64/bin/Plgd/Project.pm cp -pf pipeline/Plgd/Script.pm ../Linux-amd64/bin/Plgd/Script.pm cp -pf pipeline/Plgd/Utils.pm ../Linux-amd64/bin/Plgd/Utils.pm cc -o ../Linux-amd64/obj/libhbn.a/corelib/build_db.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/build_db.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/cmd_arg.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/cmd_arg.c g++ -o ../Linux-amd64/obj/libhbn.a/corelib/cstr_util.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp corelib/cstr_util.cpp cc -o ../Linux-amd64/obj/libhbn.a/corelib/db_format.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/db_format.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/fasta.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/fasta.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/gapped_candidate.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/gapped_candidate.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/hbn_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/hbn_aux.c corelib/hbn_aux.c: In function ‘hbn_get_cpu_count’: corelib/hbn_aux.c:357:9: warning: unused variable ‘allCPUNum_’ [-Wunused-variable] 357 | int allCPUNum_ = sysconf(_SC_NPROCESSORS_CONF); | ^~~~~~~~~~ cc -o ../Linux-amd64/obj/libhbn.a/corelib/hbn_format.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/hbn_format.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/hbn_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/hbn_hit.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/hbn_package_version.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/hbn_package_version.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/kstring.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/kstring.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/line_reader.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/line_reader.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/m4_record.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/m4_record.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/name2id_map.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/name2id_map.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/partition_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/partition_aux.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/raw_reads.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/raw_reads.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/seqdb_summary.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/seqdb_summary.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/seqdb.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/seqdb.c cc -o ../Linux-amd64/obj/libhbn.a/corelib/seq_tag.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/seq_tag.c corelib/seq_tag.c:480:1: warning: ‘examine_ovlp_quality_perfect’ defined but not used [-Wunused-function] 480 | examine_ovlp_quality_perfect(int qoff, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ corelib/seq_tag.c:9:12: warning: ‘CircularSeq’ defined but not used [-Wunused-variable] 9 | static int CircularSeq = 0; | ^~~~~~~~~~~ corelib/seq_tag.c:7:12: warning: ‘RepeatSeq’ defined but not used [-Wunused-variable] 7 | static int RepeatSeq = 0; | ^~~~~~~~~ g++ -o ../Linux-amd64/obj/libhbn.a/corelib/seq_tag_report.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp corelib/seq_tag_report.cpp cc -o ../Linux-amd64/obj/libhbn.a/corelib/small_object_alloc.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/small_object_alloc.c g++ -o ../Linux-amd64/obj/libhbn.a/corelib/string2hsp.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp corelib/string2hsp.cpp cc -o ../Linux-amd64/obj/libhbn.a/algo/chain_dp.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/chain_dp.c algo/chain_dp.c: In function ‘find_best_kmer_match’: algo/chain_dp.c:164:5: warning: ‘memset’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 164 | memset(t, 0, sizeof(int) * n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ algo/chain_dp.c: In function ‘chaining_find_candidates’: algo/chain_dp.c:257:5: warning: ‘memset’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 257 | memset(t, 0, sizeof(int) * n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o ../Linux-amd64/obj/libhbn.a/algo/diff_gapalign.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp algo/diff_gapalign.cpp cc -o ../Linux-amd64/obj/libhbn.a/algo/hash_list_bucket_sort.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/hash_list_bucket_sort.c cc -o ../Linux-amd64/obj/libhbn.a/algo/kalloc.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/kalloc.c cc -o ../Linux-amd64/obj/libhbn.a/algo/ksw2_extd2_sse.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/ksw2_extd2_sse.c algo/diff_gapalign.cpp:375:1: warning: ‘void dump_subseq(const u8*, int)’ defined but not used [-Wunused-function] 375 | dump_subseq(const u8* seq, int len) | ^~~~~~~~~~~ cc -o ../Linux-amd64/obj/libhbn.a/algo/ksw2_extz2_sse.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/ksw2_extz2_sse.c cc -o ../Linux-amd64/obj/libhbn.a/algo/ksw2_wrapper.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/ksw2_wrapper.c cc -o ../Linux-amd64/obj/libhbn.a/algo/hbn_lookup_table.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/hbn_lookup_table.c cc -o ../Linux-amd64/obj/libhbn.a/algo/hbn_traceback_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/hbn_traceback_aux.c cc -o ../Linux-amd64/obj/libhbn.a/algo/word_finder.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/word_finder.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/c_ncbi_blast_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/c_ncbi_blast_aux.c g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/ncbi_blast_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/ncbi_blast_aux.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/blast_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/blast_args.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/cmdline_flags.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/cmdline_flags.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/format_flags.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/format_flags.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_allow.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/ncbiargs_allow.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_desc.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/ncbiargs_desc.cpp ncbi_blast/cmdline_args/ncbiargs_allow.cpp:85:15: warning: ‘std::string ncbi::s_GetSymbolClass(CArgAllow_Symbols::ESymbolClass)’ defined but not used [-Wunused-function] 85 | static string s_GetSymbolClass(CArgAllow_Symbols::ESymbolClass symbol_class) | ^~~~~~~~~~~~~~~~ g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_types.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/ncbiargs_types.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr_util.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/ncbistr_util.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/ncbistr.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_cmp.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/str_cmp.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/numeric_str_interconv.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/numeric_str_interconv.cpp g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_util.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/str_util.cpp ncbi_blast/str_util/numeric_str_interconv.cpp: In function ‘ncbi::SIZE_TYPE ns_hbnstr::DoubleToString_Ecvt(double, unsigned int, char*, ncbi::SIZE_TYPE, int*, int*)’: ncbi_blast/str_util/numeric_str_interconv.cpp:2175:20: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying between 0 and 15 bytes from a string of length 31 [-Wstringop-truncation] 2175 | strncpy(buffer,digits,digits_len); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ ncbi_blast/str_util/numeric_str_interconv.cpp: In function ‘ncbi::SIZE_TYPE ns_hbnstr::DoubleToStringPosix(double, unsigned int, char*, ncbi::SIZE_TYPE)’: ncbi_blast/str_util/numeric_str_interconv.cpp:2273:16: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying between 0 and 15 bytes from a string of length 31 [-Wstringop-truncation] 2273 | strncpy(buffer_pos,digits_pos, digits_len); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbi_blast/str_util/numeric_str_interconv.cpp:2260:20: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying between 0 and 14 bytes from a string of length 30 [-Wstringop-truncation] 2260 | strncpy(buffer_pos,digits_pos,digits_len); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbi_blast/str_util/numeric_str_interconv.cpp:2234:20: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying between 1 and 14 bytes from a string of length 30 [-Wstringop-truncation] 2234 | strncpy(buffer_pos,digits_pos,digits_len); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbi_blast/str_util/numeric_str_interconv.cpp:2234:20: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying between 1 and 14 bytes from a string of length 30 [-Wstringop-truncation] ncbi_blast/str_util/numeric_str_interconv.cpp:2208:16: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying between 0 and 15 bytes from a string of length 31 [-Wstringop-truncation] 2208 | strncpy(buffer,digits, digits_len); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_encoding.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_encoding.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_hits.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_hits.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_message.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_message.c ncbi_blast/setup/blast_hits.c:3897:1: warning: ‘s_TrimResultsByTotalHSPLimitEx’ defined but not used [-Wunused-function] 3897 | s_TrimResultsByTotalHSPLimitEx(BlastHSPResults* results, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbi_blast/setup/blast_hits.c:3815:1: warning: ‘s_TrimResultsByTotalHSPLimit’ defined but not used [-Wunused-function] 3815 | s_TrimResultsByTotalHSPLimit(BlastHSPResults* results, Uint4 total_hsp_limit) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ncbi_blast/setup/blast_hits.c:3580:12: warning: ‘s_SortHspWrapRawScore’ defined but not used [-Wunused-function] 3580 | static int s_SortHspWrapRawScore(const void *x, const void *y) | ^~~~~~~~~~~~~~~~~~~~~ cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_options.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_options.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_stat.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_stat.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_parameters.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_parameters.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_program.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_program.c g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_types.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/setup/blast_types.cpp cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/boost_erf.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/boost_erf.c g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/hsp2string.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/setup/hsp2string.cpp cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/ncbi_math.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/ncbi_math.c In file included from ncbi_blast/setup/ncbi_math.c:498: ncbi_blast/setup/ncbi_erf.c: In function ‘s_IEEE754_Exp’: ncbi_blast/setup/ncbi_erf.c:40:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 40 | #define __LO(x) *(int*)&x | ^ ncbi_blast/setup/ncbi_erf.c:140:34: note: in expansion of macro ‘__LO’ 140 | if(((hx&0xfffff)|__LO(x))!=0) | ^~~~ ncbi_blast/setup/ncbi_erf.c: In function ‘BLAST_Erf’: ncbi_blast/setup/ncbi_erf.c:40:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 40 | #define __LO(x) *(int*)&x | ^ ncbi_blast/setup/ncbi_erf.c:401:9: note: in expansion of macro ‘__LO’ 401 | __LO(z) = 0; | ^~~~ ncbi_blast/setup/ncbi_erf.c: In function ‘BLAST_ErfC’: ncbi_blast/setup/ncbi_erf.c:40:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 40 | #define __LO(x) *(int*)&x | ^ ncbi_blast/setup/ncbi_erf.c:462:13: note: in expansion of macro ‘__LO’ 462 | __LO(z) = 0; | ^~~~ cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_query_info.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_query_info.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_sequence_blk.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_sequence_blk.c cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/gapinfo.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/gapinfo.c cc -o ../Linux-amd64/obj/mecat2pcan/app/mecat2pcan/pcan.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2pcan app/mecat2pcan/pcan.c g++ -o ../Linux-amd64/obj/mecat2map/app/map/cmdline_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -Iapp/map app/map/cmdline_args.cpp cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_align_one_volume.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_align_one_volume.c cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_build_seqdb.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_build_seqdb.c cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_extend_subseq_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_extend_subseq_hit.c cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_find_subseq_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_find_subseq_hit.c cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_job_control.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_job_control.c cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_options.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_options.c cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_subseq_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_subseq_hit.c app/map/cmdline_args.cpp:74:20: warning: ‘ncbi::kGroupExtension’ defined but not used [-Wunused-variable] 74 | static const char* kGroupExtension = "Extension options"; | ^~~~~~~~~~~~~~~ cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_task_struct.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_task_struct.c cc -o ../Linux-amd64/obj/mecat2map/app/map/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/main.c cc -o ../Linux-amd64/obj/mecat2map/app/map/mecat_results.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/mecat_results.c g++ -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cmdline_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cmdline_args.cpp cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cns_aux.c cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_part.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cns_one_part.c g++ -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_read.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cns_one_read.cpp app/mecat2cns/cns_one_read.cpp: In function ‘BOOL meap_consensus_one_segment(FCCnsData*, int*, int*, int, int, kstring_t*)’: app/mecat2cns/cns_one_read.cpp:34:27: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 34 | if (ks_size(*cns_seq) < min_size) return FALSE; In file included from app/mecat2cns/cns_one_read.h:4, from app/mecat2cns/cns_one_read.cpp:1: app/mecat2cns/cns_one_read.cpp: In function ‘void consensus_one_read(CnsThreadData*, int)’: app/mecat2cns/cns_one_read.cpp:242:32: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 242 | hbn_assert(read_length == kv_size(*fwd_read_v)); app/mecat2cns/../../corelib/hbn_aux.h:115:15: note: in definition of macro ‘__hbn_assert’ 115 | if (!(expr)) { \ | ^~~~ app/mecat2cns/cns_one_read.cpp:242:9: note: in expansion of macro ‘hbn_assert’ 242 | hbn_assert(read_length == kv_size(*fwd_read_v)); | ^~~~~~~~~~ cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_options.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cns_options.c cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_align_tag.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/fccns_align_tag.c cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/fccns_aux.c app/mecat2cns/fccns_aux.c: In function ‘consensus_backbone_segment’: app/mecat2cns/fccns_aux.c:137:9: warning: variable ‘g_best_ck’ set but not used [-Wunused-but-set-variable] 137 | int g_best_ck = 0; | ^~~~~~~~~ cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/fccns.c cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/hbn_task_struct.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/hbn_task_struct.c cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/main.c cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/raw_reads_reader.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/raw_reads_reader.c cc -o ../Linux-amd64/obj/mecat2viewdb/app/hbndb/viewhbndb.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/hbndb app/hbndb/viewhbndb.c g++ -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/cmdline_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/1_largest_cover_range/cmdline_args.cpp cc -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/largest_cover_range.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/1_largest_cover_range/largest_cover_range.c cc -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/1_largest_cover_range/main.c cc -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/range_list.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/common/range_list.c cc -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/m4_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/common/m4_aux.c g++ -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/cmdline_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/2_split_reads/cmdline_args.cpp cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/2_split_reads/main.c cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/split_reads.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/2_split_reads/split_reads.c cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/range_list.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/common/range_list.c cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/m4_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/common/m4_aux.c cc -o ../Linux-amd64/obj/mecat2trimbases/app/mecat2trim/3_trim_bases/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/3_trim_bases app/mecat2trim/3_trim_bases/main.c cc -o ../Linux-amd64/obj/mecat2pm4/app/mecat2pm4/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2pm4 app/mecat2pm4/main.c cc -o ../Linux-amd64/obj/mecat2extseqs/app/mecat2extseqs/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2extseqs -Iapp/mecat2extseqs/libboost app/mecat2extseqs/main.c g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/argument_parser.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/argument_parser.cpp cc -o ../Linux-amd64/obj/libfsa.a/app/fsa/getopt.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/fsa app/fsa/getopt.c g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/logger.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/logger.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/read_store.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/read_store.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/sequence.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/sequence.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/utility.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/utility.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/fasta_reader.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fasta_reader.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/fastq_reader.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fastq_reader.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_store.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap_store.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/simple_align.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/simple_align.cpp app/fsa/simple_align.cpp: In member function ‘SimpleAlign::Result SimpleAlign::Align(const std::string&, const std::string&, int, bool)’: app/fsa/simple_align.cpp:153:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 153 | if ( node.x + node.len >= query.size() || node.y + node.len >= target_.size()) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ app/fsa/simple_align.cpp:153:75: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 153 | if ( node.x + node.len >= query.size() || node.y + node.len >= target_.size()) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_filter.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap_filter.cpp g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_stat.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap_stat.cpp app/fsa/overlap_filter.cpp: In member function ‘void OverlapFilter::FilterLocalStep(Seq::Id, const std::unordered_map&)’: app/fsa/overlap_filter.cpp:413:18: warning: unused variable ‘loc’ [-Wunused-variable] 413 | auto loc = o.Location(max_overhang_); | ^~~ app/fsa/overlap_filter.cpp:447:22: warning: unused variable ‘loc’ [-Wunused-variable] 447 | auto loc = o.Location(max_overhang_); | ^~~ g++ -o ../Linux-amd64/obj/fsa_ol_filter/app/fsa/fsa_ol_filter.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fsa_ol_filter.cpp g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/fsa_assemble.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fsa_assemble.cpp g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/assembly.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/assembly.cpp g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/graph.cpp g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/string_graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/string_graph.cpp app/fsa/string_graph.cpp: In member function ‘std::vector StringNode::GetAllOutNodes()’: app/fsa/string_graph.cpp:39:21: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move] 39 | return std::move(nodes); | ~~~~~~~~~^~~~~~~ app/fsa/string_graph.cpp:39:21: note: remove ‘std::move’ call app/fsa/string_graph.cpp: In member function ‘std::vector StringNode::GetAllInNodes()’: app/fsa/string_graph.cpp:49:21: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move] 49 | return std::move(nodes); | ~~~~~~~~~^~~~~~~ app/fsa/string_graph.cpp:49:21: note: remove ‘std::move’ call g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/path_graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/path_graph.cpp g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/fsa_ctg_bridge.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fsa_ctg_bridge.cpp g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_bridge.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_bridge.cpp g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_graph.cpp g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_link.cpp g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link_store.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_link_store.cpp g++ -o ../Linux-amd64/obj/fsa_rd_stat/app/fsa/fsa_rd_stat.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fsa_rd_stat.cpp g++ -o ../Linux-amd64/obj/fsa_rd_stat/app/fsa/read_stat.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/read_stat.cpp ar -rv ../Linux-amd64/bin/libhbn.a ../Linux-amd64/obj/libhbn.a/corelib/build_db.o ../Linux-amd64/obj/libhbn.a/corelib/cmd_arg.o ../Linux-amd64/obj/libhbn.a/corelib/cstr_util.o ../Linux-amd64/obj/libhbn.a/corelib/db_format.o ../Linux-amd64/obj/libhbn.a/corelib/fasta.o ../Linux-amd64/obj/libhbn.a/corelib/gapped_candidate.o ../Linux-amd64/obj/libhbn.a/corelib/hbn_aux.o ../Linux-amd64/obj/libhbn.a/corelib/hbn_format.o ../Linux-amd64/obj/libhbn.a/corelib/hbn_hit.o ../Linux-amd64/obj/libhbn.a/corelib/hbn_package_version.o ../Linux-amd64/obj/libhbn.a/corelib/kstring.o ../Linux-amd64/obj/libhbn.a/corelib/line_reader.o ../Linux-amd64/obj/libhbn.a/corelib/m4_record.o ../Linux-amd64/obj/libhbn.a/corelib/name2id_map.o ../Linux-amd64/obj/libhbn.a/corelib/partition_aux.o ../Linux-amd64/obj/libhbn.a/corelib/raw_reads.o ../Linux-amd64/obj/libhbn.a/corelib/seqdb_summary.o ../Linux-amd64/obj/libhbn.a/corelib/seqdb.o ../Linux-amd64/obj/libhbn.a/corelib/seq_tag.o ../Linux-amd64/obj/libhbn.a/corelib/seq_tag_report.o ../Linux-amd64/obj/libhbn.a/corelib/small_object_alloc.o ../Linux-amd64/obj/libhbn.a/corelib/string2hsp.o ../Linux-amd64/obj/libhbn.a/algo/chain_dp.o ../Linux-amd64/obj/libhbn.a/algo/diff_gapalign.o ../Linux-amd64/obj/libhbn.a/algo/hash_list_bucket_sort.o ../Linux-amd64/obj/libhbn.a/algo/kalloc.o ../Linux-amd64/obj/libhbn.a/algo/ksw2_extd2_sse.o ../Linux-amd64/obj/libhbn.a/algo/ksw2_extz2_sse.o ../Linux-amd64/obj/libhbn.a/algo/ksw2_wrapper.o ../Linux-amd64/obj/libhbn.a/algo/hbn_lookup_table.o ../Linux-amd64/obj/libhbn.a/algo/hbn_traceback_aux.o ../Linux-amd64/obj/libhbn.a/algo/word_finder.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/c_ncbi_blast_aux.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/ncbi_blast_aux.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/blast_args.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/cmdline_flags.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/format_flags.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_allow.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_desc.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_types.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr_util.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_cmp.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/numeric_str_interconv.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_util.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_encoding.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_hits.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_message.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_options.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_stat.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_parameters.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_program.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_types.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/boost_erf.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/hsp2string.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/ncbi_math.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_query_info.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_sequence_blk.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/gapinfo.o ar: creating ../Linux-amd64/bin/libhbn.a a - ../Linux-amd64/obj/libhbn.a/corelib/build_db.o a - ../Linux-amd64/obj/libhbn.a/corelib/cmd_arg.o a - ../Linux-amd64/obj/libhbn.a/corelib/cstr_util.o a - ../Linux-amd64/obj/libhbn.a/corelib/db_format.o a - ../Linux-amd64/obj/libhbn.a/corelib/fasta.o a - ../Linux-amd64/obj/libhbn.a/corelib/gapped_candidate.o a - ../Linux-amd64/obj/libhbn.a/corelib/hbn_aux.o a - ../Linux-amd64/obj/libhbn.a/corelib/hbn_format.o a - ../Linux-amd64/obj/libhbn.a/corelib/hbn_hit.o a - ../Linux-amd64/obj/libhbn.a/corelib/hbn_package_version.o a - ../Linux-amd64/obj/libhbn.a/corelib/kstring.o a - ../Linux-amd64/obj/libhbn.a/corelib/line_reader.o a - ../Linux-amd64/obj/libhbn.a/corelib/m4_record.o a - ../Linux-amd64/obj/libhbn.a/corelib/name2id_map.o a - ../Linux-amd64/obj/libhbn.a/corelib/partition_aux.o a - ../Linux-amd64/obj/libhbn.a/corelib/raw_reads.o a - ../Linux-amd64/obj/libhbn.a/corelib/seqdb_summary.o a - ../Linux-amd64/obj/libhbn.a/corelib/seqdb.o a - ../Linux-amd64/obj/libhbn.a/corelib/seq_tag.o a - ../Linux-amd64/obj/libhbn.a/corelib/seq_tag_report.o a - ../Linux-amd64/obj/libhbn.a/corelib/small_object_alloc.o a - ../Linux-amd64/obj/libhbn.a/corelib/string2hsp.o a - ../Linux-amd64/obj/libhbn.a/algo/chain_dp.o a - ../Linux-amd64/obj/libhbn.a/algo/diff_gapalign.o a - ../Linux-amd64/obj/libhbn.a/algo/hash_list_bucket_sort.o a - ../Linux-amd64/obj/libhbn.a/algo/kalloc.o a - ../Linux-amd64/obj/libhbn.a/algo/ksw2_extd2_sse.o a - ../Linux-amd64/obj/libhbn.a/algo/ksw2_extz2_sse.o a - ../Linux-amd64/obj/libhbn.a/algo/ksw2_wrapper.o a - ../Linux-amd64/obj/libhbn.a/algo/hbn_lookup_table.o a - ../Linux-amd64/obj/libhbn.a/algo/hbn_traceback_aux.o a - ../Linux-amd64/obj/libhbn.a/algo/word_finder.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/c_ncbi_blast_aux.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/ncbi_blast_aux.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/blast_args.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/cmdline_flags.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/format_flags.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_allow.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_desc.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_types.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr_util.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_cmp.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/numeric_str_interconv.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_util.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_encoding.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_hits.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_message.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_options.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_stat.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_parameters.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_program.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_types.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/boost_erf.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/hsp2string.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/ncbi_math.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_query_info.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_sequence_blk.o a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/gapinfo.o ar -rv ../Linux-amd64/bin/libfsa.a ../Linux-amd64/obj/libfsa.a/app/fsa/argument_parser.o ../Linux-amd64/obj/libfsa.a/app/fsa/getopt.o ../Linux-amd64/obj/libfsa.a/app/fsa/logger.o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap.o ../Linux-amd64/obj/libfsa.a/app/fsa/read_store.o ../Linux-amd64/obj/libfsa.a/app/fsa/sequence.o ../Linux-amd64/obj/libfsa.a/app/fsa/utility.o ../Linux-amd64/obj/libfsa.a/app/fsa/fasta_reader.o ../Linux-amd64/obj/libfsa.a/app/fsa/fastq_reader.o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_store.o ../Linux-amd64/obj/libfsa.a/app/fsa/simple_align.o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_filter.o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_stat.o ar: creating ../Linux-amd64/bin/libfsa.a a - ../Linux-amd64/obj/libfsa.a/app/fsa/argument_parser.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/getopt.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/logger.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/overlap.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/read_store.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/sequence.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/utility.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/fasta_reader.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/fastq_reader.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_store.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/simple_align.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_filter.o a - ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_stat.o cc -o ../Linux-amd64/bin/mecat2pcan -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2pcan/app/mecat2pcan/pcan.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/bin/mecat2map -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2map/app/map/cmdline_args.o ../Linux-amd64/obj/mecat2map/app/map/hbn_align_one_volume.o ../Linux-amd64/obj/mecat2map/app/map/hbn_build_seqdb.o ../Linux-amd64/obj/mecat2map/app/map/hbn_extend_subseq_hit.o ../Linux-amd64/obj/mecat2map/app/map/hbn_find_subseq_hit.o ../Linux-amd64/obj/mecat2map/app/map/hbn_job_control.o ../Linux-amd64/obj/mecat2map/app/map/hbn_options.o ../Linux-amd64/obj/mecat2map/app/map/hbn_subseq_hit.o ../Linux-amd64/obj/mecat2map/app/map/hbn_task_struct.o ../Linux-amd64/obj/mecat2map/app/map/main.o ../Linux-amd64/obj/mecat2map/app/map/mecat_results.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/bin/mecat2cns -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cmdline_args.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_aux.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_part.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_read.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_options.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_align_tag.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_aux.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/hbn_task_struct.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/main.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/raw_reads_reader.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp cc -o ../Linux-amd64/bin/mecat2viewdb -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2viewdb/app/hbndb/viewhbndb.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/bin/mecat2lcr -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/cmdline_args.o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/largest_cover_range.o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/main.o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/range_list.o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/m4_aux.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/bin/mecat2splitreads -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/cmdline_args.o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/main.o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/split_reads.o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/range_list.o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/m4_aux.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp cc -o ../Linux-amd64/bin/mecat2trimbases -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2trimbases/app/mecat2trim/3_trim_bases/main.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp cc -o ../Linux-amd64/bin/mecat2pm4 -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2pm4/app/mecat2pm4/main.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp cc -o ../Linux-amd64/bin/mecat2extseqs -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2extseqs/app/mecat2extseqs/main.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/bin/fsa_ol_filter -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/fsa_ol_filter/app/fsa/fsa_ol_filter.o -lfsa -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/bin/fsa_assemble -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/fsa_assemble/app/fsa/fsa_assemble.o ../Linux-amd64/obj/fsa_assemble/app/fsa/assembly.o ../Linux-amd64/obj/fsa_assemble/app/fsa/graph.o ../Linux-amd64/obj/fsa_assemble/app/fsa/string_graph.o ../Linux-amd64/obj/fsa_assemble/app/fsa/path_graph.o -lfsa -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/bin/fsa_ctg_bridge -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/fsa_ctg_bridge.o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_bridge.o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_graph.o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link.o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link_store.o -lfsa -pthread -lm -lz -lstdc++ -fopenmp g++ -o ../Linux-amd64/bin/fsa_rd_stat -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/fsa_rd_stat/app/fsa/fsa_rd_stat.o ../Linux-amd64/obj/fsa_rd_stat/app/fsa/read_stat.o -lfsa -pthread -lm -lz -lstdc++ -fopenmp make[2]: Leaving directory '/build/mecat2-jpSdtR/mecat2-0.0+git20200428.f54c542+ds/src' make[1]: Leaving directory '/build/mecat2-jpSdtR/mecat2-0.0+git20200428.f54c542+ds' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/mecat2/ debian/rules override_dh_install make[1]: Entering directory '/build/mecat2-jpSdtR/mecat2-0.0+git20200428.f54c542+ds' dh_install sed 's/\#\!\/usr\/bin\/env perl/\#\!\/usr\/bin\/perl/' \ debian/mecat2/usr/bin/mecat.pl > debian/mecat2/usr/bin/mecat rm -f debian/mecat2/usr/bin/mecat.pl make[1]: Leaving directory '/build/mecat2-jpSdtR/mecat2-0.0+git20200428.f54c542+ds' dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/mecat2/usr/bin/fsa_assemble: .debug_info section not present dwz: debian/mecat2/usr/bin/fsa_ctg_bridge: .debug_info section not present dwz: debian/mecat2/usr/bin/fsa_ol_filter: .debug_info section not present dwz: debian/mecat2/usr/bin/fsa_rd_stat: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2cns: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2extseqs: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2lcr: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2map: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2pcan: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2pm4: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2splitreads: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2trimbases: .debug_info section not present dwz: debian/mecat2/usr/bin/mecat2viewdb: .debug_info section not present dwz: Too few files for multifile optimization dh_dwz: warning: No dwz multifile created, but not explicitly requested either so ignoring it. dh_dwz: warning: Common issues include no debug information at all (missing -g) and dh_dwz: warning: compressed debug information (#931891). dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'mecat2' in '../mecat2_0.0+git20200428.f54c542+ds-4_amd64.deb'. dpkg-deb: building package 'mecat2-dbgsym' in '../mecat2-dbgsym_0.0+git20200428.f54c542+ds-4_amd64.deb'. dpkg-genbuildinfo -O../mecat2_0.0+git20200428.f54c542+ds-4_amd64.buildinfo dpkg-genchanges -O../mecat2_0.0+git20200428.f54c542+ds-4_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 2025-08-18T12:28:14Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 18 Aug 2025 12:28:15 +0000 | +------------------------------------------------------------------------------+ mecat2_0.0+git20200428.f54c542+ds-4_amd64.changes: -------------------------------------------------- Format: 1.8 Date: Tue, 07 Nov 2023 08:44:12 +0100 Source: mecat2 Binary: mecat2 mecat2-dbgsym Architecture: source amd64 Version: 0.0+git20200428.f54c542+ds-4 Distribution: perl-5.42-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: mecat2 - ultra-fast and accurate de novo assembly tools for SMRT reads Closes: 1054708 Changes: mecat2 (0.0+git20200428.f54c542+ds-4) unstable; urgency=medium . * Team upload. * Add patch to 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mecat2_0.0+git20200428.f54c542+ds-4_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 18 Aug 2025 12:28:10 +0000 Build-Path: /build/mecat2-jpSdtR/mecat2-0.0+git20200428.f54c542+ds Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.17-4), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.7), bash (= 5.2.37-2+b5), binutils (= 2.45-4), binutils-common (= 2.45-4), binutils-x86-64-linux-gnu (= 2.45-4), bsdextrautils (= 2.41.1-1), bsdutils (= 1:2.41.1-1), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.7-3), cpp (= 4:14.2.0-1), cpp-14 (= 14.3.0-5), cpp-14-x86-64-linux-gnu (= 14.3.0-5), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.25), debianutils (= 5.23.2), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-2), diffutils (= 1:3.10-4), dpkg (= 1.22.21), dpkg-dev (= 1.22.21), dwz (= 0.15-1+b1), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.3.0-5), g++-14-x86-64-linux-gnu (= 14.3.0-5), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-14 (= 14.3.0-5), gcc-14-base (= 14.3.0-5), gcc-14-x86-64-linux-gnu (= 14.3.0-5), gcc-15-base (= 15.2.0-1), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-2+b1), gettext-base (= 0.23.1-2+b1), grep (= 3.11-4), groff-base (= 1.23.0-9), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-1), libatomic1 (= 15.2.0-1), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.5-1), libaudit1 (= 1:4.0.5-1), libbinutils (= 2.45-4), libblkid1 (= 2.41.1-1), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.41-12), libc-dev-bin (= 2.41-12), libc6 (= 2.41-12), libc6-dev (= 2.41-12), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-10+b1), libcc1-0 (= 15.2.0-1), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.45-4), libctf0 (= 2.45-4), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.280), libdebhelper-perl (= 13.25), libdpkg-perl (= 1.22.21), libelf1t64 (= 0.192-4), libfile-stripnondeterminism-perl (= 1.14.1-2), libgcc-14-dev (= 14.3.0-5), libgcc-s1 (= 15.2.0-1), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp10 (= 2:6.3.0+dfsg-3), libgomp1 (= 15.2.0-1), libgprofng0 (= 2.45-4), libhwasan0 (= 15.2.0-1), libisl23 (= 0.27-1), libitm1 (= 15.2.0-1), libjansson4 (= 2.14-2+b3), liblastlog2-2 (= 2.41.1-1), liblsan0 (= 15.2.0-1), liblzma5 (= 5.8.1-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41.1-1), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.2-1), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpcre2-8-0 (= 10.45-1), libperl5.42 (= 5.42.0-1), libpipeline1 (= 1.5.8-1), libquadmath0 (= 15.2.0-1), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsframe2 (= 2.45-4), libsmartcols1 (= 2.41.1-1), libsqlite3-0 (= 3.46.1-7), libssl3t64 (= 3.5.2-1), libstdc++-14-dev (= 14.3.0-5), libstdc++6 (= 15.2.0-1), libsystemd0 (= 258~rc2-2), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 15.2.0-1), libubsan1 (= 15.2.0-1), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 258~rc2-2), libunistring5 (= 1.3-2), libuuid1 (= 2.41.1-1), libxml2-16 (= 2.14.5+dfsg-0.1), libzstd1 (= 1.5.7+dfsg-1), linux-libc-dev (= 6.12.38-1), m4 (= 1.4.19-8), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), openssl-provider-legacy (= 3.5.2-1), patch (= 2.8-2), perl (= 5.42.0-1), perl-base (= 5.42.0-1), perl-modules-5.42 (= 5.42.0-1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.25), sysvinit-utils (= 3.14-4), tar (= 1.35+dfsg-3.1), util-linux (= 2.41.1-1), xz-utils (= 5.8.1-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1699343052" +------------------------------------------------------------------------------+ | Package contents Mon, 18 Aug 2025 12:28:15 +0000 | +------------------------------------------------------------------------------+ mecat2-dbgsym_0.0+git20200428.f54c542+ds-4_amd64.deb ---------------------------------------------------- new Debian package, version 2.0. size 108376 bytes: control archive=1152 bytes. 901 bytes, 12 lines control 1378 bytes, 13 lines md5sums Package: mecat2-dbgsym Source: mecat2 Version: 0.0+git20200428.f54c542+ds-4 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1706 Depends: mecat2 (= 0.0+git20200428.f54c542+ds-4) Section: debug Priority: optional Description: debug symbols for mecat2 Build-Ids: 0a51e31272699be77a31d414d3f0dd9c473d43b8 27fc9beeb4d00f949fb82ff7c6be46eb23dbecf2 2a15bda832c933d87b0405d924117ea358e780de 6921bb6b2d37fe2db496e9a89d2620db7fbe639c 8cca6dc40233ad8b9723b15d5e9b40d504767322 b06ff4396336d35d0742b79c3f7b5c4694fa645a b65b508a0ab3786dc40d3a425fd2b9e051ef1fb7 b8932a1b0bbfe79a1d9352d59e19951887793d8a c949608b71edc5086a4afeac5c4734025e7ed0ae c95278b7ae7d36fde56e4b3e22cefeeecaf95d1f d7f77001fb3a2595d33c1bdcb4b3be5db8261d85 f04115686a4cace496f9e0a23d2f3e7ed29ecb2b f6c97653bdbf0cfdda9fe5b91019a20373c1b2c9 drwxr-xr-x root/root 0 2023-11-07 07:44 ./ drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/ drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/lib/ drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/lib/debug/ drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/lib/debug/.build-id/0a/ -rw-r--r-- root/root 279360 2023-11-07 07:44 ./usr/lib/debug/.build-id/0a/51e31272699be77a31d414d3f0dd9c473d43b8.debug drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/lib/debug/.build-id/27/ -rw-r--r-- root/root 105984 2023-11-07 07:44 ./usr/lib/debug/.build-id/27/fc9beeb4d00f949fb82ff7c6be46eb23dbecf2.debug drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/lib/debug/.build-id/2a/ -rw-r--r-- root/root 326960 2023-11-07 07:44 ./usr/lib/debug/.build-id/2a/15bda832c933d87b0405d924117ea358e780de.debug drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/lib/debug/.build-id/69/ -rw-r--r-- root/root 34048 2023-11-07 07:44 ./usr/lib/debug/.build-id/69/21bb6b2d37fe2db496e9a89d2620db7fbe639c.debug drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/lib/debug/.build-id/8c/ -rw-r--r-- root/root 30648 2023-11-07 07:44 ./usr/lib/debug/.build-id/8c/ca6dc40233ad8b9723b15d5e9b40d504767322.debug drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/lib/debug/.build-id/b0/ -rw-r--r-- root/root 122952 2023-11-07 07:44 ./usr/lib/debug/.build-id/b0/6ff4396336d35d0742b79c3f7b5c4694fa645a.debug drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/lib/debug/.build-id/b6/ -rw-r--r-- root/root 262632 2023-11-07 07:44 ./usr/lib/debug/.build-id/b6/5b508a0ab3786dc40d3a425fd2b9e051ef1fb7.debug drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/lib/debug/.build-id/b8/ -rw-r--r-- root/root 26520 2023-11-07 07:44 ./usr/lib/debug/.build-id/b8/932a1b0bbfe79a1d9352d59e19951887793d8a.debug drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/lib/debug/.build-id/c9/ -rw-r--r-- root/root 73168 2023-11-07 07:44 ./usr/lib/debug/.build-id/c9/49608b71edc5086a4afeac5c4734025e7ed0ae.debug -rw-r--r-- root/root 260704 2023-11-07 07:44 ./usr/lib/debug/.build-id/c9/5278b7ae7d36fde56e4b3e22cefeeecaf95d1f.debug drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/lib/debug/.build-id/d7/ -rw-r--r-- root/root 38824 2023-11-07 07:44 ./usr/lib/debug/.build-id/d7/f77001fb3a2595d33c1bdcb4b3be5db8261d85.debug drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/lib/debug/.build-id/f0/ -rw-r--r-- root/root 123168 2023-11-07 07:44 ./usr/lib/debug/.build-id/f0/4115686a4cace496f9e0a23d2f3e7ed29ecb2b.debug drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/lib/debug/.build-id/f6/ -rw-r--r-- root/root 34064 2023-11-07 07:44 ./usr/lib/debug/.build-id/f6/c97653bdbf0cfdda9fe5b91019a20373c1b2c9.debug drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/share/ drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/share/doc/ lrwxrwxrwx root/root 0 2023-11-07 07:44 ./usr/share/doc/mecat2-dbgsym -> mecat2 mecat2_0.0+git20200428.f54c542+ds-4_amd64.deb --------------------------------------------- new Debian package, version 2.0. size 773788 bytes: control archive=1628 bytes. 848 bytes, 16 lines control 1911 bytes, 31 lines md5sums Package: mecat2 Version: 0.0+git20200428.f54c542+ds-4 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 4116 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libstdc++6 (>= 14), zlib1g (>= 1:1.1.4), perl:any Section: science Priority: optional Homepage: https://github.com/xiaochuanle/MECAT2 Description: ultra-fast and accurate de novo assembly tools for SMRT reads An improved version of MECAT. It is an ultra-fast and accurate mapping and error correcting de novo assembly tools for single molecula sequencing (SMRT) reads. MECAT2 consists of the following three modules: 1. mecat2map: a fast and accurate alignment tool for SMRT reads. 2. mecat2cns: correct noisy reads based on their pairwise overlaps. 3. fsa: a string graph based assembly tool. drwxr-xr-x root/root 0 2023-11-07 07:44 ./ drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/ drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/bin/ -rwxr-xr-x root/root 289824 2023-11-07 07:44 ./usr/bin/fsa_assemble -rwxr-xr-x root/root 244816 2023-11-07 07:44 ./usr/bin/fsa_ctg_bridge -rwxr-xr-x root/root 232504 2023-11-07 07:44 ./usr/bin/fsa_ol_filter -rwxr-xr-x root/root 84896 2023-11-07 07:44 ./usr/bin/fsa_rd_stat -rwxr-xr-x root/root 13160 2023-11-07 07:44 ./usr/bin/mecat -rwxr-xr-x root/root 697512 2023-11-07 07:44 ./usr/bin/mecat2cns -rwxr-xr-x root/root 220904 2023-11-07 07:44 ./usr/bin/mecat2extseqs -rwxr-xr-x root/root 590984 2023-11-07 07:44 ./usr/bin/mecat2lcr -rwxr-xr-x root/root 877864 2023-11-07 07:44 ./usr/bin/mecat2map -rwxr-xr-x root/root 85112 2023-11-07 07:44 ./usr/bin/mecat2pcan -rwxr-xr-x root/root 72824 2023-11-07 07:44 ./usr/bin/mecat2pm4 -rwxr-xr-x root/root 595080 2023-11-07 07:44 ./usr/bin/mecat2splitreads -rwxr-xr-x root/root 56376 2023-11-07 07:44 ./usr/bin/mecat2trimbases -rwxr-xr-x root/root 80984 2023-11-07 07:44 ./usr/bin/mecat2viewdb drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/share/ drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/share/doc/mecat2/ -rw-r--r-- root/root 443 2023-11-07 07:44 ./usr/share/doc/mecat2/changelog.Debian.gz -rw-r--r-- root/root 6098 2023-11-07 07:44 ./usr/share/doc/mecat2/copyright drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/share/lintian/ drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 804 2023-11-07 07:44 ./usr/share/lintian/overrides/mecat2 drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/share/man/ drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/share/man/man1/ -rw-r--r-- root/root 744 2023-11-07 07:44 ./usr/share/man/man1/fsa_assemble.1.gz -rw-r--r-- root/root 806 2023-11-07 07:44 ./usr/share/man/man1/fsa_ctg_bridge.1.gz -rw-r--r-- root/root 922 2023-11-07 07:44 ./usr/share/man/man1/fsa_ol_filter.1.gz -rw-r--r-- root/root 313 2023-11-07 07:44 ./usr/share/man/man1/fsa_rd_stat.1.gz -rw-r--r-- root/root 396 2023-11-07 07:44 ./usr/share/man/man1/mecat.1.gz -rw-r--r-- root/root 416 2023-11-07 07:44 ./usr/share/man/man1/mecat2pcan.1.gz drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/share/perl5/ drwxr-xr-x root/root 0 2023-11-07 07:44 ./usr/share/perl5/Plgd/ -rw-r--r-- root/root 80 2020-04-28 11:55 ./usr/share/perl5/Plgd/Grid.pm -rw-r--r-- root/root 2747 2020-04-28 11:55 ./usr/share/perl5/Plgd/GridLsf.pm -rw-r--r-- root/root 2122 2020-04-28 11:55 ./usr/share/perl5/Plgd/GridPbs.pm -rw-r--r-- root/root 2069 2020-04-28 11:55 ./usr/share/perl5/Plgd/GridSge.pm -rw-r--r-- root/root 3606 2020-04-28 11:55 ./usr/share/perl5/Plgd/GridSlurm.pm -rw-r--r-- root/root 8768 2020-04-28 11:55 ./usr/share/perl5/Plgd/Project.pm -rw-r--r-- root/root 4168 2020-04-28 11:55 ./usr/share/perl5/Plgd/Script.pm -rw-r--r-- root/root 4390 2020-04-28 11:55 ./usr/share/perl5/Plgd/Utils.pm +------------------------------------------------------------------------------+ | Post Build Mon, 18 Aug 2025 12:28:16 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 18 Aug 2025 12:28:16 +0000 | +------------------------------------------------------------------------------+ Purging /build/mecat2-jpSdtR Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 18 Aug 2025 12:28:18 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 685236 Build-Time: 256 Distribution: perl-5.42-throwaway Host Architecture: amd64 Install-Time: 7 Job: /srv/debomatic/incoming/mecat2_0.0+git20200428.f54c542+ds-4.dsc Machine Architecture: amd64 Package: mecat2 Package-Time: 285 Source-Version: 0.0+git20200428.f54c542+ds-4 Space: 685236 Status: successful Version: 0.0+git20200428.f54c542+ds-4 -------------------------------------------------------------------------------- Finished at 2025-08-18T12:28:14Z Build needed 00:04:45, 685236k disk space