Running as unit: rb-build-arm64_6-89754.service ==================================================================================== Wed Apr 23 18:33:51 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_6) on jenkins, called using "codethink03-arm64 codethink04-arm64" as arguments. Wed Apr 23 18:33:51 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-A04eYs9n" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Apr 23 18:33:51 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Wed Apr 23 18:33:51 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-VDfsmY' Wed Apr 23 18:33:52 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Wed Apr 23 18:33:52 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-eaZKaF' 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 codethink03-arm64.debian.net. 2nd build will be done on codethink04-arm64.debian.net. ============================================================================= Wed Apr 23 18:34:16 UTC 2025 I: starting to build libgclib/unstable/arm64 on jenkins on '2025-04-23 18:33' Wed Apr 23 18:34:16 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_6/89754/console.log 1745433256 arm64 unstable libgclib Wed Apr 23 18:34:16 UTC 2025 I: Downloading source for unstable/libgclib=0.12.7+ds-6 --2025-04-23 18:34:16-- http://deb.debian.org/debian/pool/main/libg/libgclib/libgclib_0.12.7%2bds-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2332 (2.3K) [text/prs.lines.tag] Saving to: ‘libgclib_0.12.7+ds-6.dsc’ 0K .. 100% 298M=0s 2025-04-23 18:34:16 (298 MB/s) - ‘libgclib_0.12.7+ds-6.dsc’ saved [2332/2332] --2025-04-23 18:34:16-- http://deb.debian.org/debian/pool/main/libg/libgclib/libgclib_0.12.7%2bds-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2332 (2.3K) [text/prs.lines.tag] Saving to: ‘libgclib_0.12.7+ds-6.dsc’ 0K .. 100% 298M=0s 2025-04-23 18:34:16 (298 MB/s) - ‘libgclib_0.12.7+ds-6.dsc’ saved [2332/2332] Wed Apr 23 18:34:16 UTC 2025 I: libgclib_0.12.7+ds-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libgclib Binary: libgclib-dev, libgclib3 Architecture: any Version: 0.12.7+ds-6 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Michael R. Crusoe , Étienne Mollier Homepage: https://github.com/gpertea/gclib Standards-Version: 4.7.2 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 2a242f6d4fb055134772975d3d65e8fb4a6bc2a7 15016 libgclib_0.12.7+ds-6.debian.tar.xz Checksums-Sha256: d9e5d89b1f9c696dac329a2788c535e49fabde1fec3524b6882c00309d1b375a 256645 libgclib_0.12.7+ds.orig.tar.gz 0a052550863c2a0b9b48e0763b39bc44dd1d7459c5793ae474eaaa8fb5346e4c 15016 libgclib_0.12.7+ds-6.debian.tar.xz Files: a65ac3ce19638a92ba492569997e46b0 256645 libgclib_0.12.7+ds.orig.tar.gz 909d4443a803ab241d3297d6c4da6139 15016 libgclib_0.12.7+ds-6.debian.tar.xz Dgit: 6c194945afc892cf5c482b895cdc57e9294cd956 debian archive/debian/0.12.7+ds-6 https://git.dgit.debian.org/libgclib -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmfAxWMUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdr+LA//TCabbhoD/fbs+11AWdqlO/Ing3ZZ FXhDpRGiVwhhou1wQRp/QYrTYA2QgXqxs/onxXrPdo2jeVxNum7QhNYnma0U6N0c p//A0Lg2inX7TqcSIXBX0gio9QahBRlfSdJUfrX/lofGROulN+mWBdn8MUX+XUSI /w8Cc97rGRe4vT4w3P3qIer+LRdQAUWi49pSokfh0R8q08THKFvn/wNthYx5MmnK ODk7hAZmhICgnGTGHIPTqTcAkVdGFMkrezosfQRekMMH+sHOJFBH+RNiGUy7Vi9O o/rSwlFSuT3vyJ7EF1O+sBExRP0e3WCs475Q3s/5KRQt1xmPUeGia6vAO3fE9IOr 82IxomH3WzAMZL/xTgfTj4bb3nOishRJxcWCVJFn/CoIVw4sbFQ++ldvTsYs91r3 IOYksZM7xwGFtDagCq5kgwpM5x1XIpNQ04wi4B5Bit1P36LWZU9NhTMIF0rTE8bF zQKZIgKqpk3sr0Bw4MKiGTKcC1fW57akWjy4EsbecZ4M7XkDugsQC4RZVYgRYvv6 rPM19R/Ur3jjaD4hKxH7a7M87wGtKWVjfsN/IJPChI5xxbjTO2+pMLE1z39fJ8ca 2x3v4P0bvfCapfqDIq+yHz72yRAtvcrjJ62we3mld3FN9vB5V9CAOPu0ZDDGRsnn +ht8FxPYDRGR+/4= =S9DH -----END PGP SIGNATURE----- Wed Apr 23 18:34:16 UTC 2025 I: Checking whether the package is not for us Wed Apr 23 18:34:16 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Wed Apr 23 18:34:16 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Wed Apr 23 18:34:16 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Wed Apr 23 18:34:16 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-Pg7QDx' ==================================================================================== Wed May 27 00:57:18 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "1 libgclib unstable /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx 0.12.7+ds-6" as arguments. Wed May 27 00:57:18 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-f49WskuG" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed May 27 00:57:18 UTC 2026 I: Downloading source for unstable/libgclib=0.12.7+ds-6 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-6 (dsc) [2332 B] Get:2 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-6 (tar) [257 kB] Get:3 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-6 (diff) [15.0 kB] Fetched 274 kB in 0s (1984 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-6 (dsc) [2332 B] Get:2 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-6 (tar) [257 kB] Get:3 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-6 (diff) [15.0 kB] Fetched 274 kB in 0s (1984 kB/s) Download complete and in download only mode ============================================================================= Building libgclib in unstable on arm64 on codethink03-arm64 now. Date: Wed May 27 01:57:18 BST 2026 Date UTC: Wed May 27 00:57:18 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue May 26 12:57:19 -12 2026 I: pbuilder-time-stamp: 1779843439 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-6.dsc] I: copying [./libgclib_0.12.7+ds.orig.tar.gz] I: copying [./libgclib_0.12.7+ds-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libgclib_0.12.7+ds-6.dsc: unsupported subcommand 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-6.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/5727/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='291b6f852c1c40608dfe440621e16c8f' 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='5727' 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.4u3Kp5Nx/pbuilderrc_BxMU --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.4u3Kp5Nx/b1 --logfile b1/build.log libgclib_0.12.7+ds-6.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 codethink03-arm64 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/5727/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 ... 19953 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} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{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 10.9 MB of archives. After unpacking 44.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-4 [93.9 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 1.4.19-8 [285 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 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 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 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 libunistring5 arm64 1.3-2 [453 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 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 13.24.2 [919 kB] Fetched 10.9 MB in 0s (76.3 MB/s) Preconfiguring packages ... 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 ... 19953 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-4_arm64.deb ... Unpacking bsdextrautils (2.41-4) ... 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_1.4.19-8_arm64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../15-d-shlibs_0.109_all.deb ... Unpacking d-shlibs (0.109) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... 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_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... 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 libunistring5:arm64. Preparing to unpack .../24-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.4_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... 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_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-1) ... Setting up d-shlibs (0.109) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... 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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-6_source.changes dpkg-buildpackage: info: source package libgclib dpkg-buildpackage: info: source version 0.12.7+ds-6 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 sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... 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 ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip 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 18474: 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=. 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.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 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 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 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 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 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 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 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 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 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 GFaSeqGet.cpp -fPIC -DPIC -o .libs/libgclib_la-GFaSeqGet.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-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 gdna.cpp -o libgclib_la-gdna.o >/dev/null 2>&1 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 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 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 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 /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); | ~~~~~~^~~~~~ 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 * *)_79]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ 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 ()); | ~~~~~~~~~~~~~~~~~ /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 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 -fPIC -DPIC -o .libs/libgclib_la-gstopwatch.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-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 gcdb.cpp -o libgclib_la-gcdb.o >/dev/null 2>&1 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 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 GStr.cpp -fPIC -DPIC -o .libs/libgclib_la-GStr.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 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 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 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 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 GFaSeqGet.cpp -o libgclib_la-GFaSeqGet.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 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -Werror=format-security -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 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) | ^ 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) | ^ 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 'libgclib3' in '../libgclib3_0.12.7+ds-6_arm64.deb'. dpkg-deb: building package 'libgclib-dev' in '../libgclib-dev_0.12.7+ds-6_arm64.deb'. dpkg-deb: building package 'libgclib3-dbgsym' in '../libgclib3-dbgsym_0.12.7+ds-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libgclib_0.12.7+ds-6_arm64.buildinfo dpkg-genchanges --build=binary -O../libgclib_0.12.7+ds-6_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/5727 and its subdirectories I: Current time: Tue May 26 12:58:29 -12 2026 I: pbuilder-time-stamp: 1779843509 Wed May 27 00:58:29 UTC 2026 I: Signing ./b1/libgclib_0.12.7+ds-6_arm64.buildinfo as libgclib_0.12.7+ds-6_arm64.buildinfo.asc Wed May 27 00:58:29 UTC 2026 I: Signed ./b1/libgclib_0.12.7+ds-6_arm64.buildinfo as ./b1/libgclib_0.12.7+ds-6_arm64.buildinfo.asc Wed May 27 00:58:29 UTC 2026 - build #1 for libgclib/unstable/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Wed May 27 00:58:29 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-f49WskuG, removing. /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Apr 23 18:35 b1 drwxr-xr-x 2 jenkins jenkins 4096 Apr 23 18:34 b2 -rw-r--r-- 1 jenkins jenkins 2332 Feb 27 20:13 libgclib_0.12.7+ds-6.dsc -rw------- 1 jenkins jenkins 3473 Apr 23 18:34 rbuildlog.SFpfUNk /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx/b1: total 1108 -rw-r--r-- 1 jenkins jenkins 63940 Apr 23 18:35 build.log -rw-r--r-- 1 jenkins jenkins 270396 Apr 23 18:35 libgclib-dev_0.12.7+ds-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 612520 Apr 23 18:35 libgclib3-dbgsym_0.12.7+ds-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 134204 Apr 23 18:35 libgclib3_0.12.7+ds-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 15016 Apr 23 18:35 libgclib_0.12.7+ds-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2332 Apr 23 18:35 libgclib_0.12.7+ds-6.dsc -rw-r--r-- 1 jenkins jenkins 5568 Apr 23 18:35 libgclib_0.12.7+ds-6_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6450 Apr 23 18:35 libgclib_0.12.7+ds-6_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1909 Apr 23 18:35 libgclib_0.12.7+ds-6_arm64.changes -rw-r--r-- 1 jenkins jenkins 1402 Apr 23 18:35 libgclib_0.12.7+ds-6_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx/b2: total 0 Wed Apr 23 18:35:30 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 26 12:57:19 -12 2026 I: pbuilder-time-stamp: 1779843439 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-6.dsc] I: copying [./libgclib_0.12.7+ds.orig.tar.gz] I: copying [./libgclib_0.12.7+ds-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libgclib_0.12.7+ds-6.dsc: unsupported subcommand 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-6.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/5727/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='291b6f852c1c40608dfe440621e16c8f' 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='5727' 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.4u3Kp5Nx/pbuilderrc_BxMU --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.4u3Kp5Nx/b1 --logfile b1/build.log libgclib_0.12.7+ds-6.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 codethink03-arm64 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/5727/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 ... 19953 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} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{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 10.9 MB of archives. After unpacking 44.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-4 [93.9 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 1.4.19-8 [285 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 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 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 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 libunistring5 arm64 1.3-2 [453 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 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 13.24.2 [919 kB] Fetched 10.9 MB in 0s (76.3 MB/s) Preconfiguring packages ... 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 ... 19953 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-4_arm64.deb ... Unpacking bsdextrautils (2.41-4) ... 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_1.4.19-8_arm64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../15-d-shlibs_0.109_all.deb ... Unpacking d-shlibs (0.109) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... 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_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... 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 libunistring5:arm64. Preparing to unpack .../24-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.4_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... 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_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-1) ... Setting up d-shlibs (0.109) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... 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 (13.24.2) ... Processing triggers for libc-bin (2.41-7) ... 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-6_source.changes dpkg-buildpackage: info: source package libgclib dpkg-buildpackage: info: source version 0.12.7+ds-6 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 sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... 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 ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip 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 18474: 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 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 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 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 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 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 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 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 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 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 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 GFaSeqGet.cpp -fPIC -DPIC -o .libs/libgclib_la-GFaSeqGet.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-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 gdna.cpp -o libgclib_la-gdna.o >/dev/null 2>&1 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 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 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 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 /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); | ~~~~~~^~~~~~ 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 * *)_79]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ 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 ()); | ~~~~~~~~~~~~~~~~~ /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 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 -fPIC -DPIC -o .libs/libgclib_la-gstopwatch.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-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 gcdb.cpp -o libgclib_la-gcdb.o >/dev/null 2>&1 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 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 GStr.cpp -fPIC -DPIC -o .libs/libgclib_la-GStr.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 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 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 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 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 GFaSeqGet.cpp -o libgclib_la-GFaSeqGet.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 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -Werror=format-security -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 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) | ^ 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) | ^ 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 'libgclib3' in '../libgclib3_0.12.7+ds-6_arm64.deb'. dpkg-deb: building package 'libgclib-dev' in '../libgclib-dev_0.12.7+ds-6_arm64.deb'. dpkg-deb: building package 'libgclib3-dbgsym' in '../libgclib3-dbgsym_0.12.7+ds-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libgclib_0.12.7+ds-6_arm64.buildinfo dpkg-genchanges --build=binary -O../libgclib_0.12.7+ds-6_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/5727 and its subdirectories I: Current time: Tue May 26 12:58:29 -12 2026 I: pbuilder-time-stamp: 1779843509 Wed Apr 23 18:35:31 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Wed Apr 23 18:35:31 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Wed Apr 23 18:35:31 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Wed Apr 23 18:35:31 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-aCG7g9' ==================================================================================== Wed Apr 23 18:35:33 UTC 2025 - 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.4u3Kp5Nx 0.12.7+ds-6" as arguments. Wed Apr 23 18:35:33 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-ZIA2JU32" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Apr 23 18:35:33 UTC 2025 I: Downloading source for unstable/libgclib=0.12.7+ds-6 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-6 (dsc) [2332 B] Get:2 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-6 (tar) [257 kB] Get:3 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-6 (diff) [15.0 kB] Fetched 274 kB in 0s (14.6 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-6 (dsc) [2332 B] Get:2 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-6 (tar) [257 kB] Get:3 http://deb.debian.org/debian unstable/main libgclib 0.12.7+ds-6 (diff) [15.0 kB] Fetched 274 kB in 0s (14.6 MB/s) Download complete and in download only mode ============================================================================= Re-Building libgclib in unstable on arm64 on codethink04-arm64 now. Date: Wed Apr 23 19:35:33 BST 2025 Date UTC: Wed Apr 23 18:35:33 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx/pbuilderrc_zkRy + 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.4u3Kp5Nx/pbuilderrc_zkRy --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.4u3Kp5Nx/b2 --logfile b2/build.log libgclib_0.12.7+ds-6.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: Thu Apr 24 08:35:33 +14 2025 I: pbuilder-time-stamp: 1745433333 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-6.dsc] I: copying [./libgclib_0.12.7+ds.orig.tar.gz] I: copying [./libgclib_0.12.7+ds-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libgclib_0.12.7+ds-6.dsc: unsupported subcommand 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-6.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/40990/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 Apr 23 18:35 /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/40990/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/40990/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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(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=791d83c23a0942e6aaccaed924b18a03 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=40990 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.4u3Kp5Nx/pbuilderrc_zkRy --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.4u3Kp5Nx/b2 --logfile b2/build.log libgclib_0.12.7+ds-6.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 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/40990/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 ... 19953 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} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{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 10.9 MB of archives. After unpacking 44.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-4 [93.9 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 1.4.19-8 [285 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 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 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 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 libunistring5 arm64 1.3-2 [453 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 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 13.24.2 [919 kB] Fetched 10.9 MB in 0s (82.4 MB/s) Preconfiguring packages ... 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 ... 19953 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-4_arm64.deb ... Unpacking bsdextrautils (2.41-4) ... 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_1.4.19-8_arm64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../15-d-shlibs_0.109_all.deb ... Unpacking d-shlibs (0.109) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... 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_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... 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 libunistring5:arm64. Preparing to unpack .../24-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.4_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... 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_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-1) ... Setting up d-shlibs (0.109) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... 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 (13.24.2) ... Processing triggers for libc-bin (2.41-7) ... 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/40990/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/40990/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-6_source.changes dpkg-buildpackage: info: source package libgclib dpkg-buildpackage: info: source version 0.12.7+ds-6 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 sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... 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... 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 ranlib... ranlib checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip 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 18474: 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 -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 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 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 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 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 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 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 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 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 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 GArgs.cpp -fPIC -DPIC -o .libs/libgclib_la-GArgs.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 codons.cpp -o libgclib_la-codons.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 gdna.cpp -o libgclib_la-gdna.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-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 GCdbYank.cpp -o libgclib_la-GCdbYank.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 * *)_79]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ 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); | ~~~~~~^~~~~~ /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 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-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 gsocket.cpp -fPIC -DPIC -o .libs/libgclib_la-gsocket.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 -o libgclib_la-GArgs.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 gcdb.cpp -o libgclib_la-gcdb.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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 gstopwatch.cpp -fPIC -DPIC -o .libs/libgclib_la-gstopwatch.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 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 GStr.cpp -fPIC -DPIC -o .libs/libgclib_la-GStr.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-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 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 GFaSeqGet.cpp -o libgclib_la-GFaSeqGet.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 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 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 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 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 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -Werror=format-security -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 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) | ^ 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) | ^ 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-6_arm64.deb'. dpkg-deb: building package 'libgclib3' in '../libgclib3_0.12.7+ds-6_arm64.deb'. dpkg-deb: building package 'libgclib3-dbgsym' in '../libgclib3-dbgsym_0.12.7+ds-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libgclib_0.12.7+ds-6_arm64.buildinfo dpkg-genchanges --build=binary -O../libgclib_0.12.7+ds-6_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/40990/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/40990/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/40990 and its subdirectories I: Current time: Thu Apr 24 08:36:41 +14 2025 I: pbuilder-time-stamp: 1745433401 + false + set +x Wed Apr 23 18:36:41 UTC 2025 I: Signing ./b2/libgclib_0.12.7+ds-6_arm64.buildinfo as libgclib_0.12.7+ds-6_arm64.buildinfo.asc Wed Apr 23 18:36:41 UTC 2025 I: Signed ./b2/libgclib_0.12.7+ds-6_arm64.buildinfo as ./b2/libgclib_0.12.7+ds-6_arm64.buildinfo.asc Wed Apr 23 18:36:41 UTC 2025 - build #2 for libgclib/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Wed Apr 23 18:36:41 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-ZIA2JU32, removing. /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx: total 84 drwxr-xr-x 2 jenkins jenkins 4096 Apr 23 18:35 b1 drwxr-xr-x 2 jenkins jenkins 4096 Apr 23 18:36 b2 -rw-r--r-- 1 jenkins jenkins 2332 Feb 27 20:13 libgclib_0.12.7+ds-6.dsc -rw------- 1 jenkins jenkins 67714 Apr 23 18:35 rbuildlog.SFpfUNk /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx/b1: total 1124 -rw-r--r-- 1 jenkins jenkins 63940 Apr 23 18:35 build.log -rw-r--r-- 1 jenkins jenkins 270396 Apr 23 18:35 libgclib-dev_0.12.7+ds-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 612520 Apr 23 18:35 libgclib3-dbgsym_0.12.7+ds-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 134204 Apr 23 18:35 libgclib3_0.12.7+ds-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 15016 Apr 23 18:35 libgclib_0.12.7+ds-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2332 Apr 23 18:35 libgclib_0.12.7+ds-6.dsc -rw-r--r-- 1 jenkins jenkins 5568 Apr 23 18:35 libgclib_0.12.7+ds-6_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6450 Apr 23 18:35 libgclib_0.12.7+ds-6_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1909 Apr 23 18:35 libgclib_0.12.7+ds-6_arm64.changes -rw-r--r-- 1 jenkins jenkins 1402 Apr 23 18:35 libgclib_0.12.7+ds-6_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx/b2: total 1112 -rw-r--r-- 1 jenkins jenkins 65839 Apr 23 18:36 build.log -rw-r--r-- 1 jenkins jenkins 270396 Apr 23 18:36 libgclib-dev_0.12.7+ds-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 612520 Apr 23 18:36 libgclib3-dbgsym_0.12.7+ds-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 134204 Apr 23 18:36 libgclib3_0.12.7+ds-6_arm64.deb -rw-r--r-- 1 jenkins jenkins 15016 Apr 23 18:36 libgclib_0.12.7+ds-6.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2332 Apr 23 18:36 libgclib_0.12.7+ds-6.dsc -rw-r--r-- 1 jenkins jenkins 5568 Apr 23 18:36 libgclib_0.12.7+ds-6_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 6450 Apr 23 18:36 libgclib_0.12.7+ds-6_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1909 Apr 23 18:36 libgclib_0.12.7+ds-6_arm64.changes -rw-r--r-- 1 jenkins jenkins 1402 Apr 23 18:36 libgclib_0.12.7+ds-6_source.changes Wed Apr 23 18:36:42 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Wed Apr 23 18:36:43 UTC 2025 I: libgclib_0.12.7+ds-6_arm64.changes: Format: 1.8 Date: Thu, 27 Feb 2025 20:55:27 +0100 Source: libgclib Binary: libgclib-dev libgclib3 libgclib3-dbgsym Architecture: arm64 Version: 0.12.7+ds-6 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 Closes: 1097188 Changes: libgclib (0.12.7+ds-6) unstable; urgency=medium . * d/libgclib3.symbols.amd64: flag some optional symbols. (Closes: #1097188) * d/control: declare compliance to standards version 4.7.2. * d/patches/*: normalize dep3 headers. Checksums-Sha1: b3492f79b9b6503f1d2a948008d661dc8df0c2be 270396 libgclib-dev_0.12.7+ds-6_arm64.deb af7d413b2c76187b6ad305b7ea4de071753077ce 612520 libgclib3-dbgsym_0.12.7+ds-6_arm64.deb f2a2d8c44a910ccc280d34c692aa32ef4b7184b9 134204 libgclib3_0.12.7+ds-6_arm64.deb 89e6dec92ef14b0edf853186135a9ffabfbeb1ea 5568 libgclib_0.12.7+ds-6_arm64.buildinfo Checksums-Sha256: fbc72e84f68591dfc979fcf7de85a20b4a63e9597518f94d1bf3cabb13451982 270396 libgclib-dev_0.12.7+ds-6_arm64.deb 30607fd7f300830108483318a9ba3e9b8c98a9480c4848a3569da134d36a26ee 612520 libgclib3-dbgsym_0.12.7+ds-6_arm64.deb db12b6fd8bd7aa7d298325ad7b6e57d8b8d118bcea2c30bab7611482d49a7580 134204 libgclib3_0.12.7+ds-6_arm64.deb ec66d74acfb6acc07969ba9c1eaf687d15b58b4fa0be09548d836ca59b4538f9 5568 libgclib_0.12.7+ds-6_arm64.buildinfo Files: c8aef7da19dd944b0f99eaba06ba2767 270396 libdevel optional libgclib-dev_0.12.7+ds-6_arm64.deb b5f0a991959a074da4f1476d1c48960b 612520 debug optional libgclib3-dbgsym_0.12.7+ds-6_arm64.deb b4ac91b82266b7710276397ce211818e 134204 libs optional libgclib3_0.12.7+ds-6_arm64.deb 3f400453173e0ac522081806bedfa521 5568 science optional libgclib_0.12.7+ds-6_arm64.buildinfo removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libgclib_0.12.7+ds-6.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libgclib_0.12.7+ds-6.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/libgclib_0.12.7+ds-6.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/libgclib_0.12.7+ds-6.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/libgclib_0.12.7+ds-6_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libgclib_0.12.7+ds-6.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-04-23 18:35:30.691770103 +0000 +++ b2/build.log 2025-04-23 18:36:42.322243648 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 26 12:57:19 -12 2026 -I: pbuilder-time-stamp: 1779843439 +I: Current time: Thu Apr 24 08:35:33 +14 2025 +I: pbuilder-time-stamp: 1745433333 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ 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/5727/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/40990/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 Apr 23 18:35 /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/40990/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/40990/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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(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='291b6f852c1c40608dfe440621e16c8f' - 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='5727' - PS1='# ' - PS2='> ' + INVOCATION_ID=791d83c23a0942e6aaccaed924b18a03 + 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=40990 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.4u3Kp5Nx/pbuilderrc_BxMU --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.4u3Kp5Nx/b1 --logfile b1/build.log libgclib_0.12.7+ds-6.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.4u3Kp5Nx/pbuilderrc_zkRy --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.4u3Kp5Nx/b2 --logfile b2/build.log libgclib_0.12.7+ds-6.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 codethink03-arm64 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/5727/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/40990/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -138,7 +170,7 @@ 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 13.24.2 [919 kB] -Fetched 10.9 MB in 0s (76.3 MB/s) +Fetched 10.9 MB in 0s (82.4 MB/s) Preconfiguring packages ... 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 ... 19953 files and directories currently installed.) @@ -273,7 +305,11 @@ 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-6_source.changes +I: user script /srv/workspace/pbuilder/40990/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/40990/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-6_source.changes dpkg-buildpackage: info: source package libgclib dpkg-buildpackage: info: source version 0.12.7+ds-6 dpkg-buildpackage: info: source distribution unstable @@ -329,8 +365,8 @@ checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... 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 @@ -434,30 +470,28 @@ 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 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-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 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 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 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 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./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 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-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 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 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 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 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 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 +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 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 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 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 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 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 GFaSeqGet.cpp -fPIC -DPIC -o .libs/libgclib_la-GFaSeqGet.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-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 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 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 GArgs.cpp -fPIC -DPIC -o .libs/libgclib_la-GArgs.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; @@ -470,11 +504,18 @@ 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 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 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 -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 -/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 +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 +/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 +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 +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 * *)_79]’ may be used uninitialized [-Wmaybe-uninitialized] + 254 | return *ptr!=NULL; + | ^~~~ 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: @@ -504,6 +545,7 @@ GBase.h:272:20: note: at offset 4294967295 into destination object of size 16 allocated by ‘malloc’ 272 | void *p=malloc(size); | ~~~~~~^~~~~~ +/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 In file included from GFastaFile.h:4, from GapAssem.h:3, from GapAssem.cpp:1: @@ -520,14 +562,9 @@ 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 * *)_79]’ 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-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 gsocket.cpp -fPIC -DPIC -o .libs/libgclib_la-gsocket.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 -o libgclib_la-GArgs.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); @@ -568,25 +605,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -/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 -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 -fPIC -DPIC -o .libs/libgclib_la-gstopwatch.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-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 gcdb.cpp -o libgclib_la-gcdb.o >/dev/null 2>&1 -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 { @@ -607,8 +626,21 @@ 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 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 GStr.cpp -fPIC -DPIC -o .libs/libgclib_la-GStr.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 gstopwatch.cpp -fPIC -DPIC -o .libs/libgclib_la-gstopwatch.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, @@ -617,11 +649,13 @@ 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 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 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 GStr.cpp -fPIC -DPIC -o .libs/libgclib_la-GStr.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-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 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 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 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 GFaSeqGet.cpp -o libgclib_la-GFaSeqGet.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 file included from GStr.h:5, from GStr.cpp:2: GStr.cpp: In function ‘GStr::new_data(char const*, unsigned int)’: @@ -632,6 +666,8 @@ 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 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 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 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: @@ -643,7 +679,7 @@ 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 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -Werror=format-security -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 GVec.hh: In member function 'setCapacity': GVec.hh:107:24: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] @@ -666,7 +702,7 @@ 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' @@ -687,7 +723,7 @@ 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; }; }) @@ -697,7 +733,7 @@ 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' @@ -762,8 +798,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libgclib3' in '../libgclib3_0.12.7+ds-6_arm64.deb'. dpkg-deb: building package 'libgclib-dev' in '../libgclib-dev_0.12.7+ds-6_arm64.deb'. +dpkg-deb: building package 'libgclib3' in '../libgclib3_0.12.7+ds-6_arm64.deb'. dpkg-deb: building package 'libgclib3-dbgsym' in '../libgclib3-dbgsym_0.12.7+ds-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libgclib_0.12.7+ds-6_arm64.buildinfo dpkg-genchanges --build=binary -O../libgclib_0.12.7+ds-6_arm64.changes @@ -772,12 +808,14 @@ 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/40990/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/40990/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/5727 and its subdirectories -I: Current time: Tue May 26 12:58:29 -12 2026 -I: pbuilder-time-stamp: 1779843509 +I: removing directory /srv/workspace/pbuilder/40990 and its subdirectories +I: Current time: Thu Apr 24 08:36:41 +14 2025 +I: pbuilder-time-stamp: 1745433401 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libgclib_0.12.7+ds-6.diff: 87.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/libgclib_0.12.7+ds-6.diff.gz b2/build.log: 81.9% -- replaced with stdout Compressing the 1st log... b1/build.log: 82.4% -- replaced with stdout Wed Apr 23 18:36:44 UTC 2025 I: diffoscope 294 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_libgclib_unstable_arm64_1745433404 + touch /var/log/reproducible-builds/diffoscope_stamp_libgclib_unstable_arm64_1745433404 + RESULT=0 + systemd-run '--description=diffoscope on libgclib/0.12.7+ds-6 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_6-89754 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx --run-session -c jenkins-reproducible-unstable-diffoscope-0fa9e584-5fad-4897-b5e1-a5129993330b -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx/dbd-tmp-keaB3MF ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx/libgclib_0.12.7+ds-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx/libgclib_0.12.7+ds-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx/libgclib_0.12.7+ds-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx/b1/libgclib_0.12.7+ds-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx/b2/libgclib_0.12.7+ds-6_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_6-89754.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx/libgclib_0.12.7+ds-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx/libgclib_0.12.7+ds-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx/libgclib_0.12.7+ds-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx/b1/libgclib_0.12.7+ds-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.4u3Kp5Nx/b2/libgclib_0.12.7+ds-6_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 diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.006s) 0.006s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 354ms CPU time consumed: 355ms _ _ _ _ _ _ | (_) |__ __ _ ___| (_) |__ | | | '_ \ / _` |/ __| | | '_ \ | | | |_) | (_| | (__| | | |_) | |_|_|_.__/ \__, |\___|_|_|_.__/ |___/ Wed Apr 23 18:36:45 UTC 2025 I: diffoscope 294 found no differences in the changes files, and a .buildinfo file also exists. Wed Apr 23 18:36:45 UTC 2025 I: libgclib from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-04-23 18:36:45] INFO: Starting at 2025-04-23 18:36:45.586537 [2025-04-23 18:36:45] INFO: Generating the pages of 1 package(s) [2025-04-23 18:36:45] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/libgclib didn't produce a buildlog, even though it has been built. [2025-04-23 18:36:45] INFO: Finished at 2025-04-23 18:36:45.943575, took: 0:00:00.357045 Wed Apr 23 18:36:46 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/libgclib.html Wed Apr 23 18:36:46 UTC 2025 I: Submitting .buildinfo files to external archives: Wed Apr 23 18:36:46 UTC 2025 I: Submitting 8.0K b1/libgclib_0.12.7+ds-6_arm64.buildinfo.asc Wed Apr 23 18:37:16 UTC 2025 E: Could not submit buildinfo from b1 to http://buildinfo.debian.net/api/submit Wed Apr 23 18:37:16 UTC 2025 I: Submitting 8.0K b2/libgclib_0.12.7+ds-6_arm64.buildinfo.asc Wed Apr 23 18:37:46 UTC 2025 E: Could not submit buildinfo from b2 to http://buildinfo.debian.net/api/submit Wed Apr 23 18:37:46 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Apr 23 18:37:46 UTC 2025 I: Done submitting .buildinfo files. Wed Apr 23 18:37:46 UTC 2025 I: Removing signed libgclib_0.12.7+ds-6_arm64.buildinfo.asc files: removed './b1/libgclib_0.12.7+ds-6_arm64.buildinfo.asc' removed './b2/libgclib_0.12.7+ds-6_arm64.buildinfo.asc' 1745433466 arm64 unstable libgclib Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libgclib_0.12.7+ds-6.rbuild.log: 79.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/libgclib_0.12.7+ds-6.rbuild.log.gz [2025-04-23 18:37:46] INFO: Starting at 2025-04-23 18:37:46.432105 [2025-04-23 18:37:46] INFO: Generating the pages of 1 package(s) [2025-04-23 18:37:46] INFO: Finished at 2025-04-23 18:37:46.798634, took: 0:00:00.366538 All cleanup done. Wed Apr 23 18:37:47 UTC 2025 - total duration: 0h 2m 54s. Wed Apr 23 18:37:47 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-A04eYs9n, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 3min 56.080s CPU time consumed: 6.927s