Running as unit: rb-build-arm64_3-57537.service ==================================================================================== Mon Sep 30 22:49:25 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_3) on jenkins, called using "codethink01-arm64 codethink04-arm64" as arguments. Mon Sep 30 22:49:25 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-2rXm75TF" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Sep 30 22:49:25 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Mon Sep 30 22:49:25 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-MgPr5q' Mon Sep 30 22:49:26 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Mon Sep 30 22:49:26 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-byQQfv' ok, let's check if libgclib is building anywhere yet… ok, libgclib is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of libgclib in unstable on arm64 on jenkins now. 1st build will be done on codethink01-arm64.debian.net. 2nd build will be done on codethink04-arm64.debian.net. ============================================================================= Mon Sep 30 22:49:45 UTC 2024 I: starting to build libgclib/unstable/arm64 on jenkins on '2024-09-30 22:49' Mon Sep 30 22:49:45 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_3/57537/console.log 1727736585 arm64 unstable libgclib Mon Sep 30 22:49:45 UTC 2024 I: Downloading source for unstable/libgclib=0.12.7+ds-5 --2024-09-30 22:49:45-- http://deb.debian.org/debian/pool/main/libg/libgclib/libgclib_0.12.7%2bds-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2331 (2.3K) [text/prs.lines.tag] Saving to: ‘libgclib_0.12.7+ds-5.dsc’ 0K .. 100% 371M=0s 2024-09-30 22:49:45 (371 MB/s) - ‘libgclib_0.12.7+ds-5.dsc’ saved [2331/2331] --2024-09-30 22:49:45-- http://deb.debian.org/debian/pool/main/libg/libgclib/libgclib_0.12.7%2bds-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2331 (2.3K) [text/prs.lines.tag] Saving to: ‘libgclib_0.12.7+ds-5.dsc’ 0K .. 100% 371M=0s 2024-09-30 22:49:45 (371 MB/s) - ‘libgclib_0.12.7+ds-5.dsc’ saved [2331/2331] Mon Sep 30 22:49:45 UTC 2024 I: libgclib_0.12.7+ds-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libgclib Binary: libgclib-dev, libgclib3 Architecture: any Version: 0.12.7+ds-5 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Michael R. Crusoe , Étienne Mollier Homepage: https://github.com/gpertea/gclib Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/libgclib Vcs-Git: https://salsa.debian.org/med-team/libgclib.git Testsuite: autopkgtest Testsuite-Triggers: build-essential Build-Depends: debhelper-compat (= 13), d-shlibs Package-List: libgclib-dev deb libdevel optional arch=any libgclib3 deb libs optional arch=any Checksums-Sha1: d54728a73bca7734b58bc52bae84578694918fbb 256645 libgclib_0.12.7+ds.orig.tar.gz 89900ccc1fe336c282107f4f247e62ab1b695cd0 14920 libgclib_0.12.7+ds-5.debian.tar.xz Checksums-Sha256: d9e5d89b1f9c696dac329a2788c535e49fabde1fec3524b6882c00309d1b375a 256645 libgclib_0.12.7+ds.orig.tar.gz 371133e06326d2aa8222134dd5edffe7a9cfc618d9f9def995842102aa122ade 14920 libgclib_0.12.7+ds-5.debian.tar.xz Files: a65ac3ce19638a92ba492569997e46b0 256645 libgclib_0.12.7+ds.orig.tar.gz 50d20daa4530ec4e138734aa1dbe1ae7 14920 libgclib_0.12.7+ds-5.debian.tar.xz Dgit: 38904758baca7a36b72e7b0d2f259b4a04c3b53b debian archive/debian/0.12.7+ds-5 https://git.dgit.debian.org/libgclib -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmNqvNAUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdo0kxAAkv2StsYn5DF3OKgDd2LZ8THEux66 QC3QuDmmyh9KdfDUGq7bNnCUbpRf9pByig4TuN8KAzTYsCkpyl+1TYGXD/b/qQtD fnzNSaTmbjw3nY4fCnd/dm3vsE1qo8T++2cFiK6B1cmr1vuVDDG7y6loKdo8TJgX +CemB1c670MmwphHk7epmuAQ5px+Q1p9JA+FwAUPs7SUEjh0dyEM7axdPj1GRjO2 EzZuGgHDRhPQBlz6zmXeQuYlMzYIvixM6ghXs0iriLO93F5lP2mL+7SVZasSCf4w fI/k8pGZbSGIfWsClD/2DbgH/QNkY0KcPKiQey+ndfNHdENlC3MA2hLKJ/w3jTLq B8AdQzL57ScSPMBW3LH0bdaZS0VLi8OwZdk2d12XD7BwpEgQE5BKLyLYY0DjwRBV YbB743nzDlu3yghSpIecKNgYSpSU5DiIQ20TXbOs6450Nywh5vJxZd95/p0CAOI5 jY9lo1w0mWPRdc01uKv5KfLBIPyU8sb1MPoupcnMb0pIt/RLAuDm1SrhdBPdy/GG JmZGj316K9iS7FSyTYqyuJjMTVpIvLvM5sccvf5djfGe3wnzyxx4PamvLLk/wTod +z9WhZhLQsoBRNAs4enXzPQWCj5vXCl1DOxUde6y3J6OZsg0kyjLFQUs9EAk3UCe mbhadEv2QS+1k0k= =0Nli -----END PGP SIGNATURE----- Mon Sep 30 22:49:45 UTC 2024 I: Checking whether the package is not for us Mon Sep 30 22:49:46 UTC 2024 I: Starting 1st build on remote node codethink01-arm64.debian.net. Mon Sep 30 22:49:46 UTC 2024 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Mon Sep 30 22:49:46 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Mon Sep 30 22:49:46 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-6NPYXN' ==================================================================================== Mon Nov 3 05:12:47 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink01-arm64, called using "1 libgclib unstable /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg 0.12.7+ds-5" as arguments. Mon Nov 3 05:12:47 UTC 2025 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-ILZ4Uz3E" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Nov 3 05:12:47 UTC 2025 I: Downloading source for unstable/libgclib=0.12.7+ds-5 Reading package lists... NOTICE: 'libgclib' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libgclib.git Please use: git clone https://salsa.debian.org/med-team/libgclib.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 274 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-5 (dsc) [2331 B] Get:2 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-5 (tar) [257 kB] Get:3 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-5 (diff) [14.9 kB] Fetched 274 kB in 0s (1831 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'libgclib' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libgclib.git Please use: git clone https://salsa.debian.org/med-team/libgclib.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 274 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-5 (dsc) [2331 B] Get:2 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-5 (tar) [257 kB] Get:3 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-5 (diff) [14.9 kB] Fetched 274 kB in 0s (1831 kB/s) Download complete and in download only mode ============================================================================= Building libgclib in unstable on arm64 on codethink01-arm64 now. Date: Mon Nov 3 05:12:47 GMT 2025 Date UTC: Mon Nov 3 05:12:47 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 2 17:12:47 -12 2025 I: pbuilder-time-stamp: 1762146767 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libgclib_0.12.7+ds-5.dsc] I: copying [./libgclib_0.12.7+ds.orig.tar.gz] I: copying [./libgclib_0.12.7+ds-5.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Nov 8 20:32:16 2022 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libgclib_0.12.7+ds-5.dsc: no acceptable signature found dpkg-source: info: extracting libgclib in libgclib-0.12.7+ds dpkg-source: info: unpacking libgclib_0.12.7+ds.orig.tar.gz dpkg-source: info: unpacking libgclib_0.12.7+ds-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying autoconf.patch dpkg-source: info: applying CVE-2021-42006.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1003020/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='253e5325ca4041faad50fd50c8e94fad' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1003020' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/pbuilderrc_o8yK --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/b1 --logfile b1/build.log libgclib_0.12.7+ds-5.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1003020/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), d-shlibs dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19895 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 77.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 d-shlibs all 0.107 [11.0 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Fetched 19.4 MB in 0s (122 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19895 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-8_arm64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../15-d-shlibs_0.107_all.deb ... Unpacking d-shlibs (0.107) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.191-2_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-5_arm64.deb ... Unpacking libicu72:arm64 (72.1-5) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/libgclib-0.12.7+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libgclib_0.12.7+ds-5_source.changes dpkg-buildpackage: info: source package libgclib dpkg-buildpackage: info: source version 0.12.7+ds-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' if [ -r Makefile -a -r Makefile.am ]; then dh_auto_clean; fi rm -f Makefile Makefile.in aclocal.m4 config.h.in configure debian/autoreconf.after debian/autoreconf.before find . -name "*.o" -delete make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf aclocal: warning: couldn't open directory 'config': No such file or directory libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config'. libtoolize: copying file 'config/libtool.m4' libtoolize: copying file 'config/ltoptions.m4' libtoolize: copying file 'config/ltsugar.m4' libtoolize: copying file 'config/ltversion.m4' libtoolize: copying file 'config/lt~obsolete.m4' libtoolize: Consider adding '-I config' to ACLOCAL_AMFLAGS in Makefile.am. configure.ac:30: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:30: You should run autoupdate. config/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:30: the top level configure.ac:51: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:51: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:51: the top level configure.ac:30: installing 'config/compile' configure.ac:30: installing 'config/config.guess' configure.ac:30: installing 'config/config.sub' configure.ac:18: installing 'config/install-sh' configure.ac:18: installing 'config/missing' Makefile.am: installing 'config/depcomp' dh_auto_configure ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate ./configure: line 17133: AX_CXXFLAGS: command not found checking for egrep... (cached) /usr/bin/grep -E checking for stdlib.h... (cached) yes checking whether make sets $(MAKE)... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating libgclib.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' make all-am make[2]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o mdtest.o mdtest.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-codons.lo `test -f 'codons.cpp' || echo './'`codons.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GAlnExtend.lo `test -f 'GAlnExtend.cpp' || echo './'`GAlnExtend.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GapAssem.lo `test -f 'GapAssem.cpp' || echo './'`GapAssem.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GArgs.lo `test -f 'GArgs.cpp' || echo './'`GArgs.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GBase.lo `test -f 'GBase.cpp' || echo './'`GBase.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gcdb.lo `test -f 'gcdb.cpp' || echo './'`gcdb.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GCdbYank.lo `test -f 'GCdbYank.cpp' || echo './'`GCdbYank.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gdna.lo `test -f 'gdna.cpp' || echo './'`gdna.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GFaSeqGet.lo `test -f 'GFaSeqGet.cpp' || echo './'`GFaSeqGet.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GFastaIndex.lo `test -f 'GFastaIndex.cpp' || echo './'`GFastaIndex.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gff.lo `test -f 'gff.cpp' || echo './'`gff.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gdna.cpp -fPIC -DPIC -o .libs/libgclib_la-gdna.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GCdbYank.cpp -fPIC -DPIC -o .libs/libgclib_la-GCdbYank.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c codons.cpp -fPIC -DPIC -o .libs/libgclib_la-codons.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GapAssem.cpp -fPIC -DPIC -o .libs/libgclib_la-GapAssem.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gcdb.cpp -fPIC -DPIC -o .libs/libgclib_la-gcdb.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GArgs.cpp -fPIC -DPIC -o .libs/libgclib_la-GArgs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GBase.cpp -fPIC -DPIC -o .libs/libgclib_la-GBase.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GAlnExtend.cpp -fPIC -DPIC -o .libs/libgclib_la-GAlnExtend.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gff.cpp -fPIC -DPIC -o .libs/libgclib_la-gff.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFastaIndex.cpp -fPIC -DPIC -o .libs/libgclib_la-GFastaIndex.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFaSeqGet.cpp -fPIC -DPIC -o .libs/libgclib_la-GFaSeqGet.o gcdb.cpp: In function ‘unsigned int gcdb_strlen(const char*)’: gcdb.cpp:102:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 102 | register char *t; | ^ gcdb.cpp: In constructor ‘GCdbRead::GCdbRead(int)’: gcdb.cpp:809:13: warning: comparing the result of pointer addition ‘(x + 1)’ and NULL [-Waddress] 809 | if (x + 1) { | ~~^~~ gcdb.cpp: In constructor ‘GCdbRead::GCdbRead(char*)’: gcdb.cpp:843:13: warning: comparing the result of pointer addition ‘(x + 1)’ and NULL [-Waddress] 843 | if (x + 1) { | ~~^~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gdna.cpp -o libgclib_la-gdna.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c codons.cpp -o libgclib_la-codons.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gsocket.lo `test -f 'gsocket.cpp' || echo './'`gsocket.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GArgs.cpp -o libgclib_la-GArgs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GCdbYank.cpp -o libgclib_la-GCdbYank.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gsocket.cpp -fPIC -DPIC -o .libs/libgclib_la-gsocket.o /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gstopwatch.lo `test -f 'gstopwatch.cpp' || echo './'`gstopwatch.cpp In file included from GBase.cpp:1: In member function ‘GDynArray::Push(char)’, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: GBase.h:549:26: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 549 | fArray[fCount-1] = item; | ^ In function ‘GRealloc(void**, unsigned long)’, inlined from ‘GDynArray::Clear()’ at GBase.h:633:6, inlined from ‘GDynArray::growTo(unsigned int)’ at GBase.h:577:28, inlined from ‘GDynArray::Grow()’ at GBase.h:544:12, inlined from ‘GDynArray::Push(char)’ at GBase.h:564:6, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: GBase.h:280:21: note: at offset 4294967295 into destination object of size 16 allocated by ‘realloc’ 280 | void *p=realloc(*ptr,size); | ~~~~~~~^~~~~~~~~~~ In member function ‘GDynArray::Push(char)’, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: GBase.h:549:26: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 549 | fArray[fCount-1] = item; | ^ In function ‘GRealloc(void**, unsigned long)’, inlined from ‘GDynArray::Clear()’ at GBase.h:633:6, inlined from ‘GDynArray::growTo(unsigned int)’ at GBase.h:577:28, inlined from ‘GDynArray::Grow()’ at GBase.h:544:12, inlined from ‘GDynArray::Push(char)’ at GBase.h:564:6, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: GBase.h:272:20: note: at offset 4294967295 into destination object of size 16 allocated by ‘malloc’ 272 | void *p=malloc(size); | ~~~~~~^~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gcdb.cpp -o libgclib_la-gcdb.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GStr.lo `test -f 'GStr.cpp' || echo './'`GStr.cpp In file included from gff.cpp:1: gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 242 | struct { | ^ gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 245 | struct { | ^ gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 343 | struct { | ^ gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 706 | struct { | ^ gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1165 | struct { | ^ /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GThreads.lo `test -f 'GThreads.cpp' || echo './'`GThreads.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gsocket.cpp -o libgclib_la-gsocket.o >/dev/null 2>&1 gff.cpp: In constructor ‘GffLine::GffLine(GffReader*, const char*)’: gff.cpp:426:19: warning: unknown escape sequence: '\%' 426 | GMessage("Warning: unexpected tab character in last column, line truncated:\n\%s\n",l); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GFastaFile.h:4, from GapAssem.h:3, from GapAssem.cpp:1: GapAssem.cpp: In member function ‘GASeq::refineClipping(GDynArray&, int, bool)’: GBase.h:176:28: warning: ‘gxpos’ may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ GapAssem.cpp:236:14: note: ‘gxpos’ was declared here 236 | int* gxpos; //mapping of positions from gseq to seq | ^~~~~ GBase.h:176:28: warning: ‘gseq’ may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ GapAssem.cpp:212:15: note: ‘gseq’ was declared here 212 | char* gseq; | ^~~~ In file included from GAlnExtend.h:6, from GAlnExtend.cpp:1: In function ‘GMalloc(void**, unsigned long)’, inlined from ‘GXMemPool::GXMemPool(int)’ at GAlnExtend.h:157:9, inlined from ‘CGreedyAlignData::CGreedyAlignData(int, int, int)’ at GAlnExtend.h:281:29: GBase.h:254:12: warning: ‘MEM[(void * *)_78]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GBase.cpp -o libgclib_la-GBase.o >/dev/null 2>&1 GAlnExtend.cpp: In function ‘color_fg(int, _IO_FILE*)’: GAlnExtend.cpp:13:35: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 13 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+30); | ^~ In function ‘color_fg(int, _IO_FILE*)’, inlined from ‘color_fg(int, _IO_FILE*)’ at GAlnExtend.cpp:11:6: GAlnExtend.cpp:13:34: note: directive argument in the range [-2147483618, 2147483647] 13 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+30); | ^~~~~ In file included from /usr/include/stdio.h:970, from GBase.h:63: In function ‘sprintf’, inlined from ‘color_fg(int, _IO_FILE*)’ at GAlnExtend.cpp:13:9, inlined from ‘color_fg(int, _IO_FILE*)’ at GAlnExtend.cpp:11:6: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 3 and 13 bytes into a destination of size 4 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ GAlnExtend.cpp: In function ‘color_bg(int, _IO_FILE*)’: GAlnExtend.cpp:19:35: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 19 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+40); | ^~ In function ‘color_bg(int, _IO_FILE*)’, inlined from ‘color_bg(int, _IO_FILE*)’ at GAlnExtend.cpp:17:6: GAlnExtend.cpp:19:34: note: directive argument in the range [-2147483608, 2147483647] 19 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+40); | ^~~~~ In function ‘sprintf’, inlined from ‘color_bg(int, _IO_FILE*)’ at GAlnExtend.cpp:19:9, inlined from ‘color_bg(int, _IO_FILE*)’ at GAlnExtend.cpp:17:6: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 3 and 13 bytes into a destination of size 4 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gstopwatch.cpp -fPIC -DPIC -o .libs/libgclib_la-gstopwatch.o In function ‘GMalloc(void**, unsigned long)’, inlined from ‘GXMemPool::GXMemPool(int)’ at GAlnExtend.h:157:9, inlined from ‘GXGreedyExtend(char const*, int, char const*, int, bool, int&, int&, CGreedyAlignData&, GXEditScript*)’ at GAlnExtend.cpp:311:50: GBase.h:254:12: warning: ‘MEM[(void * *)_196]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ In function ‘GMalloc(void**, unsigned long)’, inlined from ‘GXMemPool::GXMemPool(int)’ at GAlnExtend.h:157:9, inlined from ‘GXMemPool::getSpace(int)’ at GAlnExtend.h:195:40, inlined from ‘GXMemPool::getByteSpace(int)’ at GAlnExtend.h:209:27, inlined from ‘GXGreedyExtend(char const*, int, char const*, int, bool, int&, int&, CGreedyAlignData&, GXEditScript*)’ at GAlnExtend.cpp:473:64: GBase.h:254:12: warning: ‘MEM[(void * *)_317]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GThreads.cpp -fPIC -DPIC -o .libs/libgclib_la-GThreads.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GStr.cpp -fPIC -DPIC -o .libs/libgclib_la-GStr.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFastaIndex.cpp -o libgclib_la-GFastaIndex.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFaSeqGet.cpp -o libgclib_la-GFaSeqGet.o >/dev/null 2>&1 In function ‘GMalloc(void**, unsigned long)’, inlined from ‘FastaSeq::init(char const*, char const*, char const*, int, int)’ at GFastaFile.h:52:10, inlined from ‘FastaSeq::FastaSeq(char const*, char const*, char const*, int)’ at GFastaFile.h:127:15, inlined from ‘FastaSeq::FastaSeq(char const*, char const*, char const*, int)’ at GFastaFile.h:124:6, inlined from ‘GASeq::GASeq(char const*, int, int, int, int, char)’ at GapAssem.cpp:51:32: GBase.h:254:12: warning: ‘MEM[(void * *)this_10(D) + 24B]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gstopwatch.cpp -o libgclib_la-gstopwatch.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GThreads.cpp -o libgclib_la-GThreads.o >/dev/null 2>&1 In file included from GStr.h:5, from GStr.cpp:2: GStr.cpp: In function ‘GStr::new_data(char const*, unsigned int)’: GBase.h:176:28: warning: ‘data’ may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ GStr.cpp:38:15: note: ‘data’ was declared here 38 | Data* data; | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GapAssem.cpp -o libgclib_la-GapAssem.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GAlnExtend.cpp -o libgclib_la-GAlnExtend.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GStr.cpp -o libgclib_la-GStr.o >/dev/null 2>&1 In file included from gff.h:6: gff.cpp: In member function ‘BEDLine::BEDLine(GffReader*, char const*)’: GBase.h:176:28: warning: ‘bstart’ may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gff.cpp:242:18: note: ‘bstart’ was declared here 242 | char** bstart; | ^~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gff.cpp -o libgclib_la-gff.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -version-info 3:0 -lpthread -Wl,-z,relro -Wl,-z,now -Wl,-flto -o libgclib.la -rpath /usr/lib/aarch64-linux-gnu libgclib_la-codons.lo libgclib_la-GAlnExtend.lo libgclib_la-GapAssem.lo libgclib_la-GArgs.lo libgclib_la-GBase.lo libgclib_la-gcdb.lo libgclib_la-GCdbYank.lo libgclib_la-gdna.lo libgclib_la-GFaSeqGet.lo libgclib_la-GFastaIndex.lo libgclib_la-gff.lo libgclib_la-gsocket.lo libgclib_la-gstopwatch.lo libgclib_la-GStr.lo libgclib_la-GThreads.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o .libs/libgclib_la-codons.o .libs/libgclib_la-GAlnExtend.o .libs/libgclib_la-GapAssem.o .libs/libgclib_la-GArgs.o .libs/libgclib_la-GBase.o .libs/libgclib_la-gcdb.o .libs/libgclib_la-GCdbYank.o .libs/libgclib_la-gdna.o .libs/libgclib_la-GFaSeqGet.o .libs/libgclib_la-GFastaIndex.o .libs/libgclib_la-gff.o .libs/libgclib_la-gsocket.o .libs/libgclib_la-gstopwatch.o .libs/libgclib_la-GStr.o .libs/libgclib_la-GThreads.o -lpthread -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -flto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-flto -Wl,-soname -Wl,libgclib.so.3 -o .libs/libgclib.so.3.0.0 lto-wrapper: warning: using serial compilation of 5 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information In member function '__ct ', inlined from 'buildMSA' at GapAssem.cpp:1123:47: GapAssem.h:350:32: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 350 | columns=new GAlnColumn[len]; | ^ /usr/include/c++/14/new: In member function 'buildMSA': /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ GVec.hh: In member function 'setCapacity': GVec.hh:107:24: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 107 | fArray=new OBJ[NewCapacity]; | ^ /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ libtool: link: (cd ".libs" && rm -f "libgclib.so.3" && ln -s "libgclib.so.3.0.0" "libgclib.so.3") libtool: link: (cd ".libs" && rm -f "libgclib.so" && ln -s "libgclib.so.3.0.0" "libgclib.so") libtool: link: ar cr .libs/libgclib.a libgclib_la-codons.o libgclib_la-GAlnExtend.o libgclib_la-GapAssem.o libgclib_la-GArgs.o libgclib_la-GBase.o libgclib_la-gcdb.o libgclib_la-GCdbYank.o libgclib_la-gdna.o libgclib_la-GFaSeqGet.o libgclib_la-GFastaIndex.o libgclib_la-gff.o libgclib_la-gsocket.o libgclib_la-gstopwatch.o libgclib_la-GStr.o libgclib_la-GThreads.o libtool: link: ranlib .libs/libgclib.a libtool: link: ( cd ".libs" && rm -f "libgclib.la" && ln -s "../libgclib.la" "libgclib.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -Wl,-z,relro -Wl,-z,now -Wl,-flto -o mdtest mdtest.o libgclib.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-flto -o .libs/mdtest mdtest.o ./.libs/libgclib.so make[2]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' ./mdtest 7TEST^BCT 7 matching bases base mismatch [T] base mismatch [E] base mismatch [S] base mismatch [T] 3 base(s) deletion [BCT] make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/libgclib-0.12.7\+ds/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' make[2]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libgclib.la '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgclib.so.3.0.0 /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.so.3.0.0 libtool: install: (cd /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libgclib.so.3.0.0 libgclib.so.3 || { rm -f libgclib.so.3 && ln -s libgclib.so.3.0.0 libgclib.so.3; }; }) libtool: install: (cd /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libgclib.so.3.0.0 libgclib.so || { rm -f libgclib.so && ln -s libgclib.so.3.0.0 libgclib.so; }; }) libtool: install: /usr/bin/install -c .libs/libgclib.lai /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.la libtool: install: /usr/bin/install -c .libs/libgclib.a /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.a libtool: install: chmod 644 /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.a libtool: install: ranlib /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c mdtest '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin' libtool: warning: 'libgclib.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/mdtest /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin/mdtest /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/include' /usr/bin/install -c -m 644 GAlnExtend.h GArgs.h GBam.h GBase.h GBitVec.h GCdbYank.h GFaSeqGet.h GFastaFile.h GFastaIndex.h GResUsage.h GStr.h GThreads.h GapAssem.h codons.h config.h gcdb.h gdimg.h gdna.h gff.h gsocket.h gstopwatch.h proc_mem.h wyhash.h xxhash.h GHash.hh GHashMap.hh GIntHash.hh GIntervalTree.hh GList.hh GVec.hh khashl.hh '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/include' /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 libgclib.pc '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' make[2]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/tmp/usr/include usr \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/aarch64-linux-gnu/pkgconfig \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility set -e install -d -m 755 debian/libgclib-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libgclib3/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.a debian/libgclib-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.so debian/libgclib-dev/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.so.3 debian/libgclib3/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.so.3.0.0 debian/libgclib3/usr/lib/aarch64-linux-gnu PKGDEV=libgclib-dev PKGSHL=libgclib3 install -d -m 755 debian/libgclib-dev/usr mv debian/tmp/usr/include debian/libgclib-dev/usr install -d -m 755 debian/libgclib-dev/usr/lib/aarch64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libgclib-dev/usr/lib/aarch64-linux-gnu/pkgconfig mkdir debian/libgclib-dev/usr/include/gclib mv debian/libgclib-dev/usr/include/*.h* debian/libgclib-dev/usr/include/gclib sed -i '/PACKAGE_NAME/d' debian/libgclib-dev/usr/include/gclib/config.h # delete header files of not compiled C++ source files find debian/libgclib-dev -name gdimg.h -delete find debian/libgclib-dev -name GBam.h -delete make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' dh_installexamples chmod a-x debian/libgclib-dev/usr/share/doc/libgclib-dev/examples/* make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libgclib-dev' in '../libgclib-dev_0.12.7+ds-5_arm64.deb'. dpkg-deb: building package 'libgclib3-dbgsym' in '../libgclib3-dbgsym_0.12.7+ds-5_arm64.deb'. dpkg-deb: building package 'libgclib3' in '../libgclib3_0.12.7+ds-5_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libgclib_0.12.7+ds-5_arm64.buildinfo dpkg-genchanges --build=binary -O../libgclib_0.12.7+ds-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1003020 and its subdirectories I: Current time: Sun Nov 2 17:13:54 -12 2025 I: pbuilder-time-stamp: 1762146834 Mon Nov 3 05:13:54 UTC 2025 I: Signing ./b1/libgclib_0.12.7+ds-5_arm64.buildinfo as libgclib_0.12.7+ds-5_arm64.buildinfo.asc Mon Nov 3 05:13:54 UTC 2025 I: Signed ./b1/libgclib_0.12.7+ds-5_arm64.buildinfo as ./b1/libgclib_0.12.7+ds-5_arm64.buildinfo.asc Mon Nov 3 05:13:54 UTC 2025 - build #1 for libgclib/unstable/arm64 on codethink01-arm64 done. Starting cleanup. All cleanup done. Mon Nov 3 05:13:54 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-ILZ4Uz3E, removing. /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Sep 30 22:50 b1 drwxr-xr-x 2 jenkins jenkins 4096 Sep 30 22:49 b2 -rw-r--r-- 1 jenkins jenkins 2331 Nov 8 2022 libgclib_0.12.7+ds-5.dsc -rw------- 1 jenkins jenkins 3472 Sep 30 22:49 rbuildlog.KCioFy7 /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/b1: total 1108 -rw-r--r-- 1 jenkins jenkins 64110 Sep 30 22:50 build.log -rw-r--r-- 1 jenkins jenkins 270432 Sep 30 22:50 libgclib-dev_0.12.7+ds-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 612404 Sep 30 22:50 libgclib3-dbgsym_0.12.7+ds-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 134668 Sep 30 22:50 libgclib3_0.12.7+ds-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 14920 Sep 30 22:50 libgclib_0.12.7+ds-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2331 Sep 30 22:50 libgclib_0.12.7+ds-5.dsc -rw-r--r-- 1 jenkins jenkins 5768 Sep 30 22:50 libgclib_0.12.7+ds-5_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6650 Sep 30 22:50 libgclib_0.12.7+ds-5_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1980 Sep 30 22:50 libgclib_0.12.7+ds-5_arm64.changes -rw-r--r-- 1 jenkins jenkins 1473 Sep 30 22:50 libgclib_0.12.7+ds-5_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/b2: total 0 Mon Sep 30 22:50:56 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 2 17:12:47 -12 2025 I: pbuilder-time-stamp: 1762146767 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libgclib_0.12.7+ds-5.dsc] I: copying [./libgclib_0.12.7+ds.orig.tar.gz] I: copying [./libgclib_0.12.7+ds-5.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Nov 8 20:32:16 2022 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libgclib_0.12.7+ds-5.dsc: no acceptable signature found dpkg-source: info: extracting libgclib in libgclib-0.12.7+ds dpkg-source: info: unpacking libgclib_0.12.7+ds.orig.tar.gz dpkg-source: info: unpacking libgclib_0.12.7+ds-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying autoconf.patch dpkg-source: info: applying CVE-2021-42006.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1003020/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='253e5325ca4041faad50fd50c8e94fad' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1003020' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/pbuilderrc_o8yK --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/b1 --logfile b1/build.log libgclib_0.12.7+ds-5.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1003020/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), d-shlibs dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19895 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 77.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 d-shlibs all 0.107 [11.0 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Fetched 19.4 MB in 0s (122 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19895 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-8_arm64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../15-d-shlibs_0.107_all.deb ... Unpacking d-shlibs (0.107) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.191-2_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-5_arm64.deb ... Unpacking libicu72:arm64 (72.1-5) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-5) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-2) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up d-shlibs (0.107) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/libgclib-0.12.7+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libgclib_0.12.7+ds-5_source.changes dpkg-buildpackage: info: source package libgclib dpkg-buildpackage: info: source version 0.12.7+ds-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' if [ -r Makefile -a -r Makefile.am ]; then dh_auto_clean; fi rm -f Makefile Makefile.in aclocal.m4 config.h.in configure debian/autoreconf.after debian/autoreconf.before find . -name "*.o" -delete make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf aclocal: warning: couldn't open directory 'config': No such file or directory libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config'. libtoolize: copying file 'config/libtool.m4' libtoolize: copying file 'config/ltoptions.m4' libtoolize: copying file 'config/ltsugar.m4' libtoolize: copying file 'config/ltversion.m4' libtoolize: copying file 'config/lt~obsolete.m4' libtoolize: Consider adding '-I config' to ACLOCAL_AMFLAGS in Makefile.am. configure.ac:30: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:30: You should run autoupdate. config/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:30: the top level configure.ac:51: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:51: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:51: the top level configure.ac:30: installing 'config/compile' configure.ac:30: installing 'config/config.guess' configure.ac:30: installing 'config/config.sub' configure.ac:18: installing 'config/install-sh' configure.ac:18: installing 'config/missing' Makefile.am: installing 'config/depcomp' dh_auto_configure ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate ./configure: line 17133: AX_CXXFLAGS: command not found checking for egrep... (cached) /usr/bin/grep -E checking for stdlib.h... (cached) yes checking whether make sets $(MAKE)... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating libgclib.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' make all-am make[2]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o mdtest.o mdtest.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-codons.lo `test -f 'codons.cpp' || echo './'`codons.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GAlnExtend.lo `test -f 'GAlnExtend.cpp' || echo './'`GAlnExtend.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GapAssem.lo `test -f 'GapAssem.cpp' || echo './'`GapAssem.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GArgs.lo `test -f 'GArgs.cpp' || echo './'`GArgs.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GBase.lo `test -f 'GBase.cpp' || echo './'`GBase.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gcdb.lo `test -f 'gcdb.cpp' || echo './'`gcdb.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GCdbYank.lo `test -f 'GCdbYank.cpp' || echo './'`GCdbYank.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gdna.lo `test -f 'gdna.cpp' || echo './'`gdna.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GFaSeqGet.lo `test -f 'GFaSeqGet.cpp' || echo './'`GFaSeqGet.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GFastaIndex.lo `test -f 'GFastaIndex.cpp' || echo './'`GFastaIndex.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gff.lo `test -f 'gff.cpp' || echo './'`gff.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gdna.cpp -fPIC -DPIC -o .libs/libgclib_la-gdna.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GCdbYank.cpp -fPIC -DPIC -o .libs/libgclib_la-GCdbYank.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c codons.cpp -fPIC -DPIC -o .libs/libgclib_la-codons.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GapAssem.cpp -fPIC -DPIC -o .libs/libgclib_la-GapAssem.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gcdb.cpp -fPIC -DPIC -o .libs/libgclib_la-gcdb.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GArgs.cpp -fPIC -DPIC -o .libs/libgclib_la-GArgs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GBase.cpp -fPIC -DPIC -o .libs/libgclib_la-GBase.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GAlnExtend.cpp -fPIC -DPIC -o .libs/libgclib_la-GAlnExtend.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gff.cpp -fPIC -DPIC -o .libs/libgclib_la-gff.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFastaIndex.cpp -fPIC -DPIC -o .libs/libgclib_la-GFastaIndex.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFaSeqGet.cpp -fPIC -DPIC -o .libs/libgclib_la-GFaSeqGet.o gcdb.cpp: In function ‘unsigned int gcdb_strlen(const char*)’: gcdb.cpp:102:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 102 | register char *t; | ^ gcdb.cpp: In constructor ‘GCdbRead::GCdbRead(int)’: gcdb.cpp:809:13: warning: comparing the result of pointer addition ‘(x + 1)’ and NULL [-Waddress] 809 | if (x + 1) { | ~~^~~ gcdb.cpp: In constructor ‘GCdbRead::GCdbRead(char*)’: gcdb.cpp:843:13: warning: comparing the result of pointer addition ‘(x + 1)’ and NULL [-Waddress] 843 | if (x + 1) { | ~~^~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gdna.cpp -o libgclib_la-gdna.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c codons.cpp -o libgclib_la-codons.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gsocket.lo `test -f 'gsocket.cpp' || echo './'`gsocket.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GArgs.cpp -o libgclib_la-GArgs.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GCdbYank.cpp -o libgclib_la-GCdbYank.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gsocket.cpp -fPIC -DPIC -o .libs/libgclib_la-gsocket.o /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gstopwatch.lo `test -f 'gstopwatch.cpp' || echo './'`gstopwatch.cpp In file included from GBase.cpp:1: In member function ‘GDynArray::Push(char)’, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: GBase.h:549:26: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 549 | fArray[fCount-1] = item; | ^ In function ‘GRealloc(void**, unsigned long)’, inlined from ‘GDynArray::Clear()’ at GBase.h:633:6, inlined from ‘GDynArray::growTo(unsigned int)’ at GBase.h:577:28, inlined from ‘GDynArray::Grow()’ at GBase.h:544:12, inlined from ‘GDynArray::Push(char)’ at GBase.h:564:6, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: GBase.h:280:21: note: at offset 4294967295 into destination object of size 16 allocated by ‘realloc’ 280 | void *p=realloc(*ptr,size); | ~~~~~~~^~~~~~~~~~~ In member function ‘GDynArray::Push(char)’, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: GBase.h:549:26: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 549 | fArray[fCount-1] = item; | ^ In function ‘GRealloc(void**, unsigned long)’, inlined from ‘GDynArray::Clear()’ at GBase.h:633:6, inlined from ‘GDynArray::growTo(unsigned int)’ at GBase.h:577:28, inlined from ‘GDynArray::Grow()’ at GBase.h:544:12, inlined from ‘GDynArray::Push(char)’ at GBase.h:564:6, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: GBase.h:272:20: note: at offset 4294967295 into destination object of size 16 allocated by ‘malloc’ 272 | void *p=malloc(size); | ~~~~~~^~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gcdb.cpp -o libgclib_la-gcdb.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GStr.lo `test -f 'GStr.cpp' || echo './'`GStr.cpp In file included from gff.cpp:1: gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 242 | struct { | ^ gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 245 | struct { | ^ gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 343 | struct { | ^ gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 706 | struct { | ^ gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1165 | struct { | ^ /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GThreads.lo `test -f 'GThreads.cpp' || echo './'`GThreads.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gsocket.cpp -o libgclib_la-gsocket.o >/dev/null 2>&1 gff.cpp: In constructor ‘GffLine::GffLine(GffReader*, const char*)’: gff.cpp:426:19: warning: unknown escape sequence: '\%' 426 | GMessage("Warning: unexpected tab character in last column, line truncated:\n\%s\n",l); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GFastaFile.h:4, from GapAssem.h:3, from GapAssem.cpp:1: GapAssem.cpp: In member function ‘GASeq::refineClipping(GDynArray&, int, bool)’: GBase.h:176:28: warning: ‘gxpos’ may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ GapAssem.cpp:236:14: note: ‘gxpos’ was declared here 236 | int* gxpos; //mapping of positions from gseq to seq | ^~~~~ GBase.h:176:28: warning: ‘gseq’ may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ GapAssem.cpp:212:15: note: ‘gseq’ was declared here 212 | char* gseq; | ^~~~ In file included from GAlnExtend.h:6, from GAlnExtend.cpp:1: In function ‘GMalloc(void**, unsigned long)’, inlined from ‘GXMemPool::GXMemPool(int)’ at GAlnExtend.h:157:9, inlined from ‘CGreedyAlignData::CGreedyAlignData(int, int, int)’ at GAlnExtend.h:281:29: GBase.h:254:12: warning: ‘MEM[(void * *)_78]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GBase.cpp -o libgclib_la-GBase.o >/dev/null 2>&1 GAlnExtend.cpp: In function ‘color_fg(int, _IO_FILE*)’: GAlnExtend.cpp:13:35: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 13 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+30); | ^~ In function ‘color_fg(int, _IO_FILE*)’, inlined from ‘color_fg(int, _IO_FILE*)’ at GAlnExtend.cpp:11:6: GAlnExtend.cpp:13:34: note: directive argument in the range [-2147483618, 2147483647] 13 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+30); | ^~~~~ In file included from /usr/include/stdio.h:970, from GBase.h:63: In function ‘sprintf’, inlined from ‘color_fg(int, _IO_FILE*)’ at GAlnExtend.cpp:13:9, inlined from ‘color_fg(int, _IO_FILE*)’ at GAlnExtend.cpp:11:6: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 3 and 13 bytes into a destination of size 4 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ GAlnExtend.cpp: In function ‘color_bg(int, _IO_FILE*)’: GAlnExtend.cpp:19:35: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 19 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+40); | ^~ In function ‘color_bg(int, _IO_FILE*)’, inlined from ‘color_bg(int, _IO_FILE*)’ at GAlnExtend.cpp:17:6: GAlnExtend.cpp:19:34: note: directive argument in the range [-2147483608, 2147483647] 19 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+40); | ^~~~~ In function ‘sprintf’, inlined from ‘color_bg(int, _IO_FILE*)’ at GAlnExtend.cpp:19:9, inlined from ‘color_bg(int, _IO_FILE*)’ at GAlnExtend.cpp:17:6: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 3 and 13 bytes into a destination of size 4 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gstopwatch.cpp -fPIC -DPIC -o .libs/libgclib_la-gstopwatch.o In function ‘GMalloc(void**, unsigned long)’, inlined from ‘GXMemPool::GXMemPool(int)’ at GAlnExtend.h:157:9, inlined from ‘GXGreedyExtend(char const*, int, char const*, int, bool, int&, int&, CGreedyAlignData&, GXEditScript*)’ at GAlnExtend.cpp:311:50: GBase.h:254:12: warning: ‘MEM[(void * *)_196]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ In function ‘GMalloc(void**, unsigned long)’, inlined from ‘GXMemPool::GXMemPool(int)’ at GAlnExtend.h:157:9, inlined from ‘GXMemPool::getSpace(int)’ at GAlnExtend.h:195:40, inlined from ‘GXMemPool::getByteSpace(int)’ at GAlnExtend.h:209:27, inlined from ‘GXGreedyExtend(char const*, int, char const*, int, bool, int&, int&, CGreedyAlignData&, GXEditScript*)’ at GAlnExtend.cpp:473:64: GBase.h:254:12: warning: ‘MEM[(void * *)_317]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GThreads.cpp -fPIC -DPIC -o .libs/libgclib_la-GThreads.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GStr.cpp -fPIC -DPIC -o .libs/libgclib_la-GStr.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFastaIndex.cpp -o libgclib_la-GFastaIndex.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFaSeqGet.cpp -o libgclib_la-GFaSeqGet.o >/dev/null 2>&1 In function ‘GMalloc(void**, unsigned long)’, inlined from ‘FastaSeq::init(char const*, char const*, char const*, int, int)’ at GFastaFile.h:52:10, inlined from ‘FastaSeq::FastaSeq(char const*, char const*, char const*, int)’ at GFastaFile.h:127:15, inlined from ‘FastaSeq::FastaSeq(char const*, char const*, char const*, int)’ at GFastaFile.h:124:6, inlined from ‘GASeq::GASeq(char const*, int, int, int, int, char)’ at GapAssem.cpp:51:32: GBase.h:254:12: warning: ‘MEM[(void * *)this_10(D) + 24B]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gstopwatch.cpp -o libgclib_la-gstopwatch.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GThreads.cpp -o libgclib_la-GThreads.o >/dev/null 2>&1 In file included from GStr.h:5, from GStr.cpp:2: GStr.cpp: In function ‘GStr::new_data(char const*, unsigned int)’: GBase.h:176:28: warning: ‘data’ may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ GStr.cpp:38:15: note: ‘data’ was declared here 38 | Data* data; | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GapAssem.cpp -o libgclib_la-GapAssem.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GAlnExtend.cpp -o libgclib_la-GAlnExtend.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GStr.cpp -o libgclib_la-GStr.o >/dev/null 2>&1 In file included from gff.h:6: gff.cpp: In member function ‘BEDLine::BEDLine(GffReader*, char const*)’: GBase.h:176:28: warning: ‘bstart’ may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gff.cpp:242:18: note: ‘bstart’ was declared here 242 | char** bstart; | ^~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gff.cpp -o libgclib_la-gff.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -version-info 3:0 -lpthread -Wl,-z,relro -Wl,-z,now -Wl,-flto -o libgclib.la -rpath /usr/lib/aarch64-linux-gnu libgclib_la-codons.lo libgclib_la-GAlnExtend.lo libgclib_la-GapAssem.lo libgclib_la-GArgs.lo libgclib_la-GBase.lo libgclib_la-gcdb.lo libgclib_la-GCdbYank.lo libgclib_la-gdna.lo libgclib_la-GFaSeqGet.lo libgclib_la-GFastaIndex.lo libgclib_la-gff.lo libgclib_la-gsocket.lo libgclib_la-gstopwatch.lo libgclib_la-GStr.lo libgclib_la-GThreads.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o .libs/libgclib_la-codons.o .libs/libgclib_la-GAlnExtend.o .libs/libgclib_la-GapAssem.o .libs/libgclib_la-GArgs.o .libs/libgclib_la-GBase.o .libs/libgclib_la-gcdb.o .libs/libgclib_la-GCdbYank.o .libs/libgclib_la-gdna.o .libs/libgclib_la-GFaSeqGet.o .libs/libgclib_la-GFastaIndex.o .libs/libgclib_la-gff.o .libs/libgclib_la-gsocket.o .libs/libgclib_la-gstopwatch.o .libs/libgclib_la-GStr.o .libs/libgclib_la-GThreads.o -lpthread -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -flto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-flto -Wl,-soname -Wl,libgclib.so.3 -o .libs/libgclib.so.3.0.0 lto-wrapper: warning: using serial compilation of 5 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information In member function '__ct ', inlined from 'buildMSA' at GapAssem.cpp:1123:47: GapAssem.h:350:32: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 350 | columns=new GAlnColumn[len]; | ^ /usr/include/c++/14/new: In member function 'buildMSA': /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ GVec.hh: In member function 'setCapacity': GVec.hh:107:24: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 107 | fArray=new OBJ[NewCapacity]; | ^ /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ libtool: link: (cd ".libs" && rm -f "libgclib.so.3" && ln -s "libgclib.so.3.0.0" "libgclib.so.3") libtool: link: (cd ".libs" && rm -f "libgclib.so" && ln -s "libgclib.so.3.0.0" "libgclib.so") libtool: link: ar cr .libs/libgclib.a libgclib_la-codons.o libgclib_la-GAlnExtend.o libgclib_la-GapAssem.o libgclib_la-GArgs.o libgclib_la-GBase.o libgclib_la-gcdb.o libgclib_la-GCdbYank.o libgclib_la-gdna.o libgclib_la-GFaSeqGet.o libgclib_la-GFastaIndex.o libgclib_la-gff.o libgclib_la-gsocket.o libgclib_la-gstopwatch.o libgclib_la-GStr.o libgclib_la-GThreads.o libtool: link: ranlib .libs/libgclib.a libtool: link: ( cd ".libs" && rm -f "libgclib.la" && ln -s "../libgclib.la" "libgclib.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -Wl,-z,relro -Wl,-z,now -Wl,-flto -o mdtest mdtest.o libgclib.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-flto -o .libs/mdtest mdtest.o ./.libs/libgclib.so make[2]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' ./mdtest 7TEST^BCT 7 matching bases base mismatch [T] base mismatch [E] base mismatch [S] base mismatch [T] 3 base(s) deletion [BCT] make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/libgclib-0.12.7\+ds/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' make[2]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libgclib.la '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgclib.so.3.0.0 /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.so.3.0.0 libtool: install: (cd /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libgclib.so.3.0.0 libgclib.so.3 || { rm -f libgclib.so.3 && ln -s libgclib.so.3.0.0 libgclib.so.3; }; }) libtool: install: (cd /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libgclib.so.3.0.0 libgclib.so || { rm -f libgclib.so && ln -s libgclib.so.3.0.0 libgclib.so; }; }) libtool: install: /usr/bin/install -c .libs/libgclib.lai /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.la libtool: install: /usr/bin/install -c .libs/libgclib.a /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.a libtool: install: chmod 644 /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.a libtool: install: ranlib /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c mdtest '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin' libtool: warning: 'libgclib.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/mdtest /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin/mdtest /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/include' /usr/bin/install -c -m 644 GAlnExtend.h GArgs.h GBam.h GBase.h GBitVec.h GCdbYank.h GFaSeqGet.h GFastaFile.h GFastaIndex.h GResUsage.h GStr.h GThreads.h GapAssem.h codons.h config.h gcdb.h gdimg.h gdna.h gff.h gsocket.h gstopwatch.h proc_mem.h wyhash.h xxhash.h GHash.hh GHashMap.hh GIntHash.hh GIntervalTree.hh GList.hh GVec.hh khashl.hh '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/include' /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 libgclib.pc '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' make[2]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/tmp/usr/include usr \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/aarch64-linux-gnu/pkgconfig \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility set -e install -d -m 755 debian/libgclib-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libgclib3/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.a debian/libgclib-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.so debian/libgclib-dev/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.so.3 debian/libgclib3/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.so.3.0.0 debian/libgclib3/usr/lib/aarch64-linux-gnu PKGDEV=libgclib-dev PKGSHL=libgclib3 install -d -m 755 debian/libgclib-dev/usr mv debian/tmp/usr/include debian/libgclib-dev/usr install -d -m 755 debian/libgclib-dev/usr/lib/aarch64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libgclib-dev/usr/lib/aarch64-linux-gnu/pkgconfig mkdir debian/libgclib-dev/usr/include/gclib mv debian/libgclib-dev/usr/include/*.h* debian/libgclib-dev/usr/include/gclib sed -i '/PACKAGE_NAME/d' debian/libgclib-dev/usr/include/gclib/config.h # delete header files of not compiled C++ source files find debian/libgclib-dev -name gdimg.h -delete find debian/libgclib-dev -name GBam.h -delete make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' dh_installexamples chmod a-x debian/libgclib-dev/usr/share/doc/libgclib-dev/examples/* make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libgclib-dev' in '../libgclib-dev_0.12.7+ds-5_arm64.deb'. dpkg-deb: building package 'libgclib3-dbgsym' in '../libgclib3-dbgsym_0.12.7+ds-5_arm64.deb'. dpkg-deb: building package 'libgclib3' in '../libgclib3_0.12.7+ds-5_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libgclib_0.12.7+ds-5_arm64.buildinfo dpkg-genchanges --build=binary -O../libgclib_0.12.7+ds-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1003020 and its subdirectories I: Current time: Sun Nov 2 17:13:54 -12 2025 I: pbuilder-time-stamp: 1762146834 Mon Sep 30 22:50:57 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Mon Sep 30 22:50:57 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Mon Sep 30 22:50:57 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Mon Sep 30 22:50:57 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-a1jo5O' ==================================================================================== Mon Sep 30 22:50:59 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "2 libgclib unstable /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg 0.12.7+ds-5" as arguments. Mon Sep 30 22:50:59 UTC 2024 - actually running "reproducible_build.sh" (md5sum 79f74068471242981be9b3b00196cbfb) as "/tmp/jenkins-script-ouJOCk70" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Sep 30 22:50:59 UTC 2024 I: Downloading source for unstable/libgclib=0.12.7+ds-5 Reading package lists... NOTICE: 'libgclib' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libgclib.git Please use: git clone https://salsa.debian.org/med-team/libgclib.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 274 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-5 (dsc) [2331 B] Get:2 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-5 (tar) [257 kB] Get:3 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-5 (diff) [14.9 kB] Fetched 274 kB in 0s (14.1 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'libgclib' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libgclib.git Please use: git clone https://salsa.debian.org/med-team/libgclib.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 274 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-5 (dsc) [2331 B] Get:2 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-5 (tar) [257 kB] Get:3 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-5 (diff) [14.9 kB] Fetched 274 kB in 0s (14.1 MB/s) Download complete and in download only mode ============================================================================= Re-Building libgclib in unstable on arm64 on codethink04-arm64 now. Date: Mon Sep 30 23:50:59 BST 2024 Date UTC: Mon Sep 30 22:50:59 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/pbuilderrc_fuJd + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' libgclib = debian-installer -o libgclib = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' libgclib = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/pbuilderrc_fuJd --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/b2 --logfile b2/build.log libgclib_0.12.7+ds-5.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Oct 1 12:50:59 +14 2024 I: pbuilder-time-stamp: 1727736659 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libgclib_0.12.7+ds-5.dsc] I: copying [./libgclib_0.12.7+ds.orig.tar.gz] I: copying [./libgclib_0.12.7+ds-5.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Nov 8 20:32:16 2022 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libgclib_0.12.7+ds-5.dsc: no acceptable signature found dpkg-source: info: extracting libgclib in libgclib-0.12.7+ds dpkg-source: info: unpacking libgclib_0.12.7+ds.orig.tar.gz dpkg-source: info: unpacking libgclib_0.12.7+ds-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying autoconf.patch dpkg-source: info: applying CVE-2021-42006.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1786846/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Sep 30 22:51 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1786846/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1786846/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=c99bfdd955484a3cad6bee446ca4079a LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1786846 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/pbuilderrc_fuJd --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/b2 --logfile b2/build.log libgclib_0.12.7+ds-5.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1786846/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), d-shlibs dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19895 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 77.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-8 [96.6 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 d-shlibs all 0.107 [11.0 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.1 [630 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Fetched 19.4 MB in 0s (132 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19895 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-8_arm64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../15-d-shlibs_0.107_all.deb ... Unpacking d-shlibs (0.107) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.191-2_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-5_arm64.deb ... Unpacking libicu72:arm64 (72.1-5) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-5) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-2) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up d-shlibs (0.107) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1786846/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1786846/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/libgclib-0.12.7+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libgclib_0.12.7+ds-5_source.changes dpkg-buildpackage: info: source package libgclib dpkg-buildpackage: info: source version 0.12.7+ds-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' if [ -r Makefile -a -r Makefile.am ]; then dh_auto_clean; fi rm -f Makefile Makefile.in aclocal.m4 config.h.in configure debian/autoreconf.after debian/autoreconf.before find . -name "*.o" -delete make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf aclocal: warning: couldn't open directory 'config': No such file or directory libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config'. libtoolize: copying file 'config/libtool.m4' libtoolize: copying file 'config/ltoptions.m4' libtoolize: copying file 'config/ltsugar.m4' libtoolize: copying file 'config/ltversion.m4' libtoolize: copying file 'config/lt~obsolete.m4' libtoolize: Consider adding '-I config' to ACLOCAL_AMFLAGS in Makefile.am. configure.ac:30: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:30: You should run autoupdate. config/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:30: the top level configure.ac:51: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:51: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:51: the top level configure.ac:30: installing 'config/compile' configure.ac:30: installing 'config/config.guess' configure.ac:30: installing 'config/config.sub' configure.ac:18: installing 'config/install-sh' configure.ac:18: installing 'config/missing' Makefile.am: installing 'config/depcomp' dh_auto_configure ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '2222' is supported by ustar format... yes checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... 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GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate ./configure: line 17133: AX_CXXFLAGS: command not found checking for egrep... (cached) /usr/bin/grep -E checking for stdlib.h... (cached) yes checking whether make sets $(MAKE)... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating libgclib.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' make all-am make[2]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o mdtest.o mdtest.cpp /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-codons.lo `test -f 'codons.cpp' || echo './'`codons.cpp /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GAlnExtend.lo `test -f 'GAlnExtend.cpp' || echo './'`GAlnExtend.cpp /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic 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.libs/libgclib_la-GBase.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gcdb.cpp -fPIC -DPIC -o .libs/libgclib_la-gcdb.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gdna.cpp -fPIC -DPIC -o .libs/libgclib_la-gdna.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GArgs.cpp -fPIC -DPIC -o .libs/libgclib_la-GArgs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFaSeqGet.cpp -fPIC -DPIC -o .libs/libgclib_la-GFaSeqGet.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c codons.cpp -fPIC -DPIC -o .libs/libgclib_la-codons.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GAlnExtend.cpp -fPIC -DPIC -o .libs/libgclib_la-GAlnExtend.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFastaIndex.cpp -fPIC -DPIC -o .libs/libgclib_la-GFastaIndex.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gff.cpp -fPIC -DPIC -o .libs/libgclib_la-gff.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GapAssem.cpp -fPIC -DPIC -o .libs/libgclib_la-GapAssem.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GCdbYank.cpp -fPIC -DPIC -o .libs/libgclib_la-GCdbYank.o /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gsocket.lo `test -f 'gsocket.cpp' || echo './'`gsocket.cpp gcdb.cpp: In function ‘unsigned int gcdb_strlen(const char*)’: gcdb.cpp:102:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 102 | register char *t; | ^ gcdb.cpp: In constructor ‘GCdbRead::GCdbRead(int)’: gcdb.cpp:809:13: warning: comparing the result of pointer addition ‘(x + 1)’ and NULL [-Waddress] 809 | if (x + 1) { | ~~^~~ gcdb.cpp: In constructor ‘GCdbRead::GCdbRead(char*)’: gcdb.cpp:843:13: warning: comparing the result of pointer addition ‘(x + 1)’ and NULL [-Waddress] 843 | if (x + 1) { | ~~^~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gdna.cpp -o libgclib_la-gdna.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c codons.cpp -o libgclib_la-codons.o >/dev/null 2>&1 In file included from GAlnExtend.h:6, from GAlnExtend.cpp:1: In function ‘GMalloc(void**, unsigned long)’, inlined from ‘GXMemPool::GXMemPool(int)’ at GAlnExtend.h:157:9, inlined from ‘CGreedyAlignData::CGreedyAlignData(int, int, int)’ at GAlnExtend.h:281:29: GBase.h:254:12: warning: ‘MEM[(void * *)_78]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gstopwatch.lo `test -f 'gstopwatch.cpp' || echo './'`gstopwatch.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GArgs.cpp -o libgclib_la-GArgs.o >/dev/null 2>&1 In file included from GBase.cpp:1: In member function ‘GDynArray::Push(char)’, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: GBase.h:549:26: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 549 | fArray[fCount-1] = item; | ^ In function ‘GRealloc(void**, unsigned long)’, inlined from ‘GDynArray::Clear()’ at GBase.h:633:6, inlined from ‘GDynArray::growTo(unsigned int)’ at GBase.h:577:28, inlined from ‘GDynArray::Grow()’ at GBase.h:544:12, inlined from ‘GDynArray::Push(char)’ at GBase.h:564:6, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: GBase.h:280:21: note: at offset 4294967295 into destination object of size 16 allocated by ‘realloc’ 280 | void *p=realloc(*ptr,size); | ~~~~~~~^~~~~~~~~~~ In member function ‘GDynArray::Push(char)’, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: GBase.h:549:26: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 549 | fArray[fCount-1] = item; | ^ In function ‘GRealloc(void**, unsigned long)’, inlined from ‘GDynArray::Clear()’ at GBase.h:633:6, inlined from ‘GDynArray::growTo(unsigned int)’ at GBase.h:577:28, inlined from ‘GDynArray::Grow()’ at GBase.h:544:12, inlined from ‘GDynArray::Push(char)’ at GBase.h:564:6, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: GBase.h:272:20: note: at offset 4294967295 into destination object of size 16 allocated by ‘malloc’ 272 | void *p=malloc(size); | ~~~~~~^~~~~~ GAlnExtend.cpp: In function ‘color_fg(int, _IO_FILE*)’: GAlnExtend.cpp:13:35: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 13 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+30); | ^~ In function ‘color_fg(int, _IO_FILE*)’, inlined from ‘color_fg(int, _IO_FILE*)’ at GAlnExtend.cpp:11:6: GAlnExtend.cpp:13:34: note: directive argument in the range [-2147483618, 2147483647] 13 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+30); | ^~~~~ In file included from /usr/include/stdio.h:970, from GBase.h:63: In function ‘sprintf’, inlined from ‘color_fg(int, _IO_FILE*)’ at GAlnExtend.cpp:13:9, inlined from ‘color_fg(int, _IO_FILE*)’ at GAlnExtend.cpp:11:6: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 3 and 13 bytes into a destination of size 4 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ GAlnExtend.cpp: In function ‘color_bg(int, _IO_FILE*)’: GAlnExtend.cpp:19:35: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 19 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+40); | ^~ In function ‘color_bg(int, _IO_FILE*)’, inlined from ‘color_bg(int, _IO_FILE*)’ at GAlnExtend.cpp:17:6: GAlnExtend.cpp:19:34: note: directive argument in the range [-2147483608, 2147483647] 19 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+40); | ^~~~~ In function ‘sprintf’, inlined from ‘color_bg(int, _IO_FILE*)’ at GAlnExtend.cpp:19:9, inlined from ‘color_bg(int, _IO_FILE*)’ at GAlnExtend.cpp:17:6: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 3 and 13 bytes into a destination of size 4 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GCdbYank.cpp -o libgclib_la-GCdbYank.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gsocket.cpp -fPIC -DPIC -o .libs/libgclib_la-gsocket.o In function ‘GMalloc(void**, unsigned long)’, inlined from ‘GXMemPool::GXMemPool(int)’ at GAlnExtend.h:157:9, inlined from ‘GXGreedyExtend(char const*, int, char const*, int, bool, int&, int&, CGreedyAlignData&, GXEditScript*)’ at GAlnExtend.cpp:311:50: GBase.h:254:12: warning: ‘MEM[(void * *)_196]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ In function ‘GMalloc(void**, unsigned long)’, inlined from ‘GXMemPool::GXMemPool(int)’ at GAlnExtend.h:157:9, inlined from ‘GXMemPool::getSpace(int)’ at GAlnExtend.h:195:40, inlined from ‘GXMemPool::getByteSpace(int)’ at GAlnExtend.h:209:27, inlined from ‘GXGreedyExtend(char const*, int, char const*, int, bool, int&, int&, CGreedyAlignData&, GXEditScript*)’ at GAlnExtend.cpp:473:64: GBase.h:254:12: warning: ‘MEM[(void * *)_317]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ In file included from gff.cpp:1: gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 242 | struct { | ^ gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 245 | struct { | ^ gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 343 | struct { | ^ gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 706 | struct { | ^ gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1165 | struct { | ^ gff.cpp: In constructor ‘GffLine::GffLine(GffReader*, const char*)’: gff.cpp:426:19: warning: unknown escape sequence: '\%' 426 | GMessage("Warning: unexpected tab character in last column, line truncated:\n\%s\n",l); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gcdb.cpp -o libgclib_la-gcdb.o >/dev/null 2>&1 /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GStr.lo `test -f 'GStr.cpp' || echo './'`GStr.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gstopwatch.cpp -fPIC -DPIC -o .libs/libgclib_la-gstopwatch.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GBase.cpp -o libgclib_la-GBase.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFaSeqGet.cpp -o libgclib_la-GFaSeqGet.o >/dev/null 2>&1 In file included from GFastaFile.h:4, from GapAssem.h:3, from GapAssem.cpp:1: GapAssem.cpp: In member function ‘GASeq::refineClipping(GDynArray&, int, bool)’: GBase.h:176:28: warning: ‘gxpos’ may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ GapAssem.cpp:236:14: note: ‘gxpos’ was declared here 236 | int* gxpos; //mapping of positions from gseq to seq | ^~~~~ GBase.h:176:28: warning: ‘gseq’ may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ GapAssem.cpp:212:15: note: ‘gseq’ was declared here 212 | char* gseq; | ^~~~ /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GThreads.lo `test -f 'GThreads.cpp' || echo './'`GThreads.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFastaIndex.cpp -o libgclib_la-GFastaIndex.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GStr.cpp -fPIC -DPIC -o .libs/libgclib_la-GStr.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gsocket.cpp -o libgclib_la-gsocket.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gstopwatch.cpp -o libgclib_la-gstopwatch.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GThreads.cpp -fPIC -DPIC -o .libs/libgclib_la-GThreads.o In function ‘GMalloc(void**, unsigned long)’, inlined from ‘FastaSeq::init(char const*, char const*, char const*, int, int)’ at GFastaFile.h:52:10, inlined from ‘FastaSeq::FastaSeq(char const*, char const*, char const*, int)’ at GFastaFile.h:127:15, inlined from ‘FastaSeq::FastaSeq(char const*, char const*, char const*, int)’ at GFastaFile.h:124:6, inlined from ‘GASeq::GASeq(char const*, int, int, int, int, char)’ at GapAssem.cpp:51:32: GBase.h:254:12: warning: ‘MEM[(void * *)this_10(D) + 24B]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GAlnExtend.cpp -o libgclib_la-GAlnExtend.o >/dev/null 2>&1 In file included from GStr.h:5, from GStr.cpp:2: GStr.cpp: In function ‘GStr::new_data(char const*, unsigned int)’: GBase.h:176:28: warning: ‘data’ may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ GStr.cpp:38:15: note: ‘data’ was declared here 38 | Data* data; | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GThreads.cpp -o libgclib_la-GThreads.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GapAssem.cpp -o libgclib_la-GapAssem.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GStr.cpp -o libgclib_la-GStr.o >/dev/null 2>&1 In file included from gff.h:6: gff.cpp: In member function ‘BEDLine::BEDLine(GffReader*, char const*)’: GBase.h:176:28: warning: ‘bstart’ may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gff.cpp:242:18: note: ‘bstart’ was declared here 242 | char** bstart; | ^~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gff.cpp -o libgclib_la-gff.o >/dev/null 2>&1 /bin/sh ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -version-info 3:0 -lpthread -Wl,-z,relro -Wl,-z,now -Wl,-flto -o libgclib.la -rpath /usr/lib/aarch64-linux-gnu libgclib_la-codons.lo libgclib_la-GAlnExtend.lo libgclib_la-GapAssem.lo libgclib_la-GArgs.lo libgclib_la-GBase.lo libgclib_la-gcdb.lo libgclib_la-GCdbYank.lo libgclib_la-gdna.lo libgclib_la-GFaSeqGet.lo libgclib_la-GFastaIndex.lo libgclib_la-gff.lo libgclib_la-gsocket.lo libgclib_la-gstopwatch.lo libgclib_la-GStr.lo libgclib_la-GThreads.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o .libs/libgclib_la-codons.o .libs/libgclib_la-GAlnExtend.o .libs/libgclib_la-GapAssem.o .libs/libgclib_la-GArgs.o .libs/libgclib_la-GBase.o .libs/libgclib_la-gcdb.o .libs/libgclib_la-GCdbYank.o .libs/libgclib_la-gdna.o .libs/libgclib_la-GFaSeqGet.o .libs/libgclib_la-GFastaIndex.o .libs/libgclib_la-gff.o .libs/libgclib_la-gsocket.o .libs/libgclib_la-gstopwatch.o .libs/libgclib_la-GStr.o .libs/libgclib_la-GThreads.o -lpthread -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -flto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-flto -Wl,-soname -Wl,libgclib.so.3 -o .libs/libgclib.so.3.0.0 lto-wrapper: warning: using serial compilation of 5 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information In member function '__ct ', inlined from 'buildMSA' at GapAssem.cpp:1123:47: GapAssem.h:350:32: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 350 | columns=new GAlnColumn[len]; | ^ /usr/include/c++/14/new: In member function 'buildMSA': /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ GVec.hh: In member function 'setCapacity': GVec.hh:107:24: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 107 | fArray=new OBJ[NewCapacity]; | ^ /usr/include/c++/14/new:133:26: note: in a call to allocation function 'operator new []' declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ libtool: link: (cd ".libs" && rm -f "libgclib.so.3" && ln -s "libgclib.so.3.0.0" "libgclib.so.3") libtool: link: (cd ".libs" && rm -f "libgclib.so" && ln -s "libgclib.so.3.0.0" "libgclib.so") libtool: link: ar cr .libs/libgclib.a libgclib_la-codons.o libgclib_la-GAlnExtend.o libgclib_la-GapAssem.o libgclib_la-GArgs.o libgclib_la-GBase.o libgclib_la-gcdb.o libgclib_la-GCdbYank.o libgclib_la-gdna.o libgclib_la-GFaSeqGet.o libgclib_la-GFastaIndex.o libgclib_la-gff.o libgclib_la-gsocket.o libgclib_la-gstopwatch.o libgclib_la-GStr.o libgclib_la-GThreads.o libtool: link: ranlib .libs/libgclib.a libtool: link: ( cd ".libs" && rm -f "libgclib.la" && ln -s "../libgclib.la" "libgclib.la" ) /bin/sh ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -Wl,-z,relro -Wl,-z,now -Wl,-flto -o mdtest mdtest.o libgclib.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-flto -o .libs/mdtest mdtest.o ./.libs/libgclib.so make[2]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' ./mdtest 7TEST^BCT 7 matching bases base mismatch [T] base mismatch [E] base mismatch [S] base mismatch [T] 3 base(s) deletion [BCT] make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/libgclib-0.12.7\+ds/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' make[2]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/sh ./libtool --mode=install /usr/bin/install -c libgclib.la '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgclib.so.3.0.0 /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.so.3.0.0 libtool: install: (cd /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libgclib.so.3.0.0 libgclib.so.3 || { rm -f libgclib.so.3 && ln -s libgclib.so.3.0.0 libgclib.so.3; }; }) libtool: install: (cd /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libgclib.so.3.0.0 libgclib.so || { rm -f libgclib.so && ln -s libgclib.so.3.0.0 libgclib.so; }; }) libtool: install: /usr/bin/install -c .libs/libgclib.lai /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.la libtool: install: /usr/bin/install -c .libs/libgclib.a /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.a libtool: install: chmod 644 /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.a libtool: install: ranlib /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin' /bin/sh ./libtool --mode=install /usr/bin/install -c mdtest '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin' libtool: warning: 'libgclib.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/mdtest /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin/mdtest /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/include' /usr/bin/install -c -m 644 GAlnExtend.h GArgs.h GBam.h GBase.h GBitVec.h GCdbYank.h GFaSeqGet.h GFastaFile.h GFastaIndex.h GResUsage.h GStr.h GThreads.h GapAssem.h codons.h config.h gcdb.h gdimg.h gdna.h gff.h gsocket.h gstopwatch.h proc_mem.h wyhash.h xxhash.h GHash.hh GHashMap.hh GIntHash.hh GIntervalTree.hh GList.hh GVec.hh khashl.hh '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/include' /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 libgclib.pc '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' make[2]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/tmp/usr/include usr \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/aarch64-linux-gnu/pkgconfig \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility set -e install -d -m 755 debian/libgclib-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libgclib3/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.a debian/libgclib-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.so debian/libgclib-dev/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.so.3 debian/libgclib3/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.so.3.0.0 debian/libgclib3/usr/lib/aarch64-linux-gnu PKGDEV=libgclib-dev PKGSHL=libgclib3 install -d -m 755 debian/libgclib-dev/usr mv debian/tmp/usr/include debian/libgclib-dev/usr install -d -m 755 debian/libgclib-dev/usr/lib/aarch64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libgclib-dev/usr/lib/aarch64-linux-gnu/pkgconfig mkdir debian/libgclib-dev/usr/include/gclib mv debian/libgclib-dev/usr/include/*.h* debian/libgclib-dev/usr/include/gclib sed -i '/PACKAGE_NAME/d' debian/libgclib-dev/usr/include/gclib/config.h # delete header files of not compiled C++ source files find debian/libgclib-dev -name gdimg.h -delete find debian/libgclib-dev -name GBam.h -delete make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' dh_installexamples chmod a-x debian/libgclib-dev/usr/share/doc/libgclib-dev/examples/* make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libgclib-dev' in '../libgclib-dev_0.12.7+ds-5_arm64.deb'. dpkg-deb: building package 'libgclib3' in '../libgclib3_0.12.7+ds-5_arm64.deb'. dpkg-deb: building package 'libgclib3-dbgsym' in '../libgclib3-dbgsym_0.12.7+ds-5_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libgclib_0.12.7+ds-5_arm64.buildinfo dpkg-genchanges --build=binary -O../libgclib_0.12.7+ds-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1786846/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1786846/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1786846 and its subdirectories I: Current time: Tue Oct 1 12:52:16 +14 2024 I: pbuilder-time-stamp: 1727736736 + false + set +x Mon Sep 30 22:52:16 UTC 2024 I: Signing ./b2/libgclib_0.12.7+ds-5_arm64.buildinfo as libgclib_0.12.7+ds-5_arm64.buildinfo.asc Mon Sep 30 22:52:16 UTC 2024 I: Signed ./b2/libgclib_0.12.7+ds-5_arm64.buildinfo as ./b2/libgclib_0.12.7+ds-5_arm64.buildinfo.asc Mon Sep 30 22:52:16 UTC 2024 - build #2 for libgclib/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Mon Sep 30 22:52:16 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-ouJOCk70, removing. /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg: total 84 drwxr-xr-x 2 jenkins jenkins 4096 Sep 30 22:50 b1 drwxr-xr-x 2 jenkins jenkins 4096 Sep 30 22:52 b2 -rw-r--r-- 1 jenkins jenkins 2331 Nov 8 2022 libgclib_0.12.7+ds-5.dsc -rw------- 1 jenkins jenkins 67883 Sep 30 22:50 rbuildlog.KCioFy7 /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/b1: total 1124 -rw-r--r-- 1 jenkins jenkins 64110 Sep 30 22:50 build.log -rw-r--r-- 1 jenkins jenkins 270432 Sep 30 22:50 libgclib-dev_0.12.7+ds-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 612404 Sep 30 22:50 libgclib3-dbgsym_0.12.7+ds-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 134668 Sep 30 22:50 libgclib3_0.12.7+ds-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 14920 Sep 30 22:50 libgclib_0.12.7+ds-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2331 Sep 30 22:50 libgclib_0.12.7+ds-5.dsc -rw-r--r-- 1 jenkins jenkins 5768 Sep 30 22:50 libgclib_0.12.7+ds-5_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6650 Sep 30 22:50 libgclib_0.12.7+ds-5_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1980 Sep 30 22:50 libgclib_0.12.7+ds-5_arm64.changes -rw-r--r-- 1 jenkins jenkins 1473 Sep 30 22:50 libgclib_0.12.7+ds-5_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/b2: total 1112 -rw-r--r-- 1 jenkins jenkins 66017 Sep 30 22:52 build.log -rw-r--r-- 1 jenkins jenkins 270432 Sep 30 22:52 libgclib-dev_0.12.7+ds-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 612404 Sep 30 22:52 libgclib3-dbgsym_0.12.7+ds-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 134668 Sep 30 22:52 libgclib3_0.12.7+ds-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 14920 Sep 30 22:52 libgclib_0.12.7+ds-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2331 Sep 30 22:52 libgclib_0.12.7+ds-5.dsc -rw-r--r-- 1 jenkins jenkins 5768 Sep 30 22:52 libgclib_0.12.7+ds-5_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6650 Sep 30 22:52 libgclib_0.12.7+ds-5_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1980 Sep 30 22:52 libgclib_0.12.7+ds-5_arm64.changes -rw-r--r-- 1 jenkins jenkins 1473 Sep 30 22:52 libgclib_0.12.7+ds-5_source.changes Mon Sep 30 22:52:18 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Mon Sep 30 22:52:18 UTC 2024 I: libgclib_0.12.7+ds-5_arm64.changes: Format: 1.8 Date: Tue, 08 Nov 2022 21:07:26 +0100 Source: libgclib Binary: libgclib-dev libgclib3 libgclib3-dbgsym Architecture: arm64 Version: 0.12.7+ds-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: libgclib-dev - header files for Genome Code Lib (GCLib) libgclib3 - C++ library to handle biological short sequence data Changes: libgclib (0.12.7+ds-5) unstable; urgency=medium . * d/control: add myself to uploaders. * d/rules: add build option -ffat-lto-objects to restore usable code, per lintian error no-code-sections. * d/watch: fix github change; switch to git mode. * d/control: declare compliance to standards version 4.6.1. Checksums-Sha1: 0dfab77eca52007c6fdc10584f4c23217305f8c4 270432 libgclib-dev_0.12.7+ds-5_arm64.deb 1a4bf4d8a736b68dadf46517adfbc2198e7158cf 612404 libgclib3-dbgsym_0.12.7+ds-5_arm64.deb 7eb608d842156a991538c2757fe2156969cd8bc7 134668 libgclib3_0.12.7+ds-5_arm64.deb 7b5bb48a30b866134f24a98e69d89c69fce4252e 5768 libgclib_0.12.7+ds-5_arm64.buildinfo Checksums-Sha256: bca97bd45ce24887a1118809382bbda067ee836b5d3617f15d2f2265787c6579 270432 libgclib-dev_0.12.7+ds-5_arm64.deb 9ed4e0d52fab5ea94d4820b8d8bb4844c0f0809c30da1c692935d29cc26b5bcc 612404 libgclib3-dbgsym_0.12.7+ds-5_arm64.deb 60fbea11c4f1fcc95d7a22675e59a33e6b962993a8f5d60761989b622ade8e53 134668 libgclib3_0.12.7+ds-5_arm64.deb 161c15134401ccc3e584998a2382918c7e4bf3f088131cfa9bc541b4f2b38051 5768 libgclib_0.12.7+ds-5_arm64.buildinfo Files: 1d4b6c64efe21b59ec2535a12e492f12 270432 libdevel optional libgclib-dev_0.12.7+ds-5_arm64.deb 27c23b5c9e732fc158a3ef371da5d308 612404 debug optional libgclib3-dbgsym_0.12.7+ds-5_arm64.deb cfb780eca211db04d0df0a6d1510f241 134668 libs optional libgclib3_0.12.7+ds-5_arm64.deb bfcfd9f36a78a4f3c7d174a3a4a941f4 5768 science optional libgclib_0.12.7+ds-5_arm64.buildinfo removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libgclib_0.12.7+ds-5.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libgclib_0.12.7+ds-5.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/libgclib_0.12.7+ds-5.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/libgclib_0.12.7+ds-5.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/libgclib_0.12.7+ds-5_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libgclib_0.12.7+ds-5.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-09-30 22:50:56.404041046 +0000 +++ b2/build.log 2024-09-30 22:52:17.876576466 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Nov 2 17:12:47 -12 2025 -I: pbuilder-time-stamp: 1762146767 +I: Current time: Tue Oct 1 12:50:59 +14 2024 +I: pbuilder-time-stamp: 1727736659 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ dpkg-source: info: applying CVE-2021-42006.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1003020/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1786846/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 30 22:51 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1786846/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1786846/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='253e5325ca4041faad50fd50c8e94fad' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1003020' - PS1='# ' - PS2='> ' + INVOCATION_ID=c99bfdd955484a3cad6bee446ca4079a + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1786846 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/pbuilderrc_o8yK --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/b1 --logfile b1/build.log libgclib_0.12.7+ds-5.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/pbuilderrc_fuJd --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/b2 --logfile b2/build.log libgclib_0.12.7+ds-5.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink01-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1003020/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1786846/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -142,7 +174,7 @@ Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] -Fetched 19.4 MB in 0s (122 MB/s) +Fetched 19.4 MB in 0s (132 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19895 files and directories currently installed.) @@ -277,7 +309,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libgclib-0.12.7+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libgclib_0.12.7+ds-5_source.changes +I: user script /srv/workspace/pbuilder/1786846/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1786846/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libgclib-0.12.7+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libgclib_0.12.7+ds-5_source.changes dpkg-buildpackage: info: source package libgclib dpkg-buildpackage: info: source version 0.12.7+ds-5 dpkg-buildpackage: info: source distribution unstable @@ -330,8 +366,8 @@ checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking build system type... aarch64-unknown-linux-gnu @@ -435,28 +471,29 @@ make all-am make[2]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o mdtest.o mdtest.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-codons.lo `test -f 'codons.cpp' || echo './'`codons.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GAlnExtend.lo `test -f 'GAlnExtend.cpp' || echo './'`GAlnExtend.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GapAssem.lo `test -f 'GapAssem.cpp' || echo './'`GapAssem.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GArgs.lo `test -f 'GArgs.cpp' || echo './'`GArgs.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GBase.lo `test -f 'GBase.cpp' || echo './'`GBase.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gcdb.lo `test -f 'gcdb.cpp' || echo './'`gcdb.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GCdbYank.lo `test -f 'GCdbYank.cpp' || echo './'`GCdbYank.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gdna.lo `test -f 'gdna.cpp' || echo './'`gdna.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GFaSeqGet.lo `test -f 'GFaSeqGet.cpp' || echo './'`GFaSeqGet.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GFastaIndex.lo `test -f 'GFastaIndex.cpp' || echo './'`GFastaIndex.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gff.lo `test -f 'gff.cpp' || echo './'`gff.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gdna.cpp -fPIC -DPIC -o .libs/libgclib_la-gdna.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GCdbYank.cpp -fPIC -DPIC -o .libs/libgclib_la-GCdbYank.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c codons.cpp -fPIC -DPIC -o .libs/libgclib_la-codons.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GapAssem.cpp -fPIC -DPIC -o .libs/libgclib_la-GapAssem.o +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-codons.lo `test -f 'codons.cpp' || echo './'`codons.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GAlnExtend.lo `test -f 'GAlnExtend.cpp' || echo './'`GAlnExtend.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GapAssem.lo `test -f 'GapAssem.cpp' || echo './'`GapAssem.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GArgs.lo `test -f 'GArgs.cpp' || echo './'`GArgs.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GBase.lo `test -f 'GBase.cpp' || echo './'`GBase.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gcdb.lo `test -f 'gcdb.cpp' || echo './'`gcdb.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GCdbYank.lo `test -f 'GCdbYank.cpp' || echo './'`GCdbYank.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gdna.lo `test -f 'gdna.cpp' || echo './'`gdna.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GFaSeqGet.lo `test -f 'GFaSeqGet.cpp' || echo './'`GFaSeqGet.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GFastaIndex.lo `test -f 'GFastaIndex.cpp' || echo './'`GFastaIndex.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gff.lo `test -f 'gff.cpp' || echo './'`gff.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GBase.cpp -fPIC -DPIC -o .libs/libgclib_la-GBase.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gcdb.cpp -fPIC -DPIC -o .libs/libgclib_la-gcdb.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gdna.cpp -fPIC -DPIC -o .libs/libgclib_la-gdna.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GArgs.cpp -fPIC -DPIC -o .libs/libgclib_la-GArgs.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GBase.cpp -fPIC -DPIC -o .libs/libgclib_la-GBase.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFaSeqGet.cpp -fPIC -DPIC -o .libs/libgclib_la-GFaSeqGet.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c codons.cpp -fPIC -DPIC -o .libs/libgclib_la-codons.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GAlnExtend.cpp -fPIC -DPIC -o .libs/libgclib_la-GAlnExtend.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gff.cpp -fPIC -DPIC -o .libs/libgclib_la-gff.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFastaIndex.cpp -fPIC -DPIC -o .libs/libgclib_la-GFastaIndex.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFaSeqGet.cpp -fPIC -DPIC -o .libs/libgclib_la-GFaSeqGet.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gff.cpp -fPIC -DPIC -o .libs/libgclib_la-gff.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GapAssem.cpp -fPIC -DPIC -o .libs/libgclib_la-GapAssem.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GCdbYank.cpp -fPIC -DPIC -o .libs/libgclib_la-GCdbYank.o +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gsocket.lo `test -f 'gsocket.cpp' || echo './'`gsocket.cpp gcdb.cpp: In function ‘unsigned int gcdb_strlen(const char*)’: gcdb.cpp:102:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 102 | register char *t; @@ -471,11 +508,16 @@ | ~~^~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gdna.cpp -o libgclib_la-gdna.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c codons.cpp -o libgclib_la-codons.o >/dev/null 2>&1 -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gsocket.lo `test -f 'gsocket.cpp' || echo './'`gsocket.cpp +In file included from GAlnExtend.h:6, + from GAlnExtend.cpp:1: +In function ‘GMalloc(void**, unsigned long)’, + inlined from ‘GXMemPool::GXMemPool(int)’ at GAlnExtend.h:157:9, + inlined from ‘CGreedyAlignData::CGreedyAlignData(int, int, int)’ at GAlnExtend.h:281:29: +GBase.h:254:12: warning: ‘MEM[(void * *)_78]’ may be used uninitialized [-Wmaybe-uninitialized] + 254 | return *ptr!=NULL; + | ^~~~ +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gstopwatch.lo `test -f 'gstopwatch.cpp' || echo './'`gstopwatch.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GArgs.cpp -o libgclib_la-GArgs.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GCdbYank.cpp -o libgclib_la-GCdbYank.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gsocket.cpp -fPIC -DPIC -o .libs/libgclib_la-gsocket.o -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gstopwatch.lo `test -f 'gstopwatch.cpp' || echo './'`gstopwatch.cpp In file included from GBase.cpp:1: In member function ‘GDynArray::Push(char)’, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: @@ -505,55 +547,6 @@ GBase.h:272:20: note: at offset 4294967295 into destination object of size 16 allocated by ‘malloc’ 272 | void *p=malloc(size); | ~~~~~~^~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gcdb.cpp -o libgclib_la-gcdb.o >/dev/null 2>&1 -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GStr.lo `test -f 'GStr.cpp' || echo './'`GStr.cpp -In file included from gff.cpp:1: -gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 242 | struct { - | ^ -gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 245 | struct { - | ^ -gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 343 | struct { - | ^ -gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 706 | struct { - | ^ -gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] - 1165 | struct { - | ^ -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GThreads.lo `test -f 'GThreads.cpp' || echo './'`GThreads.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gsocket.cpp -o libgclib_la-gsocket.o >/dev/null 2>&1 -gff.cpp: In constructor ‘GffLine::GffLine(GffReader*, const char*)’: -gff.cpp:426:19: warning: unknown escape sequence: '\%' - 426 | GMessage("Warning: unexpected tab character in last column, line truncated:\n\%s\n",l); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from GFastaFile.h:4, - from GapAssem.h:3, - from GapAssem.cpp:1: -GapAssem.cpp: In member function ‘GASeq::refineClipping(GDynArray&, int, bool)’: -GBase.h:176:28: warning: ‘gxpos’ may be used uninitialized [-Wmaybe-uninitialized] - 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ - | ^~ -GapAssem.cpp:236:14: note: ‘gxpos’ was declared here - 236 | int* gxpos; //mapping of positions from gseq to seq - | ^~~~~ -GBase.h:176:28: warning: ‘gseq’ may be used uninitialized [-Wmaybe-uninitialized] - 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ - | ^~ -GapAssem.cpp:212:15: note: ‘gseq’ was declared here - 212 | char* gseq; - | ^~~~ -In file included from GAlnExtend.h:6, - from GAlnExtend.cpp:1: -In function ‘GMalloc(void**, unsigned long)’, - inlined from ‘GXMemPool::GXMemPool(int)’ at GAlnExtend.h:157:9, - inlined from ‘CGreedyAlignData::CGreedyAlignData(int, int, int)’ at GAlnExtend.h:281:29: -GBase.h:254:12: warning: ‘MEM[(void * *)_78]’ may be used uninitialized [-Wmaybe-uninitialized] - 254 | return *ptr!=NULL; - | ^~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GBase.cpp -o libgclib_la-GBase.o >/dev/null 2>&1 GAlnExtend.cpp: In function ‘color_fg(int, _IO_FILE*)’: GAlnExtend.cpp:13:35: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 13 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+30); @@ -594,7 +587,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gstopwatch.cpp -fPIC -DPIC -o .libs/libgclib_la-gstopwatch.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GCdbYank.cpp -o libgclib_la-GCdbYank.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gsocket.cpp -fPIC -DPIC -o .libs/libgclib_la-gsocket.o In function ‘GMalloc(void**, unsigned long)’, inlined from ‘GXMemPool::GXMemPool(int)’ at GAlnExtend.h:157:9, inlined from ‘GXGreedyExtend(char const*, int, char const*, int, bool, int&, int&, CGreedyAlignData&, GXEditScript*)’ at GAlnExtend.cpp:311:50: @@ -609,10 +603,53 @@ GBase.h:254:12: warning: ‘MEM[(void * *)_317]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GThreads.cpp -fPIC -DPIC -o .libs/libgclib_la-GThreads.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GStr.cpp -fPIC -DPIC -o .libs/libgclib_la-GStr.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFastaIndex.cpp -o libgclib_la-GFastaIndex.o >/dev/null 2>&1 +In file included from gff.cpp:1: +gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] + 242 | struct { + | ^ +gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] + 245 | struct { + | ^ +gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] + 343 | struct { + | ^ +gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] + 706 | struct { + | ^ +gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] + 1165 | struct { + | ^ +gff.cpp: In constructor ‘GffLine::GffLine(GffReader*, const char*)’: +gff.cpp:426:19: warning: unknown escape sequence: '\%' + 426 | GMessage("Warning: unexpected tab character in last column, line truncated:\n\%s\n",l); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gcdb.cpp -o libgclib_la-gcdb.o >/dev/null 2>&1 +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GStr.lo `test -f 'GStr.cpp' || echo './'`GStr.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gstopwatch.cpp -fPIC -DPIC -o .libs/libgclib_la-gstopwatch.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GBase.cpp -o libgclib_la-GBase.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFaSeqGet.cpp -o libgclib_la-GFaSeqGet.o >/dev/null 2>&1 +In file included from GFastaFile.h:4, + from GapAssem.h:3, + from GapAssem.cpp:1: +GapAssem.cpp: In member function ‘GASeq::refineClipping(GDynArray&, int, bool)’: +GBase.h:176:28: warning: ‘gxpos’ may be used uninitialized [-Wmaybe-uninitialized] + 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ + | ^~ +GapAssem.cpp:236:14: note: ‘gxpos’ was declared here + 236 | int* gxpos; //mapping of positions from gseq to seq + | ^~~~~ +GBase.h:176:28: warning: ‘gseq’ may be used uninitialized [-Wmaybe-uninitialized] + 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ + | ^~ +GapAssem.cpp:212:15: note: ‘gseq’ was declared here + 212 | char* gseq; + | ^~~~ +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GThreads.lo `test -f 'GThreads.cpp' || echo './'`GThreads.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFastaIndex.cpp -o libgclib_la-GFastaIndex.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GStr.cpp -fPIC -DPIC -o .libs/libgclib_la-GStr.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gsocket.cpp -o libgclib_la-gsocket.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gstopwatch.cpp -o libgclib_la-gstopwatch.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GThreads.cpp -fPIC -DPIC -o .libs/libgclib_la-GThreads.o In function ‘GMalloc(void**, unsigned long)’, inlined from ‘FastaSeq::init(char const*, char const*, char const*, int, int)’ at GFastaFile.h:52:10, inlined from ‘FastaSeq::FastaSeq(char const*, char const*, char const*, int)’ at GFastaFile.h:127:15, @@ -621,8 +658,7 @@ GBase.h:254:12: warning: ‘MEM[(void * *)this_10(D) + 24B]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gstopwatch.cpp -o libgclib_la-gstopwatch.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GThreads.cpp -o libgclib_la-GThreads.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GAlnExtend.cpp -o libgclib_la-GAlnExtend.o >/dev/null 2>&1 In file included from GStr.h:5, from GStr.cpp:2: GStr.cpp: In function ‘GStr::new_data(char const*, unsigned int)’: @@ -632,8 +668,8 @@ GStr.cpp:38:15: note: ‘data’ was declared here 38 | Data* data; | ^~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GThreads.cpp -o libgclib_la-GThreads.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GapAssem.cpp -o libgclib_la-GapAssem.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GAlnExtend.cpp -o libgclib_la-GAlnExtend.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GStr.cpp -o libgclib_la-GStr.o >/dev/null 2>&1 In file included from gff.h:6: gff.cpp: In member function ‘BEDLine::BEDLine(GffReader*, char const*)’: @@ -644,7 +680,7 @@ 242 | char** bstart; | ^~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gff.cpp -o libgclib_la-gff.o >/dev/null 2>&1 -/bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -version-info 3:0 -lpthread -Wl,-z,relro -Wl,-z,now -Wl,-flto -o libgclib.la -rpath /usr/lib/aarch64-linux-gnu libgclib_la-codons.lo libgclib_la-GAlnExtend.lo libgclib_la-GapAssem.lo libgclib_la-GArgs.lo libgclib_la-GBase.lo libgclib_la-gcdb.lo libgclib_la-GCdbYank.lo libgclib_la-gdna.lo libgclib_la-GFaSeqGet.lo libgclib_la-GFastaIndex.lo libgclib_la-gff.lo libgclib_la-gsocket.lo libgclib_la-gstopwatch.lo libgclib_la-GStr.lo libgclib_la-GThreads.lo +/bin/sh ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -version-info 3:0 -lpthread -Wl,-z,relro -Wl,-z,now -Wl,-flto -o libgclib.la -rpath /usr/lib/aarch64-linux-gnu libgclib_la-codons.lo libgclib_la-GAlnExtend.lo libgclib_la-GapAssem.lo libgclib_la-GArgs.lo libgclib_la-GBase.lo libgclib_la-gcdb.lo libgclib_la-GCdbYank.lo libgclib_la-gdna.lo libgclib_la-GFaSeqGet.lo libgclib_la-GFastaIndex.lo libgclib_la-gff.lo libgclib_la-gsocket.lo libgclib_la-gstopwatch.lo libgclib_la-GStr.lo libgclib_la-GThreads.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o .libs/libgclib_la-codons.o .libs/libgclib_la-GAlnExtend.o .libs/libgclib_la-GapAssem.o .libs/libgclib_la-GArgs.o .libs/libgclib_la-GBase.o .libs/libgclib_la-gcdb.o .libs/libgclib_la-GCdbYank.o .libs/libgclib_la-gdna.o .libs/libgclib_la-GFaSeqGet.o .libs/libgclib_la-GFastaIndex.o .libs/libgclib_la-gff.o .libs/libgclib_la-gsocket.o .libs/libgclib_la-gstopwatch.o .libs/libgclib_la-GStr.o .libs/libgclib_la-GThreads.o -lpthread -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -flto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-flto -Wl,-soname -Wl,libgclib.so.3 -o .libs/libgclib.so.3.0.0 lto-wrapper: warning: using serial compilation of 5 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information @@ -669,7 +705,7 @@ libtool: link: ar cr .libs/libgclib.a libgclib_la-codons.o libgclib_la-GAlnExtend.o libgclib_la-GapAssem.o libgclib_la-GArgs.o libgclib_la-GBase.o libgclib_la-gcdb.o libgclib_la-GCdbYank.o libgclib_la-gdna.o libgclib_la-GFaSeqGet.o libgclib_la-GFastaIndex.o libgclib_la-gff.o libgclib_la-gsocket.o libgclib_la-gstopwatch.o libgclib_la-GStr.o libgclib_la-GThreads.o libtool: link: ranlib .libs/libgclib.a libtool: link: ( cd ".libs" && rm -f "libgclib.la" && ln -s "../libgclib.la" "libgclib.la" ) -/bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -Wl,-z,relro -Wl,-z,now -Wl,-flto -o mdtest mdtest.o libgclib.la +/bin/sh ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -Wl,-z,relro -Wl,-z,now -Wl,-flto -o mdtest mdtest.o libgclib.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-flto -o .libs/mdtest mdtest.o ./.libs/libgclib.so make[2]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' @@ -690,7 +726,7 @@ make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' make[2]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu' - /bin/bash ./libtool --mode=install /usr/bin/install -c libgclib.la '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu' + /bin/sh ./libtool --mode=install /usr/bin/install -c libgclib.la '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgclib.so.3.0.0 /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.so.3.0.0 libtool: install: (cd /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libgclib.so.3.0.0 libgclib.so.3 || { rm -f libgclib.so.3 && ln -s libgclib.so.3.0.0 libgclib.so.3; }; }) libtool: install: (cd /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libgclib.so.3.0.0 libgclib.so || { rm -f libgclib.so && ln -s libgclib.so.3.0.0 libgclib.so; }; }) @@ -700,7 +736,7 @@ libtool: install: ranlib /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin' - /bin/bash ./libtool --mode=install /usr/bin/install -c mdtest '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin' + /bin/sh ./libtool --mode=install /usr/bin/install -c mdtest '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin' libtool: warning: 'libgclib.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/mdtest /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin/mdtest /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/include' @@ -766,8 +802,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'libgclib-dev' in '../libgclib-dev_0.12.7+ds-5_arm64.deb'. -dpkg-deb: building package 'libgclib3-dbgsym' in '../libgclib3-dbgsym_0.12.7+ds-5_arm64.deb'. dpkg-deb: building package 'libgclib3' in '../libgclib3_0.12.7+ds-5_arm64.deb'. +dpkg-deb: building package 'libgclib3-dbgsym' in '../libgclib3-dbgsym_0.12.7+ds-5_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libgclib_0.12.7+ds-5_arm64.buildinfo dpkg-genchanges --build=binary -O../libgclib_0.12.7+ds-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -775,12 +811,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1786846/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1786846/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1003020 and its subdirectories -I: Current time: Sun Nov 2 17:13:54 -12 2025 -I: pbuilder-time-stamp: 1762146834 +I: removing directory /srv/workspace/pbuilder/1786846 and its subdirectories +I: Current time: Tue Oct 1 12:52:16 +14 2024 +I: pbuilder-time-stamp: 1727736736 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libgclib_0.12.7+ds-5.diff: 87.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libgclib_0.12.7+ds-5.diff.gz b2/build.log: 81.7% -- replaced with stdout Compressing the 1st log... b1/build.log: 82.2% -- replaced with stdout Mon Sep 30 22:52:20 UTC 2024 I: diffoscope 278 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_libgclib_unstable_arm64_1727736740 + touch /var/log/reproducible-builds/diffoscope_stamp_libgclib_unstable_arm64_1727736740 + RESULT=0 + systemd-run '--description=diffoscope on libgclib/0.12.7+ds-5 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_3-57537 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg --run-session -c jenkins-reproducible-unstable-diffoscope-8edc0058-c8ff-486c-9310-bfe01f2455c1 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/dbd-tmp-M8HtXh9 ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/libgclib_0.12.7+ds-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/libgclib_0.12.7+ds-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/libgclib_0.12.7+ds-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/b1/libgclib_0.12.7+ds-5_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/b2/libgclib_0.12.7+ds-5_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_3-57537.service Warning: program compiled against libxml 212 using older 209 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/libgclib_0.12.7+ds-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/libgclib_0.12.7+ds-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/libgclib_0.12.7+ds-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/b1/libgclib_0.12.7+ds-5_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Hd74qdTg/b2/libgclib_0.12.7+ds-5_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.415s) 0.415s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.030s) 0.030s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 765ms CPU time consumed: 763ms _ _ _ _ _ _ | (_) |__ __ _ ___| (_) |__ | | | '_ \ / _` |/ __| | | '_ \ | | | |_) | (_| | (__| | | |_) | |_|_|_.__/ \__, |\___|_|_|_.__/ |___/ Mon Sep 30 22:52:21 UTC 2024 I: diffoscope 278 found no differences in the changes files, and a .buildinfo file also exists. Mon Sep 30 22:52:21 UTC 2024 I: libgclib from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-09-30 22:52:21] INFO: Starting at 2024-09-30 22:52:21.965699 [2024-09-30 22:52:22] INFO: Generating the pages of 1 package(s) [2024-09-30 22:52:22] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/libgclib didn't produce a buildlog, even though it has been built. [2024-09-30 22:52:22] INFO: Finished at 2024-09-30 22:52:22.413220, took: 0:00:00.447530 Mon Sep 30 22:52:22 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/libgclib.html Mon Sep 30 22:52:22 UTC 2024 I: Submitting .buildinfo files to external archives: Mon Sep 30 22:52:22 UTC 2024 I: Submitting 8.0K b1/libgclib_0.12.7+ds-5_arm64.buildinfo.asc https://buildinfo.debian.net/7b5bb48a30b866134f24a98e69d89c69fce4252e/libgclib_0.12.7+ds-5_arm64 Mon Sep 30 22:52:23 UTC 2024 I: Submitting 8.0K b2/libgclib_0.12.7+ds-5_arm64.buildinfo.asc https://buildinfo.debian.net/d935ad3595e2b95946f8f41f4f050dd2384f39e0/libgclib_0.12.7+ds-5_arm64 Mon Sep 30 22:52:24 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Sep 30 22:52:24 UTC 2024 I: Done submitting .buildinfo files. Mon Sep 30 22:52:24 UTC 2024 I: Removing signed libgclib_0.12.7+ds-5_arm64.buildinfo.asc files: removed './b1/libgclib_0.12.7+ds-5_arm64.buildinfo.asc' removed './b2/libgclib_0.12.7+ds-5_arm64.buildinfo.asc' 1727736744 arm64 unstable libgclib Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libgclib_0.12.7+ds-5.rbuild.log: 79.5% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libgclib_0.12.7+ds-5.rbuild.log.gz [2024-09-30 22:52:24] INFO: Starting at 2024-09-30 22:52:24.975594 [2024-09-30 22:52:25] INFO: Generating the pages of 1 package(s) [2024-09-30 22:52:25] INFO: Finished at 2024-09-30 22:52:25.421891, took: 0:00:00.446306 All cleanup done. Mon Sep 30 22:52:25 UTC 2024 - total duration: 0h 2m 56s. Mon Sep 30 22:52:25 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-2rXm75TF, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 3min 239ms CPU time consumed: 8.179s