Sun Mar 2 20:09:18 UTC 2025 I: starting to build libgclib/trixie/arm64 on jenkins on '2025-03-02 20:08' Sun Mar 2 20:09:18 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_12/84039/console.log Sun Mar 2 20:09:18 UTC 2025 I: Downloading source for trixie/libgclib=0.12.7+ds-6 --2025-03-02 20:09:18-- 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% 323M=0s 2025-03-02 20:09:18 (323 MB/s) - ‘libgclib_0.12.7+ds-6.dsc’ saved [2332/2332] Sun Mar 2 20:09:18 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----- Sun Mar 2 20:09:18 UTC 2025 I: Checking whether the package is not for us Sun Mar 2 20:09:18 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Sun Mar 2 20:09:18 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Sun Mar 2 20:13:41 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Mar 2 08:09:21 -12 2025 I: pbuilder-time-stamp: 1740946161 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/2873268/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='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='4ed4b4bde21247c3ac6131a7c8befa05' 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='2873268' 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.KLshEwdH/pbuilderrc_oDYn --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.KLshEwdH/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 codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2873268/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 ... 19916 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} 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, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 20.1 MB of archives. After unpacking 80.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Fetched 20.1 MB in 0s (47.3 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 ... 19916 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... 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_2.40.4-5_arm64.deb ... Unpacking bsdextrautils (2.40.4-5) ... 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_1.4.19-5_arm64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... 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_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... 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_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../25-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../26-libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-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 .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-6) ... Setting up bsdextrautils (2.40.4-5) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up autopoint (0.23.1-1) ... Setting up d-shlibs (0.109) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Setting up automake (1:1.17-3) ... 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 (2.5.4-3) ... 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 (13.24.1) ... Processing triggers for libc-bin (2.40-7) ... 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 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 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 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 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 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 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 gcdb.cpp -fPIC -DPIC -o .libs/libgclib_la-gcdb.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gdna.cpp -fPIC -DPIC -o .libs/libgclib_la-gdna.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFastaIndex.cpp -fPIC -DPIC -o .libs/libgclib_la-GFastaIndex.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gff.cpp -fPIC -DPIC -o .libs/libgclib_la-gff.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c 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 gsocket.cpp -fPIC -DPIC -o .libs/libgclib_la-gsocket.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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-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 GArgs.cpp -o libgclib_la-GArgs.o >/dev/null 2>&1 In file included from GBase.cpp:1: In member function ‘GDynArray::Push(char)’, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: GBase.h:549:26: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 549 | fArray[fCount-1] = item; | ^ In function ‘GRealloc(void**, unsigned long)’, inlined from ‘GDynArray::Clear()’ at GBase.h:633:6, inlined from ‘GDynArray::growTo(unsigned int)’ at GBase.h:577:28, inlined from ‘GDynArray::Grow()’ at GBase.h:544:12, inlined from ‘GDynArray::Push(char)’ at GBase.h:564:6, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: GBase.h:280:21: note: at offset 4294967295 into destination object of size 16 allocated by ‘realloc’ 280 | void *p=realloc(*ptr,size); | ~~~~~~~^~~~~~~~~~~ In member function ‘GDynArray::Push(char)’, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: GBase.h:549:26: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 549 | fArray[fCount-1] = item; | ^ In function ‘GRealloc(void**, unsigned long)’, inlined from ‘GDynArray::Clear()’ at GBase.h:633:6, inlined from ‘GDynArray::growTo(unsigned int)’ at GBase.h:577:28, inlined from ‘GDynArray::Grow()’ at GBase.h:544:12, inlined from ‘GDynArray::Push(char)’ at GBase.h:564:6, inlined from ‘fgetline(char*&, int&, _IO_FILE*, long*, int*)’ at GBase.cpp:530:11: GBase.h:272:20: note: at offset 4294967295 into destination object of size 16 allocated by ‘malloc’ 272 | void *p=malloc(size); | ~~~~~~^~~~~~ /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 GFastaFile.h:4, from GapAssem.h:3, from GapAssem.cpp:1: GapAssem.cpp: In member function ‘GASeq::refineClipping(GDynArray&, int, bool)’: GBase.h:176:28: warning: ‘gxpos’ may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ GapAssem.cpp:236:14: note: ‘gxpos’ was declared here 236 | int* gxpos; //mapping of positions from gseq to seq | ^~~~~ GBase.h:176:28: warning: ‘gseq’ may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ GapAssem.cpp:212:15: note: ‘gseq’ was declared here 212 | char* gseq; | ^~~~ In file included from GAlnExtend.h:6, from GAlnExtend.cpp:1: In function ‘GMalloc(void**, unsigned long)’, inlined from ‘GXMemPool::GXMemPool(int)’ at GAlnExtend.h:157:9, inlined from ‘CGreedyAlignData::CGreedyAlignData(int, int, int)’ at GAlnExtend.h:281:29: GBase.h:254:12: warning: ‘MEM[(void * *)_78]’ may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ /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 gcdb.cpp -o libgclib_la-gcdb.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 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-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 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 ()); | ~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-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 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 ()); | ~~~~~~~~~~~~~~~~~ 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 { | ^ 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; | ^~~~ 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 -o libgclib_la-gstopwatch.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-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 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 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 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 -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 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 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 '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: 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/2873268 and its subdirectories I: Current time: Sun Mar 2 08:13:39 -12 2025 I: pbuilder-time-stamp: 1740946419 Sun Mar 2 20:13:42 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Sun Mar 2 20:13:42 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Sun Mar 2 20:14:56 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Sun Mar 2 20:14:57 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: 4472c6314b00ca175f2f76d1cf64fc0aa1488f51 270240 libgclib-dev_0.12.7+ds-6_arm64.deb 6ccc5e7c2967fb5f8ba7abcee6957f2efb39889b 612576 libgclib3-dbgsym_0.12.7+ds-6_arm64.deb 0efacaefe06249c414275ed69bc0a118eed2b734 134176 libgclib3_0.12.7+ds-6_arm64.deb 77f24c489c83f1cf90332078356e68d7a6608ae3 5584 libgclib_0.12.7+ds-6_arm64.buildinfo Checksums-Sha256: f742a068fbe5eab1eade60ac5433023615886689f6fef4e80bbac8b6efb34699 270240 libgclib-dev_0.12.7+ds-6_arm64.deb 88512d93cce0878b291fc1609c638e32552789c323f9c06e49bca8c3b3b73e32 612576 libgclib3-dbgsym_0.12.7+ds-6_arm64.deb 5d5d8657748cd4831eaa9b6bd5d3146faf2c75c50ed965c8d22dd5ceddd6c491 134176 libgclib3_0.12.7+ds-6_arm64.deb 0bd853dc20620dae57125c025ee17f2599c4aadf459df7bd7d63889362e59e8b 5584 libgclib_0.12.7+ds-6_arm64.buildinfo Files: e630be47ac4c5a57bc17fd0c2de401eb 270240 libdevel optional libgclib-dev_0.12.7+ds-6_arm64.deb 5f7f610607e81d4c6c8c7278ca1dd069 612576 debug optional libgclib3-dbgsym_0.12.7+ds-6_arm64.deb 773d6002feb7da01e6e712e6abbc6902 134176 libs optional libgclib3_0.12.7+ds-6_arm64.deb 7508f483e82f470f250b8126f4cdd95d 5584 science optional libgclib_0.12.7+ds-6_arm64.buildinfo Sun Mar 2 20:14:58 UTC 2025 I: diffoscope 289 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_12-84039.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.KLshEwdH/libgclib_0.12.7+ds-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.KLshEwdH/libgclib_0.12.7+ds-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.KLshEwdH/libgclib_0.12.7+ds-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.KLshEwdH/b1/libgclib_0.12.7+ds-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.KLshEwdH/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: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 226ms CPU time consumed: 228ms Sun Mar 2 20:14:59 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Sun Mar 2 20:14:59 UTC 2025 I: libgclib from trixie built successfully and reproducibly on arm64. Sun Mar 2 20:15:00 UTC 2025 I: Submitting .buildinfo files to external archives: Sun Mar 2 20:15:00 UTC 2025 I: Submitting 8.0K b1/libgclib_0.12.7+ds-6_arm64.buildinfo.asc Sun Mar 2 20:15:00 UTC 2025 I: Submitting 8.0K b2/libgclib_0.12.7+ds-6_arm64.buildinfo.asc Sun Mar 2 20:15:01 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Mar 2 20:15:01 UTC 2025 I: Done submitting .buildinfo files. Sun Mar 2 20:15:01 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'