sbuild (Debian sbuild) 0.91.10 (27 June 2026) on carme.larted.org.uk +==============================================================================+ | canu 2.2+dfsg-5 (amd64) Sat, 19 Sep 2026 11:25:45 +0000 | +==============================================================================+ Package: canu Version: 2.2+dfsg-5 Source Version: 2.2+dfsg-5 Distribution: perl-5.44-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 Sat, 19 Sep 2026 11:25:46 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup canu_2.2+dfsg-5 perl-5.44-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup canu_2.2+dfsg-5 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sat, 19 Sep 2026 11:25:47 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3042 B] Get:2 http://deb.debian.org/debian unstable InRelease [193 kB] Get:3 http://deb.debian.org/debian sid InRelease [193 kB] Get:1 file:/srv/reprepro perl-5.44 InRelease [3042 B] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:5 file:/srv/reprepro perl-5.44/main amd64 Packages [605 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-2026-09-19-0804.46-F-2026-09-19-0804.46.pdiff [23.4 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2026-09-19-0804.46-F-2026-09-19-0804.46.pdiff [4327 B] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2026-09-19-0804.46-F-2026-09-19-0804.46.pdiff [23.4 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2026-09-19-0804.46-F-2026-09-19-0804.46.pdiff [4327 B] Fetched 541 kB in 3s (167 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: cpp-16 cpp-16-x86-64-linux-gnu g++-16 g++-16-x86-64-linux-gnu gcc-16 gcc-16-base gcc-16-x86-64-linux-gnu libasan8 libatomic1 libcc1-0 libgcc-16-dev libgcc-s1 libgomp1 libhwasan0 libitm1 liblsan0 libquadmath0 libstdc++-16-dev libstdc++6 libtsan2 libubsan1 21 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 72.3 MB of archives. After this operation, 636 MB disk space will be freed. Get:1 http://deb.debian.org/debian unstable/main amd64 libubsan1 amd64 16.2.0-3 [1136 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 libgomp1 amd64 16.2.0-3 [151 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libitm1 amd64 16.2.0-3 [26.9 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libatomic1 amd64 16.2.0-3 [10.4 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libasan8 amd64 16.2.0-3 [2888 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 liblsan0 amd64 16.2.0-3 [1281 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libhwasan0 amd64 16.2.0-3 [1580 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libquadmath0 amd64 16.2.0-3 [148 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 gcc-16-base amd64 16.2.0-3 [38.7 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libstdc++6 amd64 16.2.0-3 [823 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 g++-16 amd64 16.2.0-3 [35.4 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 gcc-16 amd64 16.2.0-3 [538 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 cpp-16 amd64 16.2.0-3 [1272 B] Get:14 http://deb.debian.org/debian unstable/main amd64 cpp-16-x86-64-linux-gnu amd64 16.2.0-3 [13.7 MB] Get:15 http://deb.debian.org/debian unstable/main amd64 libcc1-0 amd64 16.2.0-3 [46.1 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 gcc-16-x86-64-linux-gnu amd64 16.2.0-3 [26.6 MB] Get:17 http://deb.debian.org/debian unstable/main amd64 g++-16-x86-64-linux-gnu amd64 16.2.0-3 [15.1 MB] Get:18 http://deb.debian.org/debian unstable/main amd64 libstdc++-16-dev amd64 16.2.0-3 [2755 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libgcc-16-dev amd64 16.2.0-3 [2782 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libtsan2 amd64 16.2.0-3 [2574 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libgcc-s1 amd64 16.2.0-3 [74.0 kB] Fetched 72.3 MB in 1s (119 MB/s) (Reading database ... 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Setting up libgomp1:amd64 (16.2.0-3) ... Setting up libquadmath0:amd64 (16.2.0-3) ... Setting up libatomic1:amd64 (16.2.0-3) ... Setting up libubsan1:amd64 (16.2.0-3) ... Setting up libhwasan0:amd64 (16.2.0-3) ... Setting up libasan8:amd64 (16.2.0-3) ... Setting up cpp-16-x86-64-linux-gnu (16.2.0-3) ... Setting up libtsan2:amd64 (16.2.0-3) ... Setting up libcc1-0:amd64 (16.2.0-3) ... Setting up liblsan0:amd64 (16.2.0-3) ... Setting up libitm1:amd64 (16.2.0-3) ... Setting up libgcc-16-dev:amd64 (16.2.0-3) ... Setting up gcc-16-x86-64-linux-gnu (16.2.0-3) ... Setting up libstdc++-16-dev:amd64 (16.2.0-3) ... Setting up g++-16-x86-64-linux-gnu (16.2.0-3) ... Setting up cpp-16 (16.2.0-3) ... Setting up gcc-16 (16.2.0-3) ... Setting up g++-16 (16.2.0-3) ... Processing triggers for libc-bin (2.43-5) ... +------------------------------------------------------------------------------+ | Fetch source files Sat, 19 Sep 2026 11:26:09 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/canu_2.2+dfsg-5.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sat, 19 Sep 2026 11:26:10 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libboost-dev, libmeryl-dev, libsnappy-dev, libfilesys-df-perl, mhap, debhelper, build-essential Filtered Build-Depends: debhelper-compat (= 13), libboost-dev, libmeryl-dev, libsnappy-dev, libfilesys-df-perl, mhap, debhelper, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/canu-gvhNdT/resolver-0Y83wT/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/canu-gvhNdT/resolver-0Y83wT/apt_archive ./ InRelease Get:2 copy:/build/canu-gvhNdT/resolver-0Y83wT/apt_archive ./ Release [609 B] Ign:3 copy:/build/canu-gvhNdT/resolver-0Y83wT/apt_archive ./ Release.gpg Get:4 copy:/build/canu-gvhNdT/resolver-0Y83wT/apt_archive ./ Sources [680 B] Get:5 copy:/build/canu-gvhNdT/resolver-0Y83wT/apt_archive ./ Packages [719 B] Fetched 2008 B in 0s (109 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... Solving dependencies... The following additional packages will be installed: autoconf automake autopoint autotools-dev binfmt-support bsdextrautils ca-certificates ca-certificates-java debhelper default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz fastjar file gettext gettext-base groff-base intltool-debian jaligner jarwrapper java-common libapache-pom-java libarchive-zip-perl libatinject-jsr330-api-java libboost-dev libboost1.90-dev libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-parent-java libdebhelper-perl libelf1t64 liberror-prone-java libfastutil-java libfile-stripnondeterminism-perl libfilesys-df-perl libguava-java libjpeg62-turbo libjsr305-java liblcms2-2 libmagic-mgc libmagic1t64 libmeryl-dev libnspr4 libnss3 libpcsclite1 libpipeline1 libsnappy-dev libsnappy1v5 libssw-java libtool libuchardet0 libxml2-16 m4 man-db mhap openjdk-25-jre-headless openssl po-debconf sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make default-jre gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff libatinject-jsr330-api-java-doc libboost-doc libboost1.90-doc libboost-atomic1.90-dev libboost-chrono1.90-dev libboost-container1.90-dev libboost-context1.90-dev libboost-contract1.90-dev libboost-coroutine1.90-dev libboost-date-time1.90-dev libboost-exception1.90-dev libboost-fiber1.90-dev libboost-filesystem1.90-dev libboost-graph-parallel1.90-dev libboost-graph1.90-dev libboost-iostreams1.90-dev libboost-json1.90-dev libboost-locale1.90-dev libboost-log1.90-dev libboost-math1.90-dev libboost-mpi-python1.90-dev libboost-mpi1.90-dev libboost-nowide1.90-dev libboost-numpy1.90-dev libboost-program-options1.90-dev libboost-python1.90-dev libboost-random1.90-dev libboost-regex1.90-dev libboost-serialization1.90-dev libboost-stacktrace1.90-dev libboost-test1.90-dev libboost-thread1.90-dev libboost-timer1.90-dev libboost-type-erasure1.90-dev libboost-url1.90-dev libboost-wave1.90-dev libboost1.90-tools-dev libmpfrc++-dev libntl-dev libasm-java libxz-java libjsr305-java-doc liblcms2-utils pcscd libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic libmail-box-perl Recommended packages: curl | wget | lynx python3:any python3-requests libarchive-cpio-perl libltdl-dev libcups2t64 libfontconfig1 libfreetype6 libharfbuzz0b libasound2t64 libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binfmt-support bsdextrautils ca-certificates ca-certificates-java debhelper default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz fastjar file gettext gettext-base groff-base intltool-debian jaligner jarwrapper java-common libapache-pom-java libarchive-zip-perl libatinject-jsr330-api-java libboost-dev libboost1.90-dev libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-parent-java libdebhelper-perl libelf1t64 liberror-prone-java libfastutil-java libfile-stripnondeterminism-perl libfilesys-df-perl libguava-java libjpeg62-turbo libjsr305-java liblcms2-2 libmagic-mgc libmagic1t64 libmeryl-dev libnspr4 libnss3 libpcsclite1 libpipeline1 libsnappy-dev libsnappy1v5 libssw-java libtool libuchardet0 libxml2-16 m4 man-db mhap openjdk-25-jre-headless openssl po-debconf sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 106 MB/106 MB of archives. After this operation, 504 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.44/main amd64 libfilesys-df-perl amd64 0.92-7+b6 [11.7 kB] Get:2 copy:/build/canu-gvhNdT/resolver-0Y83wT/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [896 B] Get:3 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 binfmt-support amd64 2.2.2-8 [72.5 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.6.4-1 [1546 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20260816 [134 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-5 [334 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.3-1 [102 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.19-2 [891 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-5 [820 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20260311 [11.2 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.5 [77.7 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libtool all 2.6.2-3 [552 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 23 [12.7 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:28 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.196-1 [61.2 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.17-1 [109 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.4+dfsg-1 [683 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-5 [2704 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.5 [944 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 java-common all 0.77 [6620 B] Get:36 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.19.1-1 [164 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:3.1.3-4 [213 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.40-1 [116 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.129-1 [1553 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.5.1-1 [54.8 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 openjdk-25-jre-headless amd64 25.0.5~6ea-1 [54.0 MB] Get:42 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.25-77 [3012 B] Get:43 http://deb.debian.org/debian unstable/main amd64 fastjar amd64 2:0.98-8 [80.0 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 jaligner all 1.0+dfsg-11 [133 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 jarwrapper all 0.82 [9024 B] Get:46 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 33-2 [5852 B] Get:47 http://deb.debian.org/debian unstable/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get:48 http://deb.debian.org/debian unstable/main amd64 libboost1.90-dev amd64 1.90.0-6.1+b1 [11.3 MB] Get:49 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.90.0.2+nmu1 [3200 B] Get:50 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libcommons-codec-java all 1.22.0-1 [344 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libcommons-io-java all 2.22.0-1 [570 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libjsr305-java all 0.1~+svn49-12 [26.6 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libfastutil-java all 8.5.16+dfsg-1 [20.2 MB] Get:58 http://deb.debian.org/debian unstable/main amd64 libmeryl-dev amd64 0~20150903+r2013-10+b3 [53.9 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.3.1-1 [32.0 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libsnappy-dev amd64 1.3.1-1 [47.8 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libssw-java amd64 1.1-16 [19.8 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 mhap all 2.1.3+dfsg-3 [160 kB] Preconfiguring packages ... Fetched 106 MB in 5s (20.8 MB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... 15722 files and directories currently installed.) Preparing to unpack .../00-libpipeline1_1.5.8-3_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-3) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../01-binfmt-support_2.2.2-8_amd64.deb ... Unpacking binfmt-support (2.2.2-8) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package openssl. Preparing to unpack .../03-openssl_3.6.4-1_amd64.deb ... Unpacking openssl (3.6.4-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../04-ca-certificates_20260816_all.deb ... Unpacking ca-certificates (20260816) ... Selecting previously unselected package libmagic-mgc. 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Setting up libmagic1t64:amd64 (1:5.47-4) ... Setting up gettext-base (1.0-5) ... Setting up m4 (1.4.21-1) ... Setting up file (1:5.47-4) ... Setting up libssw-java (1.1-16) ... Setting up libelf1t64:amd64 (0.196-1) ... Setting up libsnappy1v5:amd64 (1.3.1-1) ... Setting up autotools-dev (20240727.1+nmu1) ... Setting up libjpeg62-turbo:amd64 (1:3.1.3-4) ... Setting up libnspr4:amd64 (2:4.40-1) ... Setting up libapache-pom-java (33-2) ... Setting up libatinject-jsr330-api-java (1.0+ds1-6) ... Setting up libmeryl-dev:amd64 (0~20150903+r2013-10+b3) ... Setting up autopoint (1.0-5) ... Setting up binfmt-support (2.2.2-8) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: WARNING: No init system and policy-rc.d missing! Defaulting to block. Setting up libpcsclite1:amd64 (2.5.1-1) ... Setting up autoconf (2.73-2) ... Setting up dwz (0.17-1) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2+b2) ... Setting up libboost1.90-dev:amd64 (1.90.0-6.1+b1) ... Setting up libboost-dev:amd64 (1.90.0.2+nmu1) ... Setting up openssl (3.6.4-1) ... Setting up automake (1:1.19-2) ... update-alternatives: using /usr/bin/automake-1.19 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.1-1) ... Setting up gettext (1.0-5) ... Setting up jarwrapper (0.82) ... Setting up libtool (2.6.2-3) ... Setting up libsnappy-dev:amd64 (1.3.1-1) ... Setting up libcommons-parent-java (56-1) ... Setting up libnss3:amd64 (2:3.129-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (23) ... Setting up ca-certificates (20260816) ... Updating certificates in /etc/ssl/certs... 121 added, 0 removed; done. Setting up dh-strip-nondeterminism (1.15.1-1) ... Setting up groff-base (1.24.1-1) ... Setting up ca-certificates-java (20260311) ... No JRE found. Skipping Java certificates setup. Setting up libcommons-codec-java (1.22.0-1) ... Setting up libcommons-io-java (2.22.0-1) ... Setting up po-debconf (1.0.22) ... Setting up openjdk-25-jre-headless:amd64 (25.0.5~6ea-1) ... update-alternatives: using /usr/lib/jvm/java-25-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-25-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-25-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-25-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-25-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcommons-compress-java (1.27.1-2) ... Setting up debhelper (14.5) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libguava-java (32.0.1-1) ... Processing triggers for libc-bin (2.43-5) ... Processing triggers for ca-certificates-java (20260311) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_BR_Root_CA_2_2023.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_2_2023.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_Server_Root_ECC_G1.pem Adding debian:OISTE_Server_Root_RSA_G1.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SECOM_TLS_ECC_Root_CA_2024.pem Adding debian:SECOM_TLS_RSA_Root_CA_2024.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_Root_CA14.pem Adding debian:SecureSign_Root_CA15.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_RSA_TLS_Root_CA_2022_-_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem Adding debian:Telia_EC_TLS_Root_CA_v3.pem Adding debian:Telia_RSA_TLS_Root_CA_v3.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:TrustAsia_TLS_ECC_Root_CA.pem Adding debian:TrustAsia_TLS_RSA_Root_CA.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:e-Szigno_TLS_Root_CA_2023.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up default-jre-headless (2:1.25-77) ... Setting up jaligner (1.0+dfsg-11) ... Setting up mhap (2.1.3+dfsg-3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for ca-certificates (20260816) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20260311) ... done. +------------------------------------------------------------------------------+ | Check architectures Sat, 19 Sep 2026 11:26:41 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64 arm64 mips64el ppc64el riscv64 s390x ia64 loong64 ppc64 sparc64 x32) +------------------------------------------------------------------------------+ | Build environment Sat, 19 Sep 2026 11:26:42 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.47-6 dpkg-dev_1.23.11 g++-15_15.3.0-4 g++-16_16.2.0-3 gcc-15_15.3.0-4 gcc-16_16.2.0-3 libc6-dev_2.43-5 libstdc++-15-dev_15.3.0-4 libstdc++-16-dev_16.2.0-3 libstdc++6_16.2.0-3 linux-libc-dev_7.2.6-1 Package versions: apt_3.3.3 autoconf_2.73-2 automake_1:1.19-2 autopoint_1.0-5 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-4 binfmt-support_2.2.2-8 binutils_2.47-6 binutils-common_2.47-6 binutils-x86-64-linux-gnu_2.47-6 bsdextrautils_2.42.3-1 build-essential_12.12 bzip2_1.0.8-6+b2 ca-certificates_20260816 ca-certificates-java_20260311 coreutils_9.10-1 cpp_4:16.1.0-3 cpp-15_15.3.0-4 cpp-15-x86-64-linux-gnu_15.3.0-4 cpp-16_16.2.0-3 cpp-16-x86-64-linux-gnu_16.2.0-3 cpp-x86-64-linux-gnu_4:16.1.0-3 dash_0.5.12-12 debconf_1.5.92 debhelper_14.5 debian-archive-keyring_2025.1 debianutils_5.24 default-jre-headless_2:1.25-77 dh-autoreconf_23 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-7+b1 dpkg_1.23.11 dpkg-dev_1.23.11 dwz_0.17-1 eatmydata_131-2 fastjar_2:0.98-8 file_1:5.47-4 findutils_4.11.0-2 g++_4:16.1.0-3 g++-15_15.3.0-4 g++-15-x86-64-linux-gnu_15.3.0-4 g++-16_16.2.0-3 g++-16-x86-64-linux-gnu_16.2.0-3 g++-x86-64-linux-gnu_4:16.1.0-3 gcc_4:16.1.0-3 gcc-15_15.3.0-4 gcc-15-base_15.3.0-4 gcc-15-x86-64-linux-gnu_15.3.0-4 gcc-16_16.2.0-3 gcc-16-base_16.2.0-3 gcc-16-x86-64-linux-gnu_16.2.0-3 gcc-x86-64-linux-gnu_4:16.1.0-3 gettext_1.0-5 gettext-base_1.0-5 gnupg_2.4.9-7 gnupg-l10n_2.4.9-7 gpg_2.4.9-7+b1 gpg-agent_2.4.9-7+b1 gpgconf_2.4.9-7+b1 gpgsm_2.4.9-7+b1 grep_3.12-1 groff-base_1.24.1-1 gzip_1.14-1 hostname_3.25 init-system-helpers_1.69+nmu1 intltool-debian_0.35.0+20060710.6 jaligner_1.0+dfsg-11 jarwrapper_0.82 java-common_0.77 libacl1_2.4.0-1 libapache-pom-java_33-2 libapt-pkg7.0_3.3.3 libarchive-zip-perl_1.68-1 libasan8_16.2.0-3 libassuan9_3.0.2-2+b2 libatinject-jsr330-api-java_1.0+ds1-6 libatomic1_16.2.0-3 libattr1_1:2.6.0-1 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b2 libbinutils_2.47-6 libblkid1_2.42.3-1 libboost-dev_1.90.0.2+nmu1 libboost1.90-dev_1.90.0-6.1+b1 libbz2-1.0_1.0.8-6+b2 libc-bin_2.43-5 libc-dev-bin_2.43-5 libc-gconv-modules-extra_2.43-5 libc6_2.43-5 libc6-dev_2.43-5 libcap-ng0_0.9.6-1 libcc1-0_16.2.0-3 libcommons-codec-java_1.22.0-1 libcommons-compress-java_1.27.1-2 libcommons-io-java_2.22.0-1 libcommons-parent-java_56-1 libcrypt1_1:4.5.2+20251210-1 libctf-nobfd0_2.47-6 libctf0_2.47-6 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.5 libdpkg-perl_1.23.11 libeatmydata1_131-2+b2 libelf1t64_0.196-1 liberror-prone-java_2.18.0-1 libfastutil-java_8.5.16+dfsg-1 libffi8_3.8.0-2 libfile-stripnondeterminism-perl_1.15.1-1 libfilesys-df-perl_0.92-7+b6 libgcc-15-dev_15.3.0-4 libgcc-16-dev_16.2.0-3 libgcc-s1_16.2.0-3 libgcrypt20_1.12.3-2 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgnutls30t64_3.8.13-1 libgomp1_16.2.0-3 libgpg-error0_1.61-5 libgprofng0_2.47-6 libguava-java_32.0.1-1 libhogweed6t64_3.10.2-1+b1 libhwasan0_16.2.0-3 libidn2-0_2.3.8-5 libisl23_0.28-1 libitm1_16.2.0-3 libjansson4_2.15.1-1 libjpeg62-turbo_1:3.1.3-4 libjsr305-java_0.1~+svn49-12 libksba8_1.8.1-1 liblcms2-2_2.19.1-1 libldap2_2.6.14+dfsg-2+b1 liblsan0_16.2.0-3 liblz4-1_1.10.0-10 liblzma5_5.8.4-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmeryl-dev_0~20150903+r2013-10+b3 libmount1_2.42.3-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncursesw6_6.6+20260608-2 libnettle8t64_3.10.2-1+b1 libnpth0t64_1.8-4 libnspr4_2:4.40-1 libnss3_2:3.129-1 libp11-kit0_0.26.5-1 libpam-modules_1.7.0-8 libpam-modules-bin_1.7.0-8 libpam-runtime_1.7.0-8 libpam0g_1.7.0-8 libpcre2-8-0_10.48-3 libpcsclite1_2.5.1-1 libperl5.40_5.40.1-8 libperl5.44_5.44.0-1 libpipeline1_1.5.8-3 libquadmath0_16.2.0-3 libreadline8t64_8.3-4 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.1-1+b1 libselinux1_3.11-2 libsframe3_2.47-6 libsmartcols1_2.42.3-1 libsnappy-dev_1.3.1-1 libsnappy1v5_1.3.1-1 libsqlite3-0_3.53.4-2 libssl3t64_3.6.4-1 libssw-java_1.1-16 libstdc++-15-dev_15.3.0-4 libstdc++-16-dev_16.2.0-3 libstdc++6_16.2.0-3 libsystemd0_262~rc3-1 libtasn1-6_4.21.0-2+b1 libtinfo6_6.6+20260608-2 libtool_2.6.2-3 libtsan2_16.2.0-3 libtss2-mu-4.0.1-0t64_4.1.3-7 libtss2-rc0t64_4.1.3-7 libtss2-sys1t64_4.1.3-7 libtss2-tcti-device0t64_4.1.3-7 libtss2-tcti-mssim0t64_4.1.3-7 libtss2-tcti-swtpm0t64_4.1.3-7 libubsan1_16.2.0-3 libuchardet0_0.0.8-2+b2 libudev1_262~rc3-1 libunistring5_1.4.2-1 libuuid1_2.42.3-1 libxml2-16_2.15.4+dfsg-1 libxxhash0_0.8.3-2+b2 libzstd1_1.5.7+dfsg-4 linux-libc-dev_7.2.6-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 mhap_2.1.3+dfsg-3 mount_2.42.3-1 ncurses-base_6.6+20260608-2 ncurses-bin_6.6+20260608-2 openjdk-25-jre-headless_25.0.5~6ea-1 openssl_3.6.4-1 openssl-provider-legacy_3.6.4-1 patch_2.8-2 perl_5.44.0-1 perl-base_5.44.0-1 perl-modules-5.40_5.40.1-8 perl-modules-5.44_5.44.0-1 pinentry-curses_1.3.3-3 po-debconf_1.0.22 readline-common_8.3-4 rpcsvc-proto_1.4.4-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.5.0-1 sysvinit-utils_3.18-1 tar_1.35+dfsg-6 util-linux_2.42.3-1 xz-utils_5.8.4-1 zlib1g_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Sat, 19 Sep 2026 11:26:42 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: canu Binary: canu Architecture: amd64 arm64 mips64el ppc64el riscv64 s390x ia64 loong64 ppc64 sparc64 x32 Version: 2.2+dfsg-5 Maintainer: Debian Med Packaging Team Homepage: https://canu.readthedocs.org/en/latest/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/canu Vcs-Git: https://salsa.debian.org/med-team/canu.git Testsuite: autopkgtest Testsuite-Triggers: curl, procps Build-Depends: debhelper-compat (= 13), libboost-dev, libmeryl-dev, libsnappy-dev, libfilesys-df-perl, mhap, debhelper Package-List: canu deb science optional arch=amd64,arm64,mips64el,ppc64el,riscv64,s390x,ia64,loong64,ppc64,sparc64,x32 Checksums-Sha1: 042648a09dabff2308a597f971fa1e5266c3a363 1230624 canu_2.2+dfsg.orig.tar.xz 42f967ed80bca3c884b2741e01a8239b632989d0 12360 canu_2.2+dfsg-5.debian.tar.xz Checksums-Sha256: a0e68ddd7234070e9f134374a3442590199f1f3734b1855a46a4147c97680fde 1230624 canu_2.2+dfsg.orig.tar.xz b46328555c6d70b6a8baca86a3f4521893563a55815158b3f4a3e1e0c0e2089a 12360 canu_2.2+dfsg-5.debian.tar.xz Files: f9329149a74d54458678b7a1c7c42982 1230624 canu_2.2+dfsg.orig.tar.xz e90979f8e9f152ccffe2316daab69dd8 12360 canu_2.2+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmUylAsACgkQPCZ2P2xn 5uLcGRAAmqyUQEDvN3hcZNw5uepwLYYkuFF28pQjkMNqBmcF1Kn3xwKKalWnqaGd EfbgPiyKFGVZYJcLiOeSamGA0+iepP/giaqWDJZ8RYVRJZ3GumLuT0lOT1rHLTkd qFPblGYI+CiXeZWGbajqwJQK6hyUgMjXiHhyYunL29jyfz72xikSieYk6psFj2FM sJfa3RM4dVJxs7BFaL7x+OyPJBUqTgraPN4bGkqQKDZPnhYvjbZ+F4cO1/aCzlJz e0ZF8XKs5Nk3VRJg39Bm2m4cQuaWE32LRQ1cUeih/oLCvVN/3FWIqxMgMB9JME2s pftxugnSo1gbu29kW21NqDGZD65jI5EVd3ok3STL2t0aPnRZD47R9I+Ixg8mVlBO 0GGFuEOdO1iPhhqFb2BMBuAIOwdrkRQUxamQ9IxkuDGCdCu1Gad42/zsBhZFFGLh LuOBXhovChm+Jy2ljOO0nW5ASVPFMjOQ4V/FgCMQZE7O5ewGOsHtHS6P48o3Gm0X 3RT5c2PtsMdL3//rBvuLpzro88mMZ1fAkthBLCkxnIlbi7qO4nqy9yOD5noUNscm IEqbtZjpMCGIxBJrO2/kwEejoabl/XxERr56Pv8BAF24202CTTkemPPZwSnaNOF5 ETVoIwIwIA4bHgYs/lwAPS8hL8ObUtCz3MHngI8p7D9jB2Be9Mk= =n+nH -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./canu_2.2+dfsg-5.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./canu_2.2+dfsg-5.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting canu in /build/canu-gvhNdT/canu-2.2+dfsg dpkg-source: info: unpacking canu_2.2+dfsg.orig.tar.xz dpkg-source: info: unpacking canu_2.2+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-debian-mhap-at-runtime.patch dpkg-source: info: applying external-mhap.patch dpkg-source: info: applying libsnappy dpkg-source: info: applying stacktrace dpkg-source: info: applying spelling dpkg-source: info: applying cpuid clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Time Build Commands Sat, 19 Sep 2026 11:26:43 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network canu_2.2+dfsg-5 perl-5.44-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network canu_2.2+dfsg-5 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/canu-gvhNdT/canu-2.2+dfsg SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-db1855d4-cd9c-45eb-be5d-e1e03f8c4308 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 canu dpkg-buildpackage: info: source version 2.2+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src/ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/canu-gvhNdT/canu-2.2+dfsg' rm -rf Linux-* rm -f src/canu_version.H make[1]: Leaving directory '/build/canu-gvhNdT/canu-2.2+dfsg' dh_autoreconf_clean -O--sourcedirectory=src/ dh_clean -O--sourcedirectory=src/ dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building canu using existing ../canu_2.2+dfsg.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building canu in ../canu_2.2+dfsg-5.debian.tar.xz dpkg-source: info: building canu in ../canu_2.2+dfsg-5.dsc debian/rules binary dh binary --sourcedirectory=src/ dh_update_autotools_config -O--sourcedirectory=src/ dh_autoreconf -O--sourcedirectory=src/ dh_auto_configure -O--sourcedirectory=src/ debian/rules override_dh_auto_build make[1]: Entering directory '/build/canu-gvhNdT/canu-2.2+dfsg' rm -Rf src/utility/src/utility/libbacktrace src/stores/libsnappy dh_auto_build cd src && make -j2 INSTALL="install --strip-program=true" make[2]: Entering directory '/build/canu-gvhNdT/canu-2.2+dfsg/src' /bin/sh: 1: git: not found Building release v2.2 For 'Linux' '7.0.10+deb14-amd64' as 'amd64' into '/build/canu-gvhNdT/canu-2.2+dfsg/build/{bin,obj}'. Using '/usr/bin/g++' version '16'. Using user-supplied CXXFLAGS '-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection'. g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/align-parasail-driver.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/align-parasail-driver.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/runtime.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/runtime.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/edlib.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/files.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/files.C utility/src/utility/files.C: In function ‘void AS_UTL_symlink(const char*, const char*)’: utility/src/utility/files.C:299:10: warning: ignoring return value of ‘int symlink(const char*, const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | symlink(pathToFile, pathToLink); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ utility/src/utility/files.C: In function ‘void AS_UTL_loadFileList(const char*, std::vector&)’: utility/src/utility/files.C:722:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 722 | fgets(line, FILENAME_MAX, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ utility/src/utility/files.C:728:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 728 | fgets(line, FILENAME_MAX, F); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/files-buffered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/files-buffered.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/files-compressed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/files-compressed.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/files-fasta-fastq.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/files-fasta-fastq.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/files-memoryMapped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/files-memoryMapped.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/logging.C utility/src/utility/files-memoryMapped.C: In constructor ‘memoryMappedFile::memoryMappedFile(const char*, memoryMappedFileType)’: utility/src/utility/files-memoryMapped.C:70:9: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | read(_fd, _data, _length); | ~~~~^~~~~~~~~~~~~~~~~~~~~ utility/src/utility/files-memoryMapped.C: In destructor ‘memoryMappedFile::~memoryMappedFile()’: utility/src/utility/files-memoryMapped.C:96:10: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | write(_fd, _data, _length), close(_fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/strings.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/strings.C utility/src/utility/logging.C: In member function ‘void logFileInstance::rotate()’: utility/src/utility/logging.C:157:46: warning: ‘.’ directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 157 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); | ^ In file included from /usr/include/stdio.h:974, from utility/src/utility/types.H:48, from utility/src/utility/logging.H:23, from utility/src/utility/logging.C:20: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void logFileInstance::rotate()’ at utility/src/utility/logging.C:157:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output 6 or more bytes (assuming 4102) into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utility/src/utility/logging.C: In member function ‘void logFileInstance::rotate()’: utility/src/utility/logging.C:158:46: warning: ‘.’ directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 158 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); | ^ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void logFileInstance::rotate()’ at utility/src/utility/logging.C:158:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output 6 or more bytes (assuming 4102) into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utility/src/utility/logging.C: In member function ‘void logFileInstance::rotate()’: utility/src/utility/logging.C:154:46: warning: ‘.’ directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 154 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); | ^ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void logFileInstance::rotate()’ at utility/src/utility/logging.C:154:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output 6 or more bytes (assuming 4102) into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ utility/src/utility/logging.C: In member function ‘void logFileInstance::rotate()’: utility/src/utility/logging.C:155:46: warning: ‘.’ directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 155 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s.thr%03d", _prefix, _order, _name, _threadID); | ^ utility/src/utility/logging.C:155:43: note: using the range [-2147483648, 2147483647] for directive argument 155 | snprintf(_fileName, FILENAME_MAX, "%s.%03u.%s.thr%03d", _prefix, _order, _name, _threadID); | ^~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void logFileInstance::rotate()’ at utility/src/utility/logging.C:155:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output 13 or more bytes (assuming 4109) into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void logFileInstance::rotateMessage()’ at utility/src/utility/logging.C:170:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: warning: ‘int __builtin___snprintf_chk(char*, long unsigned int, int, long unsigned int, const char*, ...)’ specified bound 1024 exceeds destination size 256 [-Wstringop-overflow=] 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/system.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/system.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/system-stackTrace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/system-stackTrace.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/sequence.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/sequence.C utility/src/utility/system-stackTrace.C: In function ‘void AS_UTL_catchCrash(int, siginfo_t*, void*)’: utility/src/utility/system-stackTrace.C:40:30: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 40 | #define WRITE_STRING(S) write(2, S, strlen(S)) | ~~~~~^~~~~~~~~~~~~~~~~ utility/src/utility/system-stackTrace.C:79:3: note: in expansion of macro ‘WRITE_STRING’ 79 | WRITE_STRING("\nFailed with '"); | ^~~~~~~~~~~~ utility/src/utility/system-stackTrace.C:40:30: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 40 | #define WRITE_STRING(S) write(2, S, strlen(S)) | ~~~~~^~~~~~~~~~~~~~~~~ utility/src/utility/system-stackTrace.C:80:3: note: in expansion of macro ‘WRITE_STRING’ 80 | WRITE_STRING(strsignal(sig_num)); | ^~~~~~~~~~~~ utility/src/utility/system-stackTrace.C:40:30: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 40 | #define WRITE_STRING(S) write(2, S, strlen(S)) | ~~~~~^~~~~~~~~~~~~~~~~ utility/src/utility/system-stackTrace.C:81:3: note: in expansion of macro ‘WRITE_STRING’ 81 | WRITE_STRING("'; backtrace (libbacktrace):\n"); | ^~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/types.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/types.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-exact.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-exact.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-files.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-files.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-histogram.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-reader.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-reader.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-block.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-writer-block.C utility/src/utility/kmers-reader.C: In member function ‘void merylFileReader::initializeFromMasterIndex(bool, bool, bool)’: utility/src/utility/kmers-reader.C:133:32: warning: ‘/merylIndex’ directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 133 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _inName); | ^~~~~~~~~~~ In file included from /usr/include/stdio.h:974, from utility/src/utility/types.H:48, from utility/src/utility/kmers.H:23, from utility/src/utility/kmers-reader.C:20: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void merylFileReader::initializeFromMasterIndex(bool, bool, bool)’ at utility/src/utility/kmers-reader.C:133:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-stream.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-writer-stream.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-writer.C utility/src/utility/kmers-writer.C:55:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp] 55 | #warning how to set prefix size for streaming operations? | ^~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers.C utility/src/utility/kmers-writer.C: In destructor ‘merylFileWriter::~merylFileWriter()’: utility/src/utility/kmers-writer.C:144:32: warning: ‘/merylIndex’ directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 144 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _outName); | ^~~~~~~~~~~ In file included from /usr/include/stdio.h:974, from utility/src/utility/types.H:48, from utility/src/utility/kmers.H:23, from utility/src/utility/kmers-writer.C:20: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘merylFileWriter::~merylFileWriter()’ at utility/src/utility/kmers-writer.C:144:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/bits.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/bits-wordArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/bits-wordArray.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/hexDump.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/md5.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/mt19937ar.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/speedCounter.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/sweatShop.C cc -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/cpuid.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/cpuid.c cc -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/memory.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/memory.c cc -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg.c cc -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg_trace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_trace.c cc -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg_qx_dispatch.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_qx_dispatch.c cc -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg_qb_de_dispatch.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_qb_de_dispatch.c cc -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg_qe_db_dispatch.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_qe_db_dispatch.c cc -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/cigar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/cigar.c g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C In file included from stores/sqStoreBlob.C:18: In function ‘void makeBlobName(const char*, uint32, char*)’, inlined from ‘void sqStoreBlobWriter::writeData(sqReadDataWriter*)’ at stores/sqStoreBlob.C:65:17: stores/sqStore.H:106:36: warning: ‘/blobs.’ directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 106 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber); In file included from /usr/include/stdio.h:974, from utility/src/utility/types.H:48, from utility/src/utility/runtime.H:26, from stores/sqStore.H:21: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void makeBlobName(const char*, uint32, char*)’ at stores/sqStore.H:106:11, inlined from ‘void sqStoreBlobWriter::writeData(sqReadDataWriter*)’ at stores/sqStoreBlob.C:65:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4114 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function ‘void makeBlobName(const char*, uint32, char*)’, inlined from ‘readBuffer* sqStoreBlobReader::getBuffer(sqReadMeta*)’ at stores/sqStoreBlob.C:113:17: stores/sqStore.H:106:36: warning: ‘/blobs.’ directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 106 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber); stores/sqStore.H:106:36: note: directive argument in the range [1, 65535] In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void makeBlobName(const char*, uint32, char*)’ at stores/sqStore.H:106:11, inlined from ‘readBuffer* sqStoreBlobReader::getBuffer(sqReadMeta*)’ at stores/sqStoreBlob.C:113:17: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4109 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:329:32: warning: ‘/version.’ directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 329 | snprintf(No, FILENAME_MAX, "%s/version.%03" F_U32P, sqStore_path(), V); In file included from /usr/include/stdio.h:974, from utility/src/utility/types.H:48, from utility/src/utility/runtime.H:26, from stores/sqStore.H:21, from stores/sqStoreConstructor.C:18: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:329:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 13 and 4109 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:337:35: warning: ‘/libraries’ directive output may be truncated writing 10 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 337 | snprintf(No, FILENAME_MAX, "%s/libraries", sqStore_path()); | ^~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:337:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 11 and 4107 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:338:32: warning: ‘/version.’ directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 338 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/libraries", sqStore_path(), V); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:338:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 23 and 4126 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:341:35: warning: ‘/reads’ directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 341 | snprintf(No, FILENAME_MAX, "%s/reads", sqStore_path()); | ^~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:341:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 7 and 4103 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:342:32: warning: ‘/version.’ directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 342 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads", sqStore_path(), V); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:342:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 19 and 4122 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:345:35: warning: ‘/reads-rawu’ directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 345 | snprintf(No, FILENAME_MAX, "%s/reads-rawu", sqStore_path()); | ^~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:345:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:346:32: warning: ‘/version.’ directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 346 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-rawu", sqStore_path(), V); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:346:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 24 and 4127 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:349:35: warning: ‘/reads-rawc’ directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 349 | snprintf(No, FILENAME_MAX, "%s/reads-rawc", sqStore_path()); | ^~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:349:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:350:32: warning: ‘/version.’ directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 350 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-rawc", sqStore_path(), V); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:350:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 24 and 4127 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:353:35: warning: ‘/reads-coru’ directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 353 | snprintf(No, FILENAME_MAX, "%s/reads-coru", sqStore_path()); | ^~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:353:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:354:32: warning: ‘/version.’ directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 354 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-coru", sqStore_path(), V); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:354:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 24 and 4127 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:357:35: warning: ‘/reads-corc’ directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 357 | snprintf(No, FILENAME_MAX, "%s/reads-corc", sqStore_path()); | ^~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:357:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:358:32: warning: ‘/version.’ directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 358 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/reads-corc", sqStore_path(), V); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:358:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 24 and 4127 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:361:35: warning: ‘/info’ directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 361 | snprintf(No, FILENAME_MAX, "%s/info", sqStore_path()); | ^~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:361:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 6 and 4102 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:362:32: warning: ‘/version.’ directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 362 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/info", sqStore_path(), V); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:362:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 18 and 4121 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:365:35: warning: ‘/info.txt’ directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 365 | snprintf(No, FILENAME_MAX, "%s/info.txt", sqStore_path()); | ^~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:365:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 10 and 4106 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:366:32: warning: ‘/version.’ directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 366 | snprintf(Nn, FILENAME_MAX, "%s/version.%03" F_U32P "/info.txt", sqStore_path(), V); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:366:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 22 and 4125 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreConstructor.C: In destructor ‘sqStore::~sqStore()’: stores/sqStoreConstructor.C:332:34: warning: ‘/version.’ directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 332 | snprintf(No, FILENAME_MAX, "%s/version.%03" F_U32P, sqStore_path(), V); In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘sqStore::~sqStore()’ at stores/sqStoreConstructor.C:332:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 13 and 4116 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C stores/ovOverlap.C:201:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp] 201 | #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING | ^~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C stores/ovOverlap.C: In member function ‘char* ovOverlap::toString(char*, ovOverlapDisplayType, bool)’: stores/ovOverlap.C:55:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘int’ [-Wformat=] 55 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 59 | dat.ovl.ahg5, dat.ovl.ahg3, | ~~~~~~~~~~~~ | | | int stores/ovOverlap.C:55:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘int’ [-Wformat=] 55 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 59 | dat.ovl.ahg5, dat.ovl.ahg3, | ~~~~~~~~~~~~ | | | int stores/ovOverlap.C:55:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 9 has type ‘int’ [-Wformat=] 55 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 60 | dat.ovl.bhg5, dat.ovl.bhg3, | ~~~~~~~~~~~~ | | | int stores/ovOverlap.C:55:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 10 has type ‘int’ [-Wformat=] 55 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 60 | dat.ovl.bhg5, dat.ovl.bhg3, | ~~~~~~~~~~~~ | | | int g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C stores/ovStoreWriter.C:33:2: warning: #warning not failing if a valid store [-Wcpp] 33 | #warning not failing if a valid store | ^~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C stores/ovStoreWriter.C: In member function ‘uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)’: stores/ovStoreWriter.C:190:37: warning: ‘/bucket’ directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 190 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum); | ^~~~~~~ In file included from /usr/include/stdio.h:974, from utility/src/utility/types.H:48, from utility/src/utility/runtime.H:26, from stores/ovStore.H:21, from stores/ovStoreWriter.C:18: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)’ at stores/ovStoreWriter.C:190:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 22 and 4130 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function ‘uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)’: stores/ovStoreWriter.C:199:37: warning: ‘/bucket’ directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 199 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, i); | ^~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)’ at stores/ovStoreWriter.C:199:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 23 and 4125 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function ‘void ovStoreSliceWriter::loadOverlapsFromBucket(uint32, uint64, ovOverlap*, uint64&)’: stores/ovStoreWriter.C:222:35: warning: ‘/bucket’ directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 222 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bucket, _sliceNum); | ^~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void ovStoreSliceWriter::loadOverlapsFromBucket(uint32, uint64, ovOverlap*, uint64&)’ at stores/ovStoreWriter.C:222:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 22 and 4130 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function ‘void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)’: stores/ovStoreWriter.C:306:40: warning: ‘/’ directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 306 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, _sliceNum); | ^ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)’ at stores/ovStoreWriter.C:306:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4114 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStore.H: In member function ‘void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)’: stores/ovStore.H:88:39: warning: ‘/’ directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 88 | snprintf(name, FILENAME_MAX, "%s/%04u.info", path, index); | ^ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void ovStoreInfo::save(const char*, uint32, bool)’ at stores/ovStore.H:88:15, inlined from ‘void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)’ at stores/ovStoreWriter.C:311:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 11 and 4113 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStore.H: In member function ‘void ovStoreSliceWriter::mergeInfoFiles()’: stores/ovStore.H:63:39: warning: ‘/’ directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 63 | snprintf(name, FILENAME_MAX, "%s/%04u.info", path, index); | ^ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void ovStoreInfo::load(const char*, uint32, bool)’ at stores/ovStore.H:63:15, inlined from ‘void ovStoreSliceWriter::mergeInfoFiles()’ at stores/ovStoreWriter.C:337:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 11 and 4113 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function ‘void ovStoreSliceWriter::mergeInfoFiles()’: stores/ovStoreWriter.C:366:42: warning: ‘/’ directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 366 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, ss); | ^ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void ovStoreSliceWriter::mergeInfoFiles()’ at stores/ovStoreWriter.C:366:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4114 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStore.H: In member function ‘void ovStoreSliceWriter::mergeInfoFiles()’: stores/ovStore.H:86:39: warning: ‘/info’ directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 86 | snprintf(name, FILENAME_MAX, "%s/info", path); | ^~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void ovStoreInfo::save(const char*, uint32, bool)’ at stores/ovStore.H:86:15, inlined from ‘void ovStoreSliceWriter::mergeInfoFiles()’ at stores/ovStoreWriter.C:389:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 6 and 4102 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function ‘void ovStoreSliceWriter::removeOverlapSlice()’: stores/ovStoreWriter.C:448:37: warning: ‘/bucket’ directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 448 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, _sliceNum); | ^~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void ovStoreSliceWriter::removeOverlapSlice()’ at stores/ovStoreWriter.C:448:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 22 and 4130 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function ‘void ovStoreSliceWriter::checkSortingIsComplete()’: stores/ovStoreWriter.C:467:38: warning: ‘/’ directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 467 | snprintf(nameF, FILENAME_MAX, "%s/%04u.info", _storePath, i); | ^ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void ovStoreSliceWriter::checkSortingIsComplete()’ at stores/ovStoreWriter.C:467:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 11 and 4113 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function ‘void ovStoreSliceWriter::checkSortingIsComplete()’: stores/ovStoreWriter.C:468:38: warning: ‘/’ directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 468 | snprintf(nameI, FILENAME_MAX, "%s/%04u.index", _storePath, i); | ^ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void ovStoreSliceWriter::checkSortingIsComplete()’ at stores/ovStoreWriter.C:468:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4114 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function ‘void ovStoreSliceWriter::removeAllIntermediateFiles()’: stores/ovStoreWriter.C:499:37: warning: ‘/’ directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 499 | snprintf(name, FILENAME_MAX, "%s/%04u.index", _storePath, ss); | ^ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void ovStoreSliceWriter::removeAllIntermediateFiles()’ at stores/ovStoreWriter.C:499:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4114 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function ‘void ovStoreSliceWriter::removeAllIntermediateFiles()’: stores/ovStoreWriter.C:502:37: warning: ‘/’ directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 502 | snprintf(name, FILENAME_MAX, "%s/%04u.info", _storePath, ss); | ^ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void ovStoreSliceWriter::removeAllIntermediateFiles()’ at stores/ovStoreWriter.C:502:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 11 and 4113 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function ‘void ovStoreSliceWriter::removeAllIntermediateFiles()’: stores/ovStoreWriter.C:519:37: warning: ‘/bucket’ directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 519 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, bb); | ^~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void ovStoreSliceWriter::removeAllIntermediateFiles()’ at stores/ovStoreWriter.C:519:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 23 and 4125 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function ‘void ovStoreSliceWriter::removeAllIntermediateFiles()’: stores/ovStoreWriter.C:523:39: warning: ‘/bucket’ directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 523 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, ss); | ^~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void ovStoreSliceWriter::removeAllIntermediateFiles()’ at stores/ovStoreWriter.C:523:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 22 and 4130 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/ovStoreWriter.C: In member function ‘void ovStoreSliceWriter::removeAllIntermediateFiles()’: stores/ovStoreWriter.C:527:37: warning: ‘/bucket’ directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 527 | snprintf(name, FILENAME_MAX, "%s/bucket%04u", _storePath, bb); | ^~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void ovStoreSliceWriter::removeAllIntermediateFiles()’ at stores/ovStoreWriter.C:527:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4114 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C stores/ovStoreHistogram.C: In member function ‘void ovErateLengthHistogram::addOverlap(ovOverlap*)’: stores/ovStoreHistogram.C:337:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘int’ [-Wformat=] 337 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 338 | overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, | ~~~~~~~~~~~~~~~~~~~~~ | | | int stores/ovStoreHistogram.C:337:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘int’ [-Wformat=] 337 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 338 | overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, | ~~~~~~~~~~~~~~~~~~~~~ | | | int stores/ovStoreHistogram.C:337:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 9 has type ‘int’ [-Wformat=] 337 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 338 | overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, 339 | overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3, | ~~~~~~~~~~~~~~~~~~~~~ | | | int stores/ovStoreHistogram.C:337:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 10 has type ‘int’ [-Wformat=] 337 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 338 | overlap->a_iid, alen, overlap->dat.ovl.ahg5, overlap->dat.ovl.ahg3, 339 | overlap->b_iid, blen, overlap->dat.ovl.bhg5, overlap->dat.ovl.bhg3, | ~~~~~~~~~~~~~~~~~~~~~ | | | int g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C stores/tgStore.C: In member function ‘void tgStore::purgeVersion(uint32)’: stores/tgStore.C:168:36: warning: ‘/seqDB.v’ directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 168 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); AS_UTL_unlink(_name); | ^~~~~~~~ stores/tgStore.C:168:33: note: using the range [-2147483648, 2147483647] for directive argument 168 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); AS_UTL_unlink(_name); | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:974, from utility/src/utility/types.H:48, from utility/src/utility/runtime.H:26, from stores/tgStore.C:18: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void tgStore::purgeVersion(uint32)’ at stores/tgStore.C:168:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 16 and 4120 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function ‘void tgStore::purgeVersion(uint32)’: stores/tgStore.C:169:36: warning: ‘/seqDB.v’ directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 169 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.ctg", _path, version); AS_UTL_unlink(_name); | ^~~~~~~~ stores/tgStore.C:169:33: note: using the range [-2147483648, 2147483647] for directive argument 169 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.ctg", _path, version); AS_UTL_unlink(_name); | ^~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void tgStore::purgeVersion(uint32)’ at stores/tgStore.C:169:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 16 and 4120 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function ‘void tgStore::purgeVersion(uint32)’: stores/tgStore.C:170:36: warning: ‘/seqDB.v’ directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 170 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.utg", _path, version); AS_UTL_unlink(_name); | ^~~~~~~~ stores/tgStore.C:170:33: note: using the range [-2147483648, 2147483647] for directive argument 170 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.utg", _path, version); AS_UTL_unlink(_name); | ^~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void tgStore::purgeVersion(uint32)’ at stores/tgStore.C:170:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 16 and 4120 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function ‘void tgStore::dumpMASR(tgStoreEntry*&, uint32&, uint32)’: stores/tgStore.C:571:36: warning: ‘/seqDB.v’ directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 571 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); | ^~~~~~~~ stores/tgStore.C:571:33: note: using the range [-2147483648, 2147483647] for directive argument 571 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); | ^~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void tgStore::dumpMASR(tgStoreEntry*&, uint32&, uint32)’ at stores/tgStore.C:571:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 16 and 4120 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function ‘void tgStore::loadMASR(tgStoreEntry*&, uint32&, uint32&, uint32)’: stores/tgStore.C:603:40: warning: ‘/seqDB.v’ directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 603 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, i); | ^~~~~~~~ stores/tgStore.C:603:37: note: directive argument in the range [1, 2147483647] 603 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, i); | ^~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void tgStore::loadMASR(tgStoreEntry*&, uint32&, uint32&, uint32)’ at stores/tgStore.C:603:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 16 and 4119 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function ‘void tgStore::loadMASR(tgStoreEntry*&, uint32&, uint32&, uint32)’: stores/tgStore.C:614:36: warning: ‘/seqDB.v’ directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 614 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); | ^~~~~~~~ stores/tgStore.C:614:33: note: using the range [-2147483648, 2147483647] for directive argument 614 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); | ^~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void tgStore::loadMASR(tgStoreEntry*&, uint32&, uint32&, uint32)’ at stores/tgStore.C:614:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 16 and 4120 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function ‘void tgStore::loadMASR(tgStoreEntry*&, uint32&, uint32&, uint32)’: stores/tgStore.C:618:38: warning: ‘/seqDB.v’ directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 618 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); | ^~~~~~~~ stores/tgStore.C:618:35: note: using the range [-2147483648, 2147483647] for directive argument 618 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); | ^~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void tgStore::loadMASR(tgStoreEntry*&, uint32&, uint32&, uint32)’ at stores/tgStore.C:618:13: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 16 and 4120 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function ‘FILE* tgStore::openDB(uint32)’: stores/tgStore.C:672:36: warning: ‘/seqDB.v’ directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 672 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); | ^~~~~~~~ stores/tgStore.C:672:33: note: using the range [-2147483648, 2147483647] for directive argument 672 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); | ^~~~~~~~~~~~~~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘FILE* tgStore::openDB(uint32)’ at stores/tgStore.C:672:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 16 and 4120 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/tgTig.C: In member function ‘bool tgTig::loadLayout(FILE*)’: stores/tgTig.C:537:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 537 | fgets(LINE, LINEmax, F); LINEnum++; | ~~~~~^~~~~~~~~~~~~~~~~~ stores/tgTig.C:667:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 667 | fgets(LINE, LINEmax, F); LINEnum++; | ~~~~~^~~~~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/objectStore.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility stores/dumpBlob.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreBuild.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreConfig.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreBucketizer.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreSorter.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreIndexer.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreDump.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreStats.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility stores/sqStoreCreate.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Istores -Iutility/src/utility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C stores/sqStoreDumpFASTQ.C: In member function ‘FILE* libOutput::openFASTQ()’: stores/sqStoreDumpFASTQ.C:70:36: warning: ‘.fastq’ directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 70 | snprintf(N, FILENAME_MAX, "%s.fastq%s", _p, _s); | ^~~~~~ In file included from /usr/include/stdio.h:974, from utility/src/utility/types.H:48, from utility/src/utility/runtime.H:26, from stores/sqStoreDumpFASTQ.C:18: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘FILE* libOutput::openFASTQ()’ at stores/sqStoreDumpFASTQ.C:70:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output 7 or more bytes (assuming 4102) into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreDumpFASTQ.C: In member function ‘FILE* libOutput::openFASTQ()’: stores/sqStoreDumpFASTQ.C:68:37: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size between 0 and 4095 [-Wformat-truncation=] 68 | snprintf(N, FILENAME_MAX, "%s.%s.fastq%s", _p, _n, _s); | ^~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘FILE* libOutput::openFASTQ()’ at stores/sqStoreDumpFASTQ.C:68:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output 8 or more bytes (assuming 8198) into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreDumpFASTQ.C: In member function ‘FILE* libOutput::openFASTA()’: stores/sqStoreDumpFASTQ.C:100:36: warning: ‘.fasta’ directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 100 | snprintf(N, FILENAME_MAX, "%s.fasta%s", _p, _s); | ^~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘FILE* libOutput::openFASTA()’ at stores/sqStoreDumpFASTQ.C:100:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output 7 or more bytes (assuming 4102) into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/sqStoreDumpFASTQ.C: In member function ‘FILE* libOutput::openFASTA()’: stores/sqStoreDumpFASTQ.C:98:37: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size between 0 and 4095 [-Wformat-truncation=] 98 | snprintf(N, FILENAME_MAX, "%s.%s.fasta%s", _p, _n, _s); | ^~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘FILE* libOutput::openFASTA()’ at stores/sqStoreDumpFASTQ.C:98:15: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output 8 or more bytes (assuming 8198) into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Iseqrequester/src/seqrequester stores/sqStoreDumpMetaData.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/sqStoreDumpMetaData/seqrequester/src/seqrequester/summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Iseqrequester/src/seqrequester seqrequester/src/seqrequester/summarize.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility stores/tgStoreCompress.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility stores/tgStoreDump.C stores/tgStoreDump.C:643:2: warning: #warning replace this with genericStatistics [-Wcpp] 643 | #warning replace this with genericStatistics | ^~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility stores/tgTigSizeAnalysis.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility stores/tgStoreLoad.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility stores/tgTigDisplay.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility stores/loadCorrectedReads.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Istores -Iutility/src/utility -IoverlapBasedTrimming stores/loadTrimmedReads.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility stores/loadErates.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/meryl.C stores/loadErates.C: In member function ‘void ovStore::addEvalues(std::vector&)’: stores/loadErates.C:59:41: warning: ‘/evalues.WORKING’ directive output may be truncated writing 16 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 59 | snprintf(evalueTemp, FILENAME_MAX, "%s/evalues.WORKING", _storePath); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:974, from utility/src/utility/types.H:48, from utility/src/utility/runtime.H:26, from stores/loadErates.C:18: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void ovStore::addEvalues(std::vector&)’ at stores/loadErates.C:59:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 17 and 4113 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ stores/loadErates.C: In member function ‘void ovStore::addEvalues(std::vector&)’: stores/loadErates.C:60:41: warning: ‘/evalues’ directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 60 | snprintf(evalueName, FILENAME_MAX, "%s/evalues", _storePath); | ^~~~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void ovStore::addEvalues(std::vector&)’ at stores/loadErates.C:60:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4105 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylCommandBuilder.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylCommandBuilder.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylCountArray.C meryl/src/meryl/merylCommandBuilder.C: In member function ‘void merylCommandBuilder::initialize(char*)’: meryl/src/meryl/merylCommandBuilder.C:160:41: warning: ‘/merylIndex’ directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 160 | snprintf(_indexName, FILENAME_MAX, "%s/merylIndex", _optString); | ^~~~~~~~~~~ In file included from /usr/include/stdio.h:974, from utility/src/utility/types.H:48, from utility/src/utility/runtime.H:26, from meryl/src/meryl/meryl.H:22, from meryl/src/meryl/merylCommandBuilder.C:19: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void merylCommandBuilder::initialize(char*)’ at meryl/src/meryl/merylCommandBuilder.C:160:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4108 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ meryl/src/meryl/merylCommandBuilder.C: In member function ‘void merylCommandBuilder::initialize(char*)’: meryl/src/meryl/merylCommandBuilder.C:161:41: warning: ‘/info’ directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 161 | snprintf(_sqInfName, FILENAME_MAX, "%s/info", _optString); | ^~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void merylCommandBuilder::initialize(char*)’ at meryl/src/meryl/merylCommandBuilder.C:161:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 6 and 4102 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ meryl/src/meryl/merylCommandBuilder.C: In member function ‘void merylCommandBuilder::initialize(char*)’: meryl/src/meryl/merylCommandBuilder.C:162:41: warning: ‘/reads’ directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 162 | snprintf(_sqRdsName, FILENAME_MAX, "%s/reads", _optString); | ^~~~~~ In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void merylCommandBuilder::initialize(char*)’ at meryl/src/meryl/merylCommandBuilder.C:162:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 7 and 4103 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylInput.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-count.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-countSimple.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp-countThreads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-countThreads.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-histogram.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-nextMer.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapCheck/overlapCheck/overlapCheck.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapCheck/overlapCheck.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C overlapInCore/overlapInCore-Build_Hash_Index.C: In function ‘void Mark_Skip_Kmers()’: overlapInCore/overlapInCore-Build_Hash_Index.C:209:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 209 | fgets(line, 1024, F); | ~~~~~^~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C overlapInCore/overlapPair.C:463:2: warning: #warning do we need to check for contained too? [-Wcpp] 463 | #warning do we need to check for contained too? | ^~~~~~~ overlapInCore/overlapImport.C: In function ‘int main(int, char**)’: overlapInCore/overlapImport.C:254:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 254 | fgets(S, 1024, in->file()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ overlapInCore/overlapImport.C:284:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 284 | fgets(S, 1024, in->file()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C overlapInCore/edalign.C: In function ‘bool readLine(FILE*, char*, int32, int32&, splitToWords&)’: overlapInCore/edalign.C:30:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 30 | fgets(line, lineMax, file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Imhap/liboverlap mhap/mhapConvert.C mhap/mhapConvert.C: In function ‘int main(int, char**)’: mhap/mhapConvert.C:147:25: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘int’ [-Wformat=] 147 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 151 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, | ~~~~~~~~~~~~~~~ | | | int mhap/mhapConvert.C:147:25: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 9 has type ‘int’ [-Wformat=] 147 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 151 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, | ~~~~~~~~~~~~~~~ | | | int mhap/mhapConvert.C:147:25: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 10 has type ‘int’ [-Wformat=] 147 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 152 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, | ~~~~~~~~~~~~~~~ | | | int mhap/mhapConvert.C:147:25: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 11 has type ‘int’ [-Wformat=] 147 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 152 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, | ~~~~~~~~~~~~~~~ | | | int g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Iminimap/liboverlap minimap/mmapConvert.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores correction/filterCorrectionOverlaps.C minimap/mmapConvert.C: In function ‘int main(int, char**)’: minimap/mmapConvert.C:127:25: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘int’ [-Wformat=] 127 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 130 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, | ~~~~~~~~~~~~~~~ | | | int minimap/mmapConvert.C:127:25: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘int’ [-Wformat=] 127 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 130 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, | ~~~~~~~~~~~~~~~ | | | int minimap/mmapConvert.C:127:25: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 9 has type ‘int’ [-Wformat=] 127 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 131 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, | ~~~~~~~~~~~~~~~ | | | int minimap/mmapConvert.C:127:25: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 10 has type ‘int’ [-Wformat=] 127 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 131 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, | ~~~~~~~~~~~~~~~ | | | int g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Iutgcns correction/generateCorrectionLayouts.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Iutgcns utgcns/stashContains.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores correction/filterCorrectionLayouts.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Iutgcns correction/falconsense.C correction/falconsense.C: In function ‘void loadReadList(const char*, uint32, uint32, std::set&)’: correction/falconsense.C:64:13: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 64 | for (fgets(L, 1024, R); | ~~~~~^~~~~~~~~~~~ correction/falconsense.C:66:13: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | fgets(L, 1024, R)) { | ~~~~~^~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Iutgcns utgcns/stashContains.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Iutgcns haplotyping/splitHaplotype.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/trimReads.C In file included from overlapBasedTrimming/trimReads.C:19: overlapBasedTrimming/trimStat.H: In member function ‘void trimStat::generatePlots(const char*, const char*, uint32)’: overlapBasedTrimming/trimStat.H:69:11: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | system(N); | ~~~~~~^~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/trimReads-bestEdge.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/trimReads-largestCovered.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads-workUnit.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads-subReads.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads-trimBad.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/adjustNormal.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/adjustFlipped.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/mergeRanges.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Analyze_Alignment.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Output.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Process_Olap.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Frags.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/computeDiff.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/computeDiff.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Read_Olaps.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/fixErrors/overlapErrorAdjustment/fixErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapErrorAdjustment/fixErrors.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/fixErrors/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapErrorAdjustment/correctOverlaps-Correct_Frags.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/computeDiff.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/computeDiff.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/bogart.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/bogart.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_AssemblyGraph.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_BestOverlapGraph.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_ChunkGraph.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_DetectSpurs.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_Instrumentation.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_FindCircular.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_FindCircular.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_Logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_Logging.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_MarkRepeatReads.C bogart/AS_BAT_Logging.C: In member function ‘void logFileInstance::open()’: bogart/AS_BAT_Logging.C:115:36: warning: ‘.num’ directive output may be truncated writing 4 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 115 | snprintf(_path, FILENAME_MAX, "%s.num%03d.log", _name, _part); | ^~~~ In member function ‘void logFileInstance::open()’, inlined from ‘void logFileInstance::open()’ at bogart/AS_BAT_Logging.C:110:1: bogart/AS_BAT_Logging.C:115:33: note: using the range [-2147483648, 2147483647] for directive argument 115 | snprintf(_path, FILENAME_MAX, "%s.num%03d.log", _name, _part); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:974, from utility/src/utility/types.H:48, from utility/src/utility/system.H:23, from bogart/AS_BAT_Logging.C:18: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void logFileInstance::open()’ at bogart/AS_BAT_Logging.C:115:11, inlined from ‘void logFileInstance::open()’ at bogart/AS_BAT_Logging.C:110:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4116 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_MergeOrphans.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_OptimizePositions.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_Outputs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_Outputs.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_OverlapCache.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_PlaceContains.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_PopulateUnitig.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_PromoteToSingleton.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_ReadInfo.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_SetParentAndHang.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_SplitDiscontinuous.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_SplitTig_AtReadEnds.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_SplitTig_AtReadEnds.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_TigVector.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig_AddRead.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/layoutReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/layoutReads.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_Instrumentation.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_Instrumentation.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_Logging.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_Logging.C bogart/AS_BAT_Logging.C: In member function ‘void logFileInstance::open()’: bogart/AS_BAT_Logging.C:115:36: warning: ‘.num’ directive output may be truncated writing 4 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 115 | snprintf(_path, FILENAME_MAX, "%s.num%03d.log", _name, _part); | ^~~~ In member function ‘void logFileInstance::open()’, inlined from ‘void logFileInstance::open()’ at bogart/AS_BAT_Logging.C:110:1: bogart/AS_BAT_Logging.C:115:33: note: using the range [-2147483648, 2147483647] for directive argument 115 | snprintf(_path, FILENAME_MAX, "%s.num%03d.log", _name, _part); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:974, from utility/src/utility/types.H:48, from utility/src/utility/system.H:23, from bogart/AS_BAT_Logging.C:18: In function ‘int snprintf(char*, size_t, const char*, ...)’, inlined from ‘void logFileInstance::open()’ at bogart/AS_BAT_Logging.C:115:11, inlined from ‘void logFileInstance::open()’ at bogart/AS_BAT_Logging.C:110:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 12 and 4116 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_OptimizePositions.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_OptimizePositions.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_Outputs.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_Outputs.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_OverlapCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_OverlapCache.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_PlaceContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_PlaceContains.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_PlaceReadUsingOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_PlaceReadUsingOverlaps.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_ReadInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_ReadInfo.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_SetParentAndHang.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_SetParentAndHang.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_TigVector.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_TigVector.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_Unitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_Unitig_AddRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig_AddRead.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/utgcns/utgcns/utgcns.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Iutility/src/parasail -Istores -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/utgcns.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/utgcns/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Iutility/src/parasail -Istores -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Iutility/src/parasail -Istores -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/canu-gvhNdT/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/canu-gvhNdT/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C gfa/alignGFA.C: In function ‘void dotplot(uint32, bool, char*, uint32, bool, char*)’: gfa/alignGFA.C:148:9: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 148 | system(Pname); | ~~~~~~^~~~~~~ cp -pf pipelines/canu.pl /build/canu-gvhNdT/canu-2.2+dfsg/build/bin/canu cp -pf pipelines/canu-time.pl /build/canu-gvhNdT/canu-2.2+dfsg/build/bin/canu-time cp -pf pipelines/draw-tig.pl /build/canu-gvhNdT/canu-2.2+dfsg/build/bin/draw-tig cp -pf pipelines/canu/Consensus.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/CorrectReads.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/HaplotypeReads.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/Configure.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/Defaults.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/Execution.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/SequenceStore.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_Cloud.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_DNANexus.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_LSF.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_Local.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_PBSTorque.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_SGE.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/Grid_Slurm.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/Meryl.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/Output.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapBasedTrimming.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapErrorAdjustment.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapInCore.pm /build/canu-gvhNdT/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/OverlapMhap.pm 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/build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -lcanu -lsnappy -lbacktrace g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/bin/mergeRanges -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-gvhNdT/canu-2.2+dfsg/build/lib /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -lcanu -lsnappy -lbacktrace g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/bin/overlapAlign -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-gvhNdT/canu-2.2+dfsg/build/lib /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/overlapAlign.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/trimRead.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -lcanu -lsnappy -lbacktrace g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/bin/findErrors -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-gvhNdT/canu-2.2+dfsg/build/lib /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Process_Olap.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Frags.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/computeDiff.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Read_Olaps.o -lcanu -lsnappy -lbacktrace g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/bin/fixErrors -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-gvhNdT/canu-2.2+dfsg/build/lib /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/fixErrors/overlapErrorAdjustment/fixErrors.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/fixErrors/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -lcanu -lsnappy -lbacktrace g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/bin/findErrors-Dump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-gvhNdT/canu-2.2+dfsg/build/lib /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -lcanu -lsnappy -lbacktrace g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/bin/correctOverlaps -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-gvhNdT/canu-2.2+dfsg/build/lib /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/computeDiff.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -lcanu -lsnappy -lbacktrace g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/bin/bogart -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-gvhNdT/canu-2.2+dfsg/build/lib /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/bogart.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_DetectSpurs.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_Instrumentation.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_FindCircular.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_Logging.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_MarkRepeatReads.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_MergeOrphans.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_OptimizePositions.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_Outputs.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_OverlapCache.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_PlaceContains.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_PlaceReadUsingOverlaps.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_PopulateUnitig.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_PromoteToSingleton.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_SplitTig_AtReadEnds.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_TigVector.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_Unitig.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_Unitig_AddRead.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu -lsnappy -lbacktrace g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/bin/layoutReads -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-gvhNdT/canu-2.2+dfsg/build/lib /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/layoutReads.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_Instrumentation.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_Logging.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_OptimizePositions.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_Outputs.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_OverlapCache.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_PlaceContains.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_PlaceReadUsingOverlaps.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_ReadInfo.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_SetParentAndHang.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_TigVector.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_Unitig.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_Unitig_AddRead.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/layoutReads/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.o -lcanu -lsnappy -lbacktrace g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/bin/utgcns -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-gvhNdT/canu-2.2+dfsg/build/lib /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/utgcns/utgcns/utgcns.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/utgcns/utgcns/stashContains.o /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/utgcns/utgcns/unitigConsensus.o -lcanu -lsnappy -lbacktrace g++ -o /build/canu-gvhNdT/canu-2.2+dfsg/build/bin/alignGFA -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/canu-gvhNdT/canu-2.2+dfsg/build/lib /build/canu-gvhNdT/canu-2.2+dfsg/build/obj/bin/alignGFA/gfa/alignGFA.o -lcanu -lsnappy -lbacktrace Success! canu installed in /build/canu-gvhNdT/canu-2.2+dfsg/build/bin/canu make[2]: Leaving directory '/build/canu-gvhNdT/canu-2.2+dfsg/src' find build \ -name OverlapMhap.pm \ -exec sed -i 's#\(\s*my \$javaPath = \).*#\1 "/usr/lib/jvm/java-8-openjdk-amd64/bin/java";#' {} + make[1]: Leaving directory '/build/canu-gvhNdT/canu-2.2+dfsg' dh_auto_test -O--sourcedirectory=src/ create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src/ dh_prep -O--sourcedirectory=src/ dh_auto_install --destdir=debian/canu/ -O--sourcedirectory=src/ debian/rules override_dh_install make[1]: Entering directory '/build/canu-gvhNdT/canu-2.2+dfsg' dh_install for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done rm -Rf debian/canu/build make[1]: Leaving directory '/build/canu-gvhNdT/canu-2.2+dfsg' dh_installdocs -O--sourcedirectory=src/ dh_installchangelogs -O--sourcedirectory=src/ dh_installman -O--sourcedirectory=src/ dh_installsystemduser -O--sourcedirectory=src/ dh_perl -O--sourcedirectory=src/ dh_link -O--sourcedirectory=src/ dh_strip_nondeterminism -O--sourcedirectory=src/ dh_compress -O--sourcedirectory=src/ dh_fixperms -O--sourcedirectory=src/ dh_missing -O--sourcedirectory=src/ dh_dwz -a -O--sourcedirectory=src/ dh_strip -a -O--sourcedirectory=src/ dh_makeshlibs -a -O--sourcedirectory=src/ dh_shlibdeps -a -O--sourcedirectory=src/ dh_installdeb -O--sourcedirectory=src/ dh_gencontrol -O--sourcedirectory=src/ dh_md5sums -O--sourcedirectory=src/ dh_builddeb -O--sourcedirectory=src/ dpkg-deb: building package 'canu' in '../canu_2.2+dfsg-5_amd64.deb'. dpkg-deb: building package 'canu-dbgsym' in '../canu-dbgsym_2.2+dfsg-5_amd64.deb'. dpkg-genbuildinfo -O../canu_2.2+dfsg-5_amd64.buildinfo dpkg-genchanges -O../canu_2.2+dfsg-5_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2026-09-19T11:30:22Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sat, 19 Sep 2026 11:30:22 +0000 | +------------------------------------------------------------------------------+ canu_2.2+dfsg-5_amd64.changes: ------------------------------ Format: 1.8 Date: Fri, 20 Oct 2023 16:51:22 +0200 Source: canu Binary: canu canu-dbgsym Architecture: source amd64 Version: 2.2+dfsg-5 Distribution: perl-5.44-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: canu - single molecule sequence assembler for genomes Changes: canu (2.2+dfsg-5) unstable; urgency=medium . * d/tests/run-unit-test: preserve more logs Checksums-Sha1: 766cd67c2283e816f6d8c73e8dcb12fdfa1acd3f 1248 canu_2.2+dfsg-5.dsc 42f967ed80bca3c884b2741e01a8239b632989d0 12360 canu_2.2+dfsg-5.debian.tar.xz 3c81c31df95ed2137eeff56c281fce0c8251fb24 15806348 canu-dbgsym_2.2+dfsg-5_amd64.deb 32ce49ef561db2e0c5d1c7e4a9cdae388d251c0e 6216 canu_2.2+dfsg-5_amd64.buildinfo 9ea79e63ba71f0ca85f2674d3cfb3c8ff89670d9 1513976 canu_2.2+dfsg-5_amd64.deb Checksums-Sha256: 8cd93e3c21c72b6201eae89de68868377656a751213d8196edd2dbe8e5829874 1248 canu_2.2+dfsg-5.dsc b46328555c6d70b6a8baca86a3f4521893563a55815158b3f4a3e1e0c0e2089a 12360 canu_2.2+dfsg-5.debian.tar.xz faa8f6ca7af8a94faad8d6824f2d3982d399aeac04aad234aa14d0fc0b5aa4c4 15806348 canu-dbgsym_2.2+dfsg-5_amd64.deb 964f870a93219fd0fb2bde2e39abc21c0d8ade5ec3ae6bbde4c64d7ca50648a3 6216 canu_2.2+dfsg-5_amd64.buildinfo 35fbaa861bda8efec421d50e88883ca7bd15e254c09e2009f49dad510cde34dc 1513976 canu_2.2+dfsg-5_amd64.deb Files: 5c480594c47dd973500b5f8575bde772 1248 science optional canu_2.2+dfsg-5.dsc e90979f8e9f152ccffe2316daab69dd8 12360 science optional canu_2.2+dfsg-5.debian.tar.xz eab0769461b6be2871043e9be6019d8c 15806348 debug optional canu-dbgsym_2.2+dfsg-5_amd64.deb db1c12310a57ef5839ddac8e812d783b 6216 science optional canu_2.2+dfsg-5_amd64.buildinfo 6748ac0c3a44557c1e12db454a41c6d9 1513976 science optional canu_2.2+dfsg-5_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sat, 19 Sep 2026 11:30:22 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: canu Binary: canu canu-dbgsym Architecture: amd64 source Version: 2.2+dfsg-5 Checksums-Md5: 5c480594c47dd973500b5f8575bde772 1248 canu_2.2+dfsg-5.dsc eab0769461b6be2871043e9be6019d8c 15806348 canu-dbgsym_2.2+dfsg-5_amd64.deb 6748ac0c3a44557c1e12db454a41c6d9 1513976 canu_2.2+dfsg-5_amd64.deb Checksums-Sha1: 766cd67c2283e816f6d8c73e8dcb12fdfa1acd3f 1248 canu_2.2+dfsg-5.dsc 3c81c31df95ed2137eeff56c281fce0c8251fb24 15806348 canu-dbgsym_2.2+dfsg-5_amd64.deb 9ea79e63ba71f0ca85f2674d3cfb3c8ff89670d9 1513976 canu_2.2+dfsg-5_amd64.deb Checksums-Sha256: 8cd93e3c21c72b6201eae89de68868377656a751213d8196edd2dbe8e5829874 1248 canu_2.2+dfsg-5.dsc faa8f6ca7af8a94faad8d6824f2d3982d399aeac04aad234aa14d0fc0b5aa4c4 15806348 canu-dbgsym_2.2+dfsg-5_amd64.deb 35fbaa861bda8efec421d50e88883ca7bd15e254c09e2009f49dad510cde34dc 1513976 canu_2.2+dfsg-5_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 19 Sep 2026 11:30:21 +0000 Build-Path: /build/canu-gvhNdT/canu-2.2+dfsg Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.19-2), autopoint (= 1.0-5), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-4), binfmt-support (= 2.2.2-8), binutils (= 2.47-6), binutils-common (= 2.47-6), binutils-x86-64-linux-gnu (= 2.47-6), bsdextrautils (= 2.42.3-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), ca-certificates (= 20260816), ca-certificates-java (= 20260311), coreutils (= 9.10-1), cpp (= 4:16.1.0-3), cpp-15 (= 15.3.0-4), cpp-15-x86-64-linux-gnu (= 15.3.0-4), cpp-16 (= 16.2.0-3), cpp-16-x86-64-linux-gnu (= 16.2.0-3), cpp-x86-64-linux-gnu (= 4:16.1.0-3), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.5), debianutils (= 5.24), default-jre-headless (= 2:1.25-77), dh-autoreconf (= 23), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.11), dpkg-dev (= 1.23.11), dwz (= 0.17-1), fastjar (= 2:0.98-8), file (= 1:5.47-4), findutils (= 4.11.0-2), g++ (= 4:16.1.0-3), g++-16 (= 16.2.0-3), g++-16-x86-64-linux-gnu (= 16.2.0-3), g++-x86-64-linux-gnu (= 4:16.1.0-3), gcc (= 4:16.1.0-3), gcc-15 (= 15.3.0-4), gcc-15-base (= 15.3.0-4), gcc-15-x86-64-linux-gnu (= 15.3.0-4), gcc-16 (= 16.2.0-3), gcc-16-base (= 16.2.0-3), gcc-16-x86-64-linux-gnu (= 16.2.0-3), gcc-x86-64-linux-gnu (= 4:16.1.0-3), gettext (= 1.0-5), gettext-base (= 1.0-5), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.14-1), hostname (= 3.25), init-system-helpers (= 1.69+nmu1), intltool-debian (= 0.35.0+20060710.6), jaligner (= 1.0+dfsg-11), jarwrapper (= 0.82), java-common (= 0.77), libacl1 (= 2.4.0-1), libapache-pom-java (= 33-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 16.2.0-3), libatinject-jsr330-api-java (= 1.0+ds1-6), libatomic1 (= 16.2.0-3), libattr1 (= 1:2.6.0-1), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b2), libbinutils (= 2.47-6), libblkid1 (= 2.42.3-1), libboost-dev (= 1.90.0.2+nmu1), libboost1.90-dev (= 1.90.0-6.1+b1), libbz2-1.0 (= 1.0.8-6+b2), libc-bin (= 2.43-5), libc-dev-bin (= 2.43-5), libc-gconv-modules-extra (= 2.43-5), libc6 (= 2.43-5), libc6-dev (= 2.43-5), libcap-ng0 (= 0.9.6-1), libcc1-0 (= 16.2.0-3), libcommons-codec-java (= 1.22.0-1), libcommons-compress-java (= 1.27.1-2), libcommons-io-java (= 2.22.0-1), libcommons-parent-java (= 56-1), libcrypt1 (= 1:4.5.2+20251210-1), libctf-nobfd0 (= 2.47-6), libctf0 (= 2.47-6), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.5), libdpkg-perl (= 1.23.11), libelf1t64 (= 0.196-1), liberror-prone-java (= 2.18.0-1), libfastutil-java (= 8.5.16+dfsg-1), libfile-stripnondeterminism-perl (= 1.15.1-1), libfilesys-df-perl (= 0.92-7+b6), libgcc-15-dev (= 15.3.0-4), libgcc-16-dev (= 16.2.0-3), libgcc-s1 (= 16.2.0-3), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgomp1 (= 16.2.0-3), libgprofng0 (= 2.47-6), libguava-java (= 32.0.1-1), libhwasan0 (= 16.2.0-3), libisl23 (= 0.28-1), libitm1 (= 16.2.0-3), libjansson4 (= 2.15.1-1), libjpeg62-turbo (= 1:3.1.3-4), libjsr305-java (= 0.1~+svn49-12), liblcms2-2 (= 2.19.1-1), liblsan0 (= 16.2.0-3), liblzma5 (= 5.8.4-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libmeryl-dev (= 0~20150903+r2013-10+b3), libmount1 (= 2.42.3-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libnspr4 (= 2:4.40-1), libnss3 (= 2:3.129-1), libpam-modules (= 1.7.0-8), libpam-modules-bin (= 1.7.0-8), libpam-runtime (= 1.7.0-8), libpam0g (= 1.7.0-8), libpcre2-8-0 (= 10.48-3), libpcsclite1 (= 2.5.1-1), libperl5.44 (= 5.44.0-1), libpipeline1 (= 1.5.8-3), libquadmath0 (= 16.2.0-3), libseccomp2 (= 2.6.1-1+b1), libselinux1 (= 3.11-2), libsframe3 (= 2.47-6), libsmartcols1 (= 2.42.3-1), libsnappy-dev (= 1.3.1-1), libsnappy1v5 (= 1.3.1-1), libsqlite3-0 (= 3.53.4-2), libssl3t64 (= 3.6.4-1), libssw-java (= 1.1-16), libstdc++-16-dev (= 16.2.0-3), libstdc++6 (= 16.2.0-3), libsystemd0 (= 262~rc3-1), libtinfo6 (= 6.6+20260608-2), libtool (= 2.6.2-3), libtsan2 (= 16.2.0-3), libubsan1 (= 16.2.0-3), libuchardet0 (= 0.0.8-2+b2), libudev1 (= 262~rc3-1), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.3-1), libxml2-16 (= 2.15.4+dfsg-1), libzstd1 (= 1.5.7+dfsg-4), linux-libc-dev (= 7.2.6-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), mhap (= 2.1.3+dfsg-3), ncurses-base (= 6.6+20260608-2), ncurses-bin (= 6.6+20260608-2), openjdk-25-jre-headless (= 25.0.5~6ea-1), openssl (= 3.6.4-1), openssl-provider-legacy (= 3.6.4-1), patch (= 2.8-2), perl (= 5.44.0-1), perl-base (= 5.44.0-1), perl-modules-5.44 (= 5.44.0-1), po-debconf (= 1.0.22), sed (= 4.9-3), sensible-utils (= 0.0.26), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-6), util-linux (= 2.42.3-1), xz-utils (= 5.8.4-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1697813482" +------------------------------------------------------------------------------+ | Package contents Sat, 19 Sep 2026 11:30:22 +0000 | 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./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2023-10-20 14:51 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 572544 2023-10-20 14:51 ./usr/lib/debug/.dwz/x86_64-linux-gnu/canu.debug drwxr-xr-x root/root 0 2023-10-20 14:51 ./usr/share/ drwxr-xr-x root/root 0 2023-10-20 14:51 ./usr/share/doc/ lrwxrwxrwx root/root 0 2023-10-20 14:51 ./usr/share/doc/canu-dbgsym -> canu canu_2.2+dfsg-5_amd64.deb ------------------------- new Debian package, version 2.0. size 1513976 bytes: control archive=3016 bytes. 883 bytes, 21 lines control 5698 bytes, 82 lines md5sums Package: canu Version: 2.2+dfsg-5 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 13927 Depends: libc6 (>= 2.38), libgcc-s1 (>= 4.2), libgomp1 (>= 6), libsnappy1v5 (>= 1.3.1), libstdc++6 (>= 11), perl:any, libfilesys-df-perl, mhap, gnuplot-nox | gnuplot Suggests: nanopolish Section: science Priority: optional Homepage: https://canu.readthedocs.org/en/latest/ Description: single molecule sequence assembler for genomes Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II or Oxford Nanopore MinION). . Canu is a hierarchical assembly pipeline which runs in four steps: . * Detect overlaps in high-noise sequences using MHAP * Generate corrected sequence consensus * Trim corrected sequences * Assemble trimmed corrected sequences drwxr-xr-x root/root 0 2023-10-20 14:51 ./ drwxr-xr-x root/root 0 2023-10-20 14:51 ./usr/ drwxr-xr-x root/root 0 2023-10-20 14:51 ./usr/bin/ -rwxr-xr-x root/root 109 2023-08-18 16:12 ./usr/bin/canu drwxr-xr-x root/root 0 2023-10-20 14:51 ./usr/lib/ drwxr-xr-x root/root 0 2023-10-20 14:51 ./usr/lib/canu/ drwxr-xr-x root/root 0 2023-10-20 14:51 ./usr/lib/canu/bin/ -rwxr-xr-x root/root 276880 2023-10-20 14:51 ./usr/lib/canu/bin/alignGFA -rwxr-xr-x root/root 597560 2023-10-20 14:51 ./usr/lib/canu/bin/bogart -rwxr-xr-x root/root 40570 2023-10-20 14:51 ./usr/lib/canu/bin/canu -rwxr-xr-x root/root 10839 2023-10-20 14:51 ./usr/lib/canu/bin/canu-time -rw-r--r-- root/root 83 2023-10-20 14:51 ./usr/lib/canu/bin/canu.defaults -rwxr-xr-x root/root 260496 2023-10-20 14:51 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+------------------------------------------------------------------------------+ | Cleanup Sat, 19 Sep 2026 11:30:24 +0000 | +------------------------------------------------------------------------------+ Purging /build/canu-gvhNdT Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sat, 19 Sep 2026 11:30:25 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 215804 Build-Time: 219 Distribution: perl-5.44-throwaway Host Architecture: amd64 Install-Time: 31 Job: /srv/debomatic/incoming/canu_2.2+dfsg-5.dsc Machine Architecture: amd64 Package: canu Package-Time: 277 Source-Version: 2.2+dfsg-5 Space: 215804 Status: successful Version: 2.2+dfsg-5 -------------------------------------------------------------------------------- Finished at 2026-09-19T11:30:22Z Build needed 00:04:37, 215804k disk space