Running as unit: rb-build-i386_10-32491.service ==================================================================================== Fri Nov 22 17:37:32 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_i386_10) on jenkins, called using "ionos16-i386 ionos12-i386" as arguments. Fri Nov 22 17:37:32 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-H7TIpOVg" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Nov 22 17:37:32 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos16-i386.debian.net is marked as down. Fri Nov 22 17:37:32 UTC 2024 - checking via ssh if ionos16-i386.debian.net is up. removed '/tmp/read-only-fs-test-VF3aO5' Fri Nov 22 17:37:33 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos12-i386.debian.net is marked as down. Fri Nov 22 17:37:33 UTC 2024 - checking via ssh if ionos12-i386.debian.net is up. removed '/tmp/read-only-fs-test-poPMpb' ok, let's check if baitfisher is building anywhere yet… ok, baitfisher is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of baitfisher in trixie on i386 on jenkins now. 1st build will be done on ionos16-i386.debian.net. 2nd build will be done on ionos12-i386.debian.net. ============================================================================= Fri Nov 22 17:37:52 UTC 2024 I: starting to build baitfisher/trixie/i386 on jenkins on '2024-11-22 17:37' Fri Nov 22 17:37:52 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_10/32491/console.log 1732297072 i386 trixie baitfisher Fri Nov 22 17:37:52 UTC 2024 I: Downloading source for trixie/baitfisher=1.2.7+git20211020.de26d5c+dfsg-1 --2024-11-22 17:37:52-- http://deb.debian.org/debian/pool/main/b/baitfisher/baitfisher_1.2.7%2bgit20211020.de26d5c%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2207 (2.2K) [text/prs.lines.tag] Saving to: ‘baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc’ 0K .. 100% 283M=0s 2024-11-22 17:37:52 (283 MB/s) - ‘baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc’ saved [2207/2207] --2024-11-22 17:37:52-- http://deb.debian.org/debian/pool/main/b/baitfisher/baitfisher_1.2.7%2bgit20211020.de26d5c%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2207 (2.2K) [text/prs.lines.tag] Saving to: ‘baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc’ 0K .. 100% 283M=0s 2024-11-22 17:37:52 (283 MB/s) - ‘baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc’ saved [2207/2207] Fri Nov 22 17:37:52 UTC 2024 I: baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: baitfisher Binary: baitfisher Architecture: any Version: 1.2.7+git20211020.de26d5c+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou Homepage: https://github.com/cmayer/BaitFisher-package Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/baitfisher Vcs-Git: https://salsa.debian.org/med-team/baitfisher.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), help2man, libtclap-dev, debhelper Package-List: baitfisher deb science optional arch=any Checksums-Sha1: f0cae180075c9828b1be29d86fe0ccdf52477e84 3454988 baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz dd97ea2367b2a5b4180f2a7befd665d5a8c39f04 4828 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.debian.tar.xz Checksums-Sha256: 18173901d19d48a42d2f73d43f20fcbe7e9a7bc7be0d085cf396b9e06dae8103 3454988 baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz 49509da2d04fab1652eefface87d35909767be86e14f5c7911a56147d5228e4b 4828 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.debian.tar.xz Files: ea5113239392acc66501bb398a69a45d 3454988 baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz 5b8c24f27d1c2cee82497f185822079c 4828 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmHjyAMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFdvA//Req8A8j+tQvY3xW+fGtZFJ4POl6V730b zrUZocHnRS304pI9ITFbNU1H1QOGuNt2BiiY98ZiTdH2r8SD2B/MYR1tzbRut38D O4UB/fVROljYebNL6wgC+UlMOHNT3zvL4gxJ2434ppJ50aZz6mYhS3mhXsn0tZ3W hHLzU/y4xpxSP5JXRuICrrblfqBr/a3Fcm1v7RMoDJW8wvLo+HV0N3RDsfT678ca gE54I/OqlcElctL4xKOpamvirHfZgPINyti19v61G/nbqvCITvB3wmmBvPwPkqIb t8m0yIqC5douWBdscWBi0+sz10Cuvo/Y3MLc/0nECz4qKBjiy9wZH9S90GtZuc/U FZSaQRC7AQYfBpXt9+iuX//qDGeaTWQ8v4PFH3alE2Y0cOZBmIwq60hC7Ae+nJek TuFAF5bB9Gwr9rT0Ly9ebXeou0zrCSd8eIRtMbG5l8oRiq3mOeqajU0ag9xKg5n1 mVGOOoGxjdTU8ClwKI1GOihbun2ZXAyDl5ajuniyg/lYwXd+VE7DPsRHs0loL3xm I/7sZl3ZOzgABveawxjLGLdYdMcSH/dmFbZr+vgMLCjfNWABZBqBnLouvFT3cjHZ z8SYHji6AyXRp51h2sdVPxJXIz4m+tKUBlTkB5ZEOwT5gEWOdizO8kNwfJjKhJhU II8PRlSY/KI= =WH+G -----END PGP SIGNATURE----- Fri Nov 22 17:37:52 UTC 2024 I: Checking whether the package is not for us Fri Nov 22 17:37:52 UTC 2024 I: Starting 1st build on remote node ionos16-i386.debian.net. Fri Nov 22 17:37:52 UTC 2024 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Fri Nov 22 17:37:52 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos16-i386.debian.net is marked as down. Fri Nov 22 17:37:52 UTC 2024 - checking via ssh if ionos16-i386.debian.net is up. removed '/tmp/read-only-fs-test-3Gtlt3' ==================================================================================== Fri Dec 26 00:00:53 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos16-i386, called using "1 baitfisher trixie /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1 1.2.7+git20211020.de26d5c+dfsg-1" as arguments. Fri Dec 26 00:00:53 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-9BVRnu10" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Dec 26 00:00:53 UTC 2025 I: Downloading source for trixie/baitfisher=1.2.7+git20211020.de26d5c+dfsg-1 Reading package lists... NOTICE: 'baitfisher' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/baitfisher.git Please use: git clone https://salsa.debian.org/med-team/baitfisher.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3462 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-1 (dsc) [2207 B] Get:2 http://deb.debian.org/debian trixie/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-1 (tar) [3455 kB] Get:3 http://deb.debian.org/debian trixie/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-1 (diff) [4828 B] Fetched 3462 kB in 0s (55.2 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'baitfisher' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/baitfisher.git Please use: git clone https://salsa.debian.org/med-team/baitfisher.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3462 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-1 (dsc) [2207 B] Get:2 http://deb.debian.org/debian trixie/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-1 (tar) [3455 kB] Get:3 http://deb.debian.org/debian trixie/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-1 (diff) [4828 B] Fetched 3462 kB in 0s (55.2 MB/s) Download complete and in download only mode ============================================================================= Building baitfisher in trixie on i386 on ionos16-i386 now. Date: Fri Dec 26 01:00:53 CET 2025 Date UTC: Fri Dec 26 00:00:53 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Dec 25 12:00:53 -12 2025 I: pbuilder-time-stamp: 1766707253 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: using eatmydata during job I: Copying source file I: copying [baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc] I: copying [./baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz] I: copying [./baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jan 16 07:23:47 2022 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting baitfisher in baitfisher-1.2.7+git20211020.de26d5c+dfsg dpkg-source: info: unpacking baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz dpkg-source: info: unpacking baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_example.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/62718/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='2b90faab0db6451d89cf2880c37b693b' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='62718' 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.sFBewwk1/pbuilderrc_rMQ3 --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.sFBewwk1/b1 --logfile b1/build.log baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos16-i386 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/62718/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: i386 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), help2man, libtclap-dev, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19956 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 help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-dev is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtclap-dev{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 23.7 MB of archives. After unpacking 91.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 liblocale-gettext-perl i386 1.07-7+b1 [15.4 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-11 [95.6 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 help2man i386 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libtclap-dev i386 1.2.5-1+b1 [3360 kB] Fetched 23.7 MB in 0s (72.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19956 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_i386.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3+b1_i386.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_i386.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-5_i386.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg/ && 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 > ../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_source.changes dpkg-buildpackage: info: source package baitfisher dpkg-buildpackage: info: source version 1.2.7+git20211020.de26d5c+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_auto_clean make -j22 clean make[1]: Entering directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' rm -f *.o rm -f BaitFisher-v1.2.8 rm -f BaitFilter-v1.0.6 make[1]: Leaving directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j22 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bait-fisher-helper.cpp -o bait-fisher-helper.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bait-fisher.cpp -o bait-fisher.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c Csequence_cluster_and_center_sequence.cpp -o Csequence_cluster_and_center_sequence.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c mydir-unix.cpp -o mydir-unix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bait-filter.cpp -o bait-filter.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c global-types-and-parameters.cpp -o global-types-and-parameters.o In file included from CBlastParser.h:47, from CBaitRecord.h:37, from bait-filter.cpp:33: CFile/CFile2_1.h: In member function 'char CFile::getchar()': CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 256 | register char c; | ^ In file included from bait-fisher-helper.cpp:31: CFile/CFile2_1.h: In member function 'char CFile::getchar()': CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 256 | register char c; | ^ In file included from CSeqNameList.h:38, from CBlastParser.h:52: CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&, unsigned int&)': CSequence_Mol2_1.h:300:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 300 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine_toupper(CFile&)': CSequence_Mol2_1.h:321:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 321 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:340:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 340 | register char c; | ^ CSequence_Mol2_1.h:342:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 342 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:424:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 424 | register char c; | ^ CSequence_Mol2_1.h:425:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 425 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:426:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 426 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:429:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 429 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:430:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 430 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:431:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 431 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:432:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 432 | register bool removestars_bool = (pflag & removestars); // handled | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:433:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 433 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig); // handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:571:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 571 | register char c; | ^ CSequence_Mol2_1.h:572:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 572 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:573:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 573 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:578:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 578 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:580:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 580 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:582:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 582 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig);// handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:685:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 685 | register char c; | ^ CSequence_Mol2_1.h:687:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 687 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:764:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 764 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_gaps2ambig(CFile&)': CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 825 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2627 | register bool removegaps_bool = (pflag & removegaps); // | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2628 | register bool removestars_bool = (pflag & removestars); // | ^~~~~~~~~~~~~~~~ In file included from CSequence_Mol2_1.h:50, from CSequences2.h:42, from Csequence_cluster_and_center_sequence.h:44, from Csequence_cluster_and_center_sequence.cpp:27: CFile/CFile2_1.h: In member function 'char CFile::getchar()': CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 256 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&, unsigned int&)': CSequence_Mol2_1.h:300:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 300 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine_toupper(CFile&)': CSequence_Mol2_1.h:321:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 321 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:340:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 340 | register char c; | ^ CSequence_Mol2_1.h:342:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 342 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:424:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 424 | register char c; | ^ CSequence_Mol2_1.h:425:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 425 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:426:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 426 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:429:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 429 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:430:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 430 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:431:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 431 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:432:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 432 | register bool removestars_bool = (pflag & removestars); // handled | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:433:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 433 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig); // handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:571:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 571 | register char c; | ^ CSequence_Mol2_1.h:572:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 572 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:573:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 573 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:578:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 578 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:580:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 580 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:582:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 582 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig);// handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:685:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 685 | register char c; | ^ CSequence_Mol2_1.h:687:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 687 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:764:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 764 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_gaps2ambig(CFile&)': CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 825 | register char c; | ^ In file included from CSequences2.h:42, from bait-fisher-helper.cpp:32: CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&, unsigned int&)': CSequence_Mol2_1.h:300:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 300 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine_toupper(CFile&)': CSequence_Mol2_1.h:321:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 321 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:340:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 340 | register char c; | ^ CSequence_Mol2_1.h:342:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 342 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ In file included from CSequence_Mol2_1.h:50, from GFF-class.h:34, from bait-fisher.cpp:30: CFile/CFile2_1.h: In member function 'char CFile::getchar()': CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 256 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:424:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 424 | register char c; | ^ CSequence_Mol2_1.h:425:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 425 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:426:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 426 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:429:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 429 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:430:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 430 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:431:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 431 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:432:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 432 | register bool removestars_bool = (pflag & removestars); // handled | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:433:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 433 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig); // handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:571:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 571 | register char c; | ^ CSequence_Mol2_1.h:572:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 572 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:573:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 573 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:578:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 578 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:580:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 580 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:582:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 582 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig);// handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:685:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 685 | register char c; | ^ CSequence_Mol2_1.h:687:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 687 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:764:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 764 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_gaps2ambig(CFile&)': CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 825 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2627 | register bool removegaps_bool = (pflag & removegaps); // | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2628 | register bool removestars_bool = (pflag & removestars); // | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&, unsigned int&)': CSequence_Mol2_1.h:300:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 300 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine_toupper(CFile&)': CSequence_Mol2_1.h:321:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 321 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:340:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 340 | register char c; | ^ CSequence_Mol2_1.h:342:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 342 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:424:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 424 | register char c; | ^ CSequence_Mol2_1.h:425:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 425 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:426:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 426 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:429:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 429 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:430:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 430 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:431:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 431 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:432:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 432 | register bool removestars_bool = (pflag & removestars); // handled | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:433:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 433 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig); // handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:571:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 571 | register char c; | ^ CSequence_Mol2_1.h:572:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 572 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:573:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 573 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:578:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 578 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:580:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 580 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:582:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 582 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig);// handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:685:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 685 | register char c; | ^ CSequence_Mol2_1.h:687:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 687 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:764:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 764 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_gaps2ambig(CFile&)': CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 825 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2627 | register bool removegaps_bool = (pflag & removegaps); // | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2628 | register bool removestars_bool = (pflag & removestars); // | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2627 | register bool removegaps_bool = (pflag & removegaps); // | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2628 | register bool removestars_bool = (pflag & removestars); // | ^~~~~~~~~~~~~~~~ g++ -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lstdc++ bait-filter.o global-types-and-parameters.o -o BaitFilter-v1.0.6 g++ -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lstdc++ bait-fisher-helper.o bait-fisher.o Csequence_cluster_and_center_sequence.o mydir-unix.o -o BaitFisher-v1.2.8 make[1]: Leaving directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install --destdir=debian/baitfisher/ debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' cp BaitFilter-v* debian/baitfisher/usr/bin/BaitFilter cp BaitFisher-v* debian/baitfisher/usr/bin/BaitFisher dh_install for sh in `grep -Rl '#!/usr/bin/bash' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/bash?#!/bin/bash?' ${sh} ; \ done make[1]: Leaving directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' help2man --no-discard-stderr -o BaitFilter.1 ./BaitFilter-v* help2man --no-discard-stderr -o BaitFisher.1 ./BaitFisher-v* dh_installman make[1]: Leaving directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' dh_lintian 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'baitfisher' in '../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb'. dpkg-deb: building package 'baitfisher-dbgsym' in '../baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo dpkg-genchanges --build=binary -O../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.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: including full 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/62718 and its subdirectories I: Current time: Thu Dec 25 12:01:29 -12 2025 I: pbuilder-time-stamp: 1766707289 Fri Dec 26 00:01:29 UTC 2025 I: Signing ./b1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo as baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo.asc Fri Dec 26 00:01:29 UTC 2025 I: Signed ./b1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo as ./b1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo.asc Fri Dec 26 00:01:29 UTC 2025 - build #1 for baitfisher/trixie/i386 on ionos16-i386 done. Starting cleanup. All cleanup done. Fri Dec 26 00:01:29 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-9BVRnu10, removing. /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 17:38 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 17:37 b2 -rw-r--r-- 1 jenkins jenkins 2207 Jan 16 2022 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc -rw------- 1 jenkins jenkins 3451 Nov 22 17:37 rbuildlog.WfluC1Z /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/b1: total 5524 -rw-r--r-- 1 jenkins jenkins 1879068 Nov 22 17:38 baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb -rw-r--r-- 1 jenkins jenkins 4828 Nov 22 17:38 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2207 Nov 22 17:38 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 5211 Nov 22 17:38 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo -rw-r--r-- 1 jenkins jenkins 6093 Nov 22 17:38 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1733 Nov 22 17:38 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.changes -rw-r--r-- 1 jenkins jenkins 227724 Nov 22 17:38 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb -rw-r--r-- 1 jenkins jenkins 1926 Nov 22 17:38 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 3454988 Nov 22 17:38 baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz -rw-r--r-- 1 jenkins jenkins 52896 Nov 22 17:38 build.log /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/b2: total 0 Fri Nov 22 17:38:30 UTC 2024 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Dec 25 12:00:53 -12 2025 I: pbuilder-time-stamp: 1766707253 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: using eatmydata during job I: Copying source file I: copying [baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc] I: copying [./baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz] I: copying [./baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jan 16 07:23:47 2022 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting baitfisher in baitfisher-1.2.7+git20211020.de26d5c+dfsg dpkg-source: info: unpacking baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz dpkg-source: info: unpacking baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_example.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/62718/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='2b90faab0db6451d89cf2880c37b693b' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='62718' 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.sFBewwk1/pbuilderrc_rMQ3 --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.sFBewwk1/b1 --logfile b1/build.log baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos16-i386 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/62718/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: i386 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), help2man, libtclap-dev, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19956 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 help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-dev is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtclap-dev{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 23.7 MB of archives. After unpacking 91.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 liblocale-gettext-perl i386 1.07-7+b1 [15.4 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-11 [95.6 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 help2man i386 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libtclap-dev i386 1.2.5-1+b1 [3360 kB] Fetched 23.7 MB in 0s (72.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19956 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_i386.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. 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Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:i386 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up libtclap-dev (1.2.5-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg/ && 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 > ../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_source.changes dpkg-buildpackage: info: source package baitfisher dpkg-buildpackage: info: source version 1.2.7+git20211020.de26d5c+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_auto_clean make -j22 clean make[1]: Entering directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' rm -f *.o rm -f BaitFisher-v1.2.8 rm -f BaitFilter-v1.0.6 make[1]: Leaving directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j22 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bait-fisher-helper.cpp -o bait-fisher-helper.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bait-fisher.cpp -o bait-fisher.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c Csequence_cluster_and_center_sequence.cpp -o Csequence_cluster_and_center_sequence.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c mydir-unix.cpp -o mydir-unix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bait-filter.cpp -o bait-filter.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c global-types-and-parameters.cpp -o global-types-and-parameters.o In file included from CBlastParser.h:47, from CBaitRecord.h:37, from bait-filter.cpp:33: CFile/CFile2_1.h: In member function 'char CFile::getchar()': CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 256 | register char c; | ^ In file included from bait-fisher-helper.cpp:31: CFile/CFile2_1.h: In member function 'char CFile::getchar()': CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 256 | register char c; | ^ In file included from CSeqNameList.h:38, from CBlastParser.h:52: CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&, unsigned int&)': CSequence_Mol2_1.h:300:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 300 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine_toupper(CFile&)': CSequence_Mol2_1.h:321:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 321 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:340:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 340 | register char c; | ^ CSequence_Mol2_1.h:342:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 342 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:424:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 424 | register char c; | ^ CSequence_Mol2_1.h:425:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 425 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:426:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 426 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:429:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 429 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:430:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 430 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:431:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 431 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:432:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 432 | register bool removestars_bool = (pflag & removestars); // handled | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:433:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 433 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig); // handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:571:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 571 | register char c; | ^ CSequence_Mol2_1.h:572:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 572 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:573:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 573 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:578:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 578 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:580:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 580 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:582:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 582 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig);// handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:685:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 685 | register char c; | ^ CSequence_Mol2_1.h:687:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 687 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:764:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 764 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_gaps2ambig(CFile&)': CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 825 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2627 | register bool removegaps_bool = (pflag & removegaps); // | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2628 | register bool removestars_bool = (pflag & removestars); // | ^~~~~~~~~~~~~~~~ In file included from CSequence_Mol2_1.h:50, from CSequences2.h:42, from Csequence_cluster_and_center_sequence.h:44, from Csequence_cluster_and_center_sequence.cpp:27: CFile/CFile2_1.h: In member function 'char CFile::getchar()': CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 256 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&, unsigned int&)': CSequence_Mol2_1.h:300:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 300 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine_toupper(CFile&)': CSequence_Mol2_1.h:321:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 321 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:340:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 340 | register char c; | ^ CSequence_Mol2_1.h:342:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 342 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:424:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 424 | register char c; | ^ CSequence_Mol2_1.h:425:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 425 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:426:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 426 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:429:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 429 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:430:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 430 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:431:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 431 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:432:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 432 | register bool removestars_bool = (pflag & removestars); // handled | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:433:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 433 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig); // handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:571:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 571 | register char c; | ^ CSequence_Mol2_1.h:572:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 572 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:573:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 573 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:578:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 578 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:580:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 580 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:582:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 582 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig);// handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:685:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 685 | register char c; | ^ CSequence_Mol2_1.h:687:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 687 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:764:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 764 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_gaps2ambig(CFile&)': CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 825 | register char c; | ^ In file included from CSequences2.h:42, from bait-fisher-helper.cpp:32: CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&, unsigned int&)': CSequence_Mol2_1.h:300:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 300 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine_toupper(CFile&)': CSequence_Mol2_1.h:321:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 321 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:340:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 340 | register char c; | ^ CSequence_Mol2_1.h:342:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 342 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ In file included from CSequence_Mol2_1.h:50, from GFF-class.h:34, from bait-fisher.cpp:30: CFile/CFile2_1.h: In member function 'char CFile::getchar()': CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 256 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:424:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 424 | register char c; | ^ CSequence_Mol2_1.h:425:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 425 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:426:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 426 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:429:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 429 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:430:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 430 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:431:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 431 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:432:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 432 | register bool removestars_bool = (pflag & removestars); // handled | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:433:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 433 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig); // handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:571:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 571 | register char c; | ^ CSequence_Mol2_1.h:572:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 572 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:573:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 573 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:578:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 578 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:580:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 580 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:582:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 582 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig);// handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:685:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 685 | register char c; | ^ CSequence_Mol2_1.h:687:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 687 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:764:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 764 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_gaps2ambig(CFile&)': CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 825 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2627 | register bool removegaps_bool = (pflag & removegaps); // | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2628 | register bool removestars_bool = (pflag & removestars); // | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&, unsigned int&)': CSequence_Mol2_1.h:300:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 300 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine_toupper(CFile&)': CSequence_Mol2_1.h:321:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 321 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:340:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 340 | register char c; | ^ CSequence_Mol2_1.h:342:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 342 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:424:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 424 | register char c; | ^ CSequence_Mol2_1.h:425:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 425 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:426:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 426 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:429:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 429 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:430:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 430 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:431:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 431 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:432:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 432 | register bool removestars_bool = (pflag & removestars); // handled | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:433:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 433 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig); // handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:571:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 571 | register char c; | ^ CSequence_Mol2_1.h:572:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 572 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:573:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 573 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:578:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 578 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:580:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 580 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:582:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 582 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig);// handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:685:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 685 | register char c; | ^ CSequence_Mol2_1.h:687:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 687 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:764:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 764 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_gaps2ambig(CFile&)': CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 825 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2627 | register bool removegaps_bool = (pflag & removegaps); // | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2628 | register bool removestars_bool = (pflag & removestars); // | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2627 | register bool removegaps_bool = (pflag & removegaps); // | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2628 | register bool removestars_bool = (pflag & removestars); // | ^~~~~~~~~~~~~~~~ g++ -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lstdc++ bait-filter.o global-types-and-parameters.o -o BaitFilter-v1.0.6 g++ -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lstdc++ bait-fisher-helper.o bait-fisher.o Csequence_cluster_and_center_sequence.o mydir-unix.o -o BaitFisher-v1.2.8 make[1]: Leaving directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install --destdir=debian/baitfisher/ debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' cp BaitFilter-v* debian/baitfisher/usr/bin/BaitFilter cp BaitFisher-v* debian/baitfisher/usr/bin/BaitFisher dh_install for sh in `grep -Rl '#!/usr/bin/bash' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/bash?#!/bin/bash?' ${sh} ; \ done make[1]: Leaving directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' help2man --no-discard-stderr -o BaitFilter.1 ./BaitFilter-v* help2man --no-discard-stderr -o BaitFisher.1 ./BaitFisher-v* dh_installman make[1]: Leaving directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' dh_lintian 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'baitfisher' in '../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb'. dpkg-deb: building package 'baitfisher-dbgsym' in '../baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo dpkg-genchanges --build=binary -O../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.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: including full 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/62718 and its subdirectories I: Current time: Thu Dec 25 12:01:29 -12 2025 I: pbuilder-time-stamp: 1766707289 Fri Nov 22 17:38:31 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net. Fri Nov 22 17:38:31 UTC 2024 I: Preparing to do remote build '2' on ionos12-i386.debian.net. Fri Nov 22 17:38:31 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos12-i386.debian.net is marked as down. Fri Nov 22 17:38:31 UTC 2024 - checking via ssh if ionos12-i386.debian.net is up. removed '/tmp/read-only-fs-test-UEhNYC' ==================================================================================== Fri Nov 22 17:38:32 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos12-i386, called using "2 baitfisher trixie /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1 1.2.7+git20211020.de26d5c+dfsg-1" as arguments. Fri Nov 22 17:38:32 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-w6Ns2pM8" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Nov 22 17:38:32 UTC 2024 I: Downloading source for trixie/baitfisher=1.2.7+git20211020.de26d5c+dfsg-1 Reading package lists... NOTICE: 'baitfisher' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/baitfisher.git Please use: git clone https://salsa.debian.org/med-team/baitfisher.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3462 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-1 (dsc) [2207 B] Get:2 http://deb.debian.org/debian trixie/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-1 (tar) [3455 kB] Get:3 http://deb.debian.org/debian trixie/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-1 (diff) [4828 B] Fetched 3462 kB in 0s (18.0 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'baitfisher' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/baitfisher.git Please use: git clone https://salsa.debian.org/med-team/baitfisher.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3462 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-1 (dsc) [2207 B] Get:2 http://deb.debian.org/debian trixie/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-1 (tar) [3455 kB] Get:3 http://deb.debian.org/debian trixie/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-1 (diff) [4828 B] Fetched 3462 kB in 0s (18.0 MB/s) Download complete and in download only mode ============================================================================= Re-Building baitfisher in trixie on i386 on ionos12-i386 now. Date: Fri Nov 22 18:38:32 CET 2024 Date UTC: Fri Nov 22 17:38:32 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1 + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/pbuilderrc_fgNt + case ${ARCH} in + let NUM_CPU-=3 + case $ARCH in + locale=de_CH + language=de + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' baitfisher = debian-installer -o baitfisher = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' baitfisher = u-boot ']' + case "${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.sFBewwk1/pbuilderrc_fgNt --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/b2 --logfile b2/build.log baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.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: Sat Nov 23 07:38:33 +14 2024 I: pbuilder-time-stamp: 1732297113 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: using eatmydata during job I: Copying source file I: copying [baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc] I: copying [./baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz] I: copying [./baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jan 16 07:23:47 2022 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting baitfisher in baitfisher-1.2.7+git20211020.de26d5c+dfsg dpkg-source: info: unpacking baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz dpkg-source: info: unpacking baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_example.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/25494/tmp/hooks/D01_modify_environment starting debug: Running on ionos12-i386. 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 Nov 22 17:38 /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/25494/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/25494/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=927c7715c27540a98003c5eae9ee4248 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-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=25494 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.sFBewwk1/pbuilderrc_fgNt --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/b2 --logfile b2/build.log baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/25494/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: i386 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), help2man, libtclap-dev, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19956 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 help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-dev is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtclap-dev{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 23.7 MB of archives. After unpacking 91.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 liblocale-gettext-perl i386 1.07-7+b1 [15.4 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-11 [95.6 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 help2man i386 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libtclap-dev i386 1.2.5-1+b1 [3360 kB] Fetched 23.7 MB in 1s (27.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19956 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_i386.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3+b1_i386.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_i386.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-5_i386.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-11_i386.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../09-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../22-libelf1t64_0.192-4_i386.deb ... Unpacking libelf1t64:i386 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../24-libicu72_72.1-5+b1_i386.deb ... Unpacking libicu72:i386 (72.1-5+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.22.5-2_i386.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package help2man. Preparing to unpack .../30-help2man_1.49.3_i386.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package libtclap-dev. Preparing to unpack .../31-libtclap-dev_1.2.5-1+b1_i386.deb ... Unpacking libtclap-dev (1.2.5-1+b1) ... Setting up libpipeline1:i386 (1.5.8-1) ... Setting up libicu72:i386 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/25494/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/25494/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg/ && 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 > ../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_source.changes dpkg-buildpackage: info: source package baitfisher dpkg-buildpackage: info: source version 1.2.7+git20211020.de26d5c+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_auto_clean make -j10 clean make[1]: Entering directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' rm -f *.o rm -f BaitFisher-v1.2.8 rm -f BaitFilter-v1.0.6 make[1]: Leaving directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j10 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bait-fisher-helper.cpp -o bait-fisher-helper.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bait-fisher.cpp -o bait-fisher.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c Csequence_cluster_and_center_sequence.cpp -o Csequence_cluster_and_center_sequence.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c mydir-unix.cpp -o mydir-unix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bait-filter.cpp -o bait-filter.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c global-types-and-parameters.cpp -o global-types-and-parameters.o In file included from bait-fisher-helper.cpp:31: CFile/CFile2_1.h: In member function 'char CFile::getchar()': CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 256 | register char c; | ^ In file included from CBlastParser.h:47, from CBaitRecord.h:37, from bait-filter.cpp:33: CFile/CFile2_1.h: In member function 'char CFile::getchar()': CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 256 | register char c; | ^ In file included from CSequences2.h:42, from bait-fisher-helper.cpp:32: CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&, unsigned int&)': CSequence_Mol2_1.h:300:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 300 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine_toupper(CFile&)': CSequence_Mol2_1.h:321:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 321 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:340:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 340 | register char c; | ^ CSequence_Mol2_1.h:342:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 342 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:424:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 424 | register char c; | ^ CSequence_Mol2_1.h:425:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 425 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:426:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 426 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:429:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 429 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:430:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 430 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:431:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 431 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:432:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 432 | register bool removestars_bool = (pflag & removestars); // handled | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:433:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 433 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig); // handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:571:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 571 | register char c; | ^ CSequence_Mol2_1.h:572:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 572 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:573:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 573 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:578:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 578 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:580:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 580 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:582:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 582 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig);// handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:685:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 685 | register char c; | ^ CSequence_Mol2_1.h:687:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 687 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:764:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 764 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_gaps2ambig(CFile&)': CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 825 | register char c; | ^ In file included from CSeqNameList.h:38, from CBlastParser.h:52: CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&, unsigned int&)': CSequence_Mol2_1.h:300:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 300 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine_toupper(CFile&)': CSequence_Mol2_1.h:321:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 321 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:340:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 340 | register char c; | ^ CSequence_Mol2_1.h:342:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 342 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:424:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 424 | register char c; | ^ CSequence_Mol2_1.h:425:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 425 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:426:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 426 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:429:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 429 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:430:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 430 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:431:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 431 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:432:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 432 | register bool removestars_bool = (pflag & removestars); // handled | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:433:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 433 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig); // handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:571:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 571 | register char c; | ^ CSequence_Mol2_1.h:572:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 572 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:573:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 573 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:578:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 578 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:580:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 580 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:582:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 582 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig);// handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:685:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 685 | register char c; | ^ CSequence_Mol2_1.h:687:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 687 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:764:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 764 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_gaps2ambig(CFile&)': CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 825 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2627 | register bool removegaps_bool = (pflag & removegaps); // | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2628 | register bool removestars_bool = (pflag & removestars); // | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2627 | register bool removegaps_bool = (pflag & removegaps); // | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2628 | register bool removestars_bool = (pflag & removestars); // | ^~~~~~~~~~~~~~~~ In file included from CSequence_Mol2_1.h:50, from CSequences2.h:42, from Csequence_cluster_and_center_sequence.h:44, from Csequence_cluster_and_center_sequence.cpp:27: CFile/CFile2_1.h: In member function 'char CFile::getchar()': CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 256 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&, unsigned int&)': CSequence_Mol2_1.h:300:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 300 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine_toupper(CFile&)': CSequence_Mol2_1.h:321:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 321 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:340:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 340 | register char c; | ^ CSequence_Mol2_1.h:342:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 342 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:424:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 424 | register char c; | ^ CSequence_Mol2_1.h:425:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 425 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:426:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 426 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:429:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 429 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:430:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 430 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:431:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 431 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:432:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 432 | register bool removestars_bool = (pflag & removestars); // handled | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:433:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 433 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig); // handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:571:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 571 | register char c; | ^ CSequence_Mol2_1.h:572:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 572 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:573:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 573 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:578:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 578 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:580:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 580 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:582:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 582 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig);// handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:685:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 685 | register char c; | ^ CSequence_Mol2_1.h:687:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 687 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:764:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 764 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_gaps2ambig(CFile&)': CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 825 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2627 | register bool removegaps_bool = (pflag & removegaps); // | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2628 | register bool removestars_bool = (pflag & removestars); // | ^~~~~~~~~~~~~~~~ In file included from CSequence_Mol2_1.h:50, from GFF-class.h:34, from bait-fisher.cpp:30: CFile/CFile2_1.h: In member function 'char CFile::getchar()': CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 256 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&, unsigned int&)': CSequence_Mol2_1.h:300:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 300 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine_toupper(CFile&)': CSequence_Mol2_1.h:321:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 321 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:340:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 340 | register char c; | ^ CSequence_Mol2_1.h:342:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 342 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:424:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 424 | register char c; | ^ CSequence_Mol2_1.h:425:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 425 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:426:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 426 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:429:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 429 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:430:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 430 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:431:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 431 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:432:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 432 | register bool removestars_bool = (pflag & removestars); // handled | ^~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:433:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 433 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig); // handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:571:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 571 | register char c; | ^ CSequence_Mol2_1.h:572:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 572 | register char c_upper; | ^~~~~~~ CSequence_Mol2_1.h:573:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 573 | register char local_general_ambig = general_ambig; | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:578:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 578 | register bool convert_toupper_bool = (pflag & convert_toupper); // handled | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:580:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 580 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:582:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 582 | register bool gaps_to_ambig_bool = (pflag & gaps_to_ambig);// handled | ^~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:685:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 685 | register char c; | ^ CSequence_Mol2_1.h:687:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 687 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfProtein_toupper_removegaps(CFile&, unsigned int&)': CSequence_Mol2_1.h:764:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 764 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_toupper_ambig2N_gaps2ambig(CFile&)': CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 825 | register char c; | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // | ^~~~~~~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2627 | register bool removegaps_bool = (pflag & removegaps); // | ^~~~~~~~~~~~~~~ CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2628 | register bool removestars_bool = (pflag & removestars); // | ^~~~~~~~~~~~~~~~ g++ -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lstdc++ bait-filter.o global-types-and-parameters.o -o BaitFilter-v1.0.6 g++ -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lstdc++ bait-fisher-helper.o bait-fisher.o Csequence_cluster_and_center_sequence.o mydir-unix.o -o BaitFisher-v1.2.8 make[1]: Leaving directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install --destdir=debian/baitfisher/ debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' cp BaitFilter-v* debian/baitfisher/usr/bin/BaitFilter cp BaitFisher-v* debian/baitfisher/usr/bin/BaitFisher dh_install for sh in `grep -Rl '#!/usr/bin/bash' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/bash?#!/bin/bash?' ${sh} ; \ done make[1]: Leaving directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' help2man --no-discard-stderr -o BaitFilter.1 ./BaitFilter-v* help2man --no-discard-stderr -o BaitFisher.1 ./BaitFisher-v* dh_installman make[1]: Leaving directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' dh_lintian 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'baitfisher' in '../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb'. dpkg-deb: building package 'baitfisher-dbgsym' in '../baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo dpkg-genchanges --build=binary -O../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.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: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/25494/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/25494/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/25494 and its subdirectories I: Current time: Sat Nov 23 07:39:36 +14 2024 I: pbuilder-time-stamp: 1732297176 + false + set +x Fri Nov 22 17:39:36 UTC 2024 I: Signing ./b2/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo as baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo.asc Fri Nov 22 17:39:36 UTC 2024 I: Signed ./b2/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo as ./b2/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo.asc Fri Nov 22 17:39:36 UTC 2024 - build #2 for baitfisher/trixie/i386 on ionos12-i386 done. Starting cleanup. All cleanup done. Fri Nov 22 17:39:36 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-w6Ns2pM8, removing. /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1: total 72 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 17:38 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 17:39 b2 -rw-r--r-- 1 jenkins jenkins 2207 Jan 16 2022 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc -rw------- 1 jenkins jenkins 56633 Nov 22 17:38 rbuildlog.WfluC1Z /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/b1: total 5540 -rw-r--r-- 1 jenkins jenkins 1879068 Nov 22 17:38 baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb -rw-r--r-- 1 jenkins jenkins 4828 Nov 22 17:38 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2207 Nov 22 17:38 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 5211 Nov 22 17:38 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo -rw-r--r-- 1 jenkins jenkins 6093 Nov 22 17:38 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1733 Nov 22 17:38 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.changes -rw-r--r-- 1 jenkins jenkins 227724 Nov 22 17:38 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb -rw-r--r-- 1 jenkins jenkins 1926 Nov 22 17:38 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 3454988 Nov 22 17:38 baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz -rw-r--r-- 1 jenkins jenkins 52896 Nov 22 17:38 build.log /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/b2: total 5528 -rw-r--r-- 1 jenkins jenkins 1879068 Nov 22 17:39 baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb -rw-r--r-- 1 jenkins jenkins 4828 Nov 22 17:39 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2207 Nov 22 17:39 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc -rw-r--r-- 1 jenkins jenkins 5211 Nov 22 17:39 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo -rw-r--r-- 1 jenkins jenkins 6093 Nov 22 17:39 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1733 Nov 22 17:39 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.changes -rw-r--r-- 1 jenkins jenkins 227724 Nov 22 17:39 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb -rw-r--r-- 1 jenkins jenkins 1926 Nov 22 17:39 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_source.changes -rw-r--r-- 1 jenkins jenkins 3454988 Nov 22 17:39 baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz -rw-r--r-- 1 jenkins jenkins 54802 Nov 22 17:39 build.log Fri Nov 22 17:39:36 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. Fri Nov 22 17:39:37 UTC 2024 I: baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.changes: Format: 1.8 Date: Sun, 16 Jan 2022 08:18:11 +0100 Source: baitfisher Binary: baitfisher baitfisher-dbgsym Architecture: i386 Version: 1.2.7+git20211020.de26d5c+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: baitfisher - software package for designing hybrid enrichment probes Changes: baitfisher (1.2.7+git20211020.de26d5c+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.6.0 (routine-update) * Add missing build dependency on dh addon. Checksums-Sha1: a034b8068a38e14e544b67b6fd52bc0b5e2fc796 1879068 baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb 8b99dda21abfce894d2624afcaa2d71079050417 5211 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo e8f29607b10927608c32ce8a1bdcd4d0d5f8c050 227724 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb Checksums-Sha256: c02a3f11f359fc7c5cd6d2acc9db2891960099fdc6e77c708222c8f1693289a2 1879068 baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb 6a384bfdafb09e5870e9162d31fc1a33e3486193890115c8da6de933c41ebc15 5211 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo 7ed01ba30b7ec90ad89f5bd1d2b20fdab25b2fcbd9ba416dc1f789a59727a27c 227724 baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb Files: d418393143d2778f002386a3ee4c172e 1879068 debug optional baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb 045288561ef81574afe1b1994234508c 5211 science optional baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo 86803cc3c2262f5b9301e2eb79b63c3b 227724 science optional baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/i386/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-22 17:38:30.673142807 +0000 +++ b2/build.log 2024-11-22 17:39:36.878136627 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Dec 25 12:00:53 -12 2025 -I: pbuilder-time-stamp: 1766707253 +I: Current time: Sat Nov 23 07:38:33 +14 2024 +I: pbuilder-time-stamp: 1732297113 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -29,54 +29,86 @@ dpkg-source: info: applying fix_example.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/62718/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/25494/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +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 Nov 22 17:38 /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/25494/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/25494/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='2b90faab0db6451d89cf2880c37b693b' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='62718' - PS1='# ' - PS2='> ' + INVOCATION_ID=927c7715c27540a98003c5eae9ee4248 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-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=25494 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.sFBewwk1/pbuilderrc_rMQ3 --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.sFBewwk1/b1 --logfile b1/build.log baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.sFBewwk1/pbuilderrc_fgNt --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/b2 --logfile b2/build.log baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos16-i386 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/62718/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/25494/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -150,7 +182,7 @@ Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 help2man i386 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libtclap-dev i386 1.2.5-1+b1 [3360 kB] -Fetched 23.7 MB in 0s (72.3 MB/s) +Fetched 23.7 MB in 1s (27.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19956 files and directories currently installed.) @@ -293,7 +325,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg/ && 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 > ../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/25494/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/25494/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg/ && 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 > ../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_source.changes dpkg-buildpackage: info: source package baitfisher dpkg-buildpackage: info: source version 1.2.7+git20211020.de26d5c+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -303,7 +339,7 @@ debian/rules clean dh clean dh_auto_clean - make -j22 clean + make -j10 clean make[1]: Entering directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' rm -f *.o rm -f BaitFisher-v1.2.8 @@ -316,7 +352,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j22 "INSTALL=install --strip-program=true" + make -j10 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bait-fisher-helper.cpp -o bait-fisher-helper.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bait-fisher.cpp -o bait-fisher.o @@ -324,20 +360,20 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c mydir-unix.cpp -o mydir-unix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bait-filter.cpp -o bait-filter.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c global-types-and-parameters.cpp -o global-types-and-parameters.o -In file included from CBlastParser.h:47, - from CBaitRecord.h:37, - from bait-filter.cpp:33: +In file included from bait-fisher-helper.cpp:31: CFile/CFile2_1.h: In member function 'char CFile::getchar()': CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 256 | register char c; | ^ -In file included from bait-fisher-helper.cpp:31: +In file included from CBlastParser.h:47, + from CBaitRecord.h:37, + from bait-filter.cpp:33: CFile/CFile2_1.h: In member function 'char CFile::getchar()': CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 256 | register char c; | ^ -In file included from CSeqNameList.h:38, - from CBlastParser.h:52: +In file included from CSequences2.h:42, + from bait-fisher-helper.cpp:32: CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; @@ -416,27 +452,8 @@ CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 825 | register char c; | ^ -CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': -CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // - | ^~~~~~~~~~~~~~~~~~~~ -CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // - | ^~~~~~~~~~~~~~~~~~~~ -CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2627 | register bool removegaps_bool = (pflag & removegaps); // - | ^~~~~~~~~~~~~~~ -CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2628 | register bool removestars_bool = (pflag & removestars); // - | ^~~~~~~~~~~~~~~~ -In file included from CSequence_Mol2_1.h:50, - from CSequences2.h:42, - from Csequence_cluster_and_center_sequence.h:44, - from Csequence_cluster_and_center_sequence.cpp:27: -CFile/CFile2_1.h: In member function 'char CFile::getchar()': -CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 256 | register char c; - | ^ +In file included from CSeqNameList.h:38, + from CBlastParser.h:52: CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; @@ -515,8 +532,40 @@ CSequence_Mol2_1.h:825:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 825 | register char c; | ^ -In file included from CSequences2.h:42, - from bait-fisher-helper.cpp:32: +CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': +CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // + | ^~~~~~~~~~~~~~~~~~~~ +CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // + | ^~~~~~~~~~~~~~~~~~~~ +CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2627 | register bool removegaps_bool = (pflag & removegaps); // + | ^~~~~~~~~~~~~~~ +CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2628 | register bool removestars_bool = (pflag & removestars); // + | ^~~~~~~~~~~~~~~~ +CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': +CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // + | ^~~~~~~~~~~~~~~~~~~~ +CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // + | ^~~~~~~~~~~~~~~~~~~~ +CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2627 | register bool removegaps_bool = (pflag & removegaps); // + | ^~~~~~~~~~~~~~~ +CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2628 | register bool removestars_bool = (pflag & removestars); // + | ^~~~~~~~~~~~~~~~ +In file included from CSequence_Mol2_1.h:50, + from CSequences2.h:42, + from Csequence_cluster_and_center_sequence.h:44, + from Csequence_cluster_and_center_sequence.cpp:27: +CFile/CFile2_1.h: In member function 'char CFile::getchar()': +CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 256 | register char c; + | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; @@ -536,13 +585,6 @@ CSequence_Mol2_1.h:342:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 342 | register char local_general_ambig = toupper(general_ambig); | ^~~~~~~~~~~~~~~~~~~ -In file included from CSequence_Mol2_1.h:50, - from GFF-class.h:34, - from bait-fisher.cpp:30: -CFile/CFile2_1.h: In member function 'char CFile::getchar()': -CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 256 | register char c; - | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getLineOfDNA_generic(CFile&, unsigned int&, processing_flag)': CSequence_Mol2_1.h:424:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 424 | register char c; @@ -615,6 +657,13 @@ CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2628 | register bool removestars_bool = (pflag & removestars); // | ^~~~~~~~~~~~~~~~ +In file included from CSequence_Mol2_1.h:50, + from GFF-class.h:34, + from bait-fisher.cpp:30: +CFile/CFile2_1.h: In member function 'char CFile::getchar()': +CFile/CFile2_1.h:256:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 256 | register char c; + | ^ CSequence_Mol2_1.h: In member function 'void CSequence_Mol::getRawLine(CFile&)': CSequence_Mol2_1.h:283:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 283 | register char c; @@ -706,19 +755,6 @@ CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2628 | register bool removestars_bool = (pflag & removestars); // | ^~~~~~~~~~~~~~~~ -CSequence_Mol2_1.h: In member function 'void CSequence_Mol::readFastaSequence_generic(CFile&, processing_flag)': -CSequence_Mol2_1.h:2625:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2625 | register bool convert_toupper_bool = (pflag & convert_toupper); // - | ^~~~~~~~~~~~~~~~~~~~ -CSequence_Mol2_1.h:2626:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2626 | register bool convert_ambig2N_bool = (pflag & convert_ambig2N); // - | ^~~~~~~~~~~~~~~~~~~~ -CSequence_Mol2_1.h:2627:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2627 | register bool removegaps_bool = (pflag & removegaps); // - | ^~~~~~~~~~~~~~~ -CSequence_Mol2_1.h:2628:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2628 | register bool removestars_bool = (pflag & removestars); // - | ^~~~~~~~~~~~~~~~ g++ -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lstdc++ bait-filter.o global-types-and-parameters.o -o BaitFilter-v1.0.6 g++ -I . -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lstdc++ bait-fisher-helper.o bait-fisher.o Csequence_cluster_and_center_sequence.o mydir-unix.o -o BaitFisher-v1.2.8 make[1]: Leaving directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' @@ -769,12 +805,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/25494/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/25494/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/62718 and its subdirectories -I: Current time: Thu Dec 25 12:01:29 -12 2025 -I: pbuilder-time-stamp: 1766707289 +I: removing directory /srv/workspace/pbuilder/25494 and its subdirectories +I: Current time: Sat Nov 23 07:39:36 +14 2024 +I: pbuilder-time-stamp: 1732297176 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.diff: 79.5% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.diff.gz b2/build.log: 86.6% -- replaced with stdout Compressing the 1st log... b1/build.log: 87.4% -- replaced with stdout Fri Nov 22 17:39:38 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_baitfisher_trixie_i386_1732297178 + touch /var/log/reproducible-builds/diffoscope_stamp_baitfisher_trixie_i386_1732297178 + RESULT=0 + systemd-run '--description=diffoscope on baitfisher/1.2.7+git20211020.de26d5c+dfsg-1 in trixie/i386' --slice=rb-build-diffoscope.slice -u rb-diffoscope-i386_10-32491 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1 --run-session -c jenkins-reproducible-trixie-diffoscope-b9c92118-8f20-4410-ad85-9c7777f48010 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/dbd-tmp-CT8EeKM ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/b1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/b2/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.changes' + false + set +x Running as unit: rb-diffoscope-i386_10-32491.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/b1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.sFBewwk1/b2/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.351s) 0.351s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.033s) 0.033s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 651ms CPU time consumed: 650ms _ _ _ __ _ _ | |__ __ _(_) |_ / _(_)___| |__ ___ _ __ | '_ \ / _` | | __| |_| / __| '_ \ / _ \ '__| | |_) | (_| | | |_| _| \__ \ | | | __/ | |_.__/ \__,_|_|\__|_| |_|___/_| |_|\___|_| Fri Nov 22 17:39:39 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Fri Nov 22 17:39:39 UTC 2024 I: baitfisher from trixie built successfully and reproducibly on i386. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-22 17:39:39] INFO: Starting at 2024-11-22 17:39:39.990845 [2024-11-22 17:39:40] INFO: Generating the pages of 1 package(s) [2024-11-22 17:39:40] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/i386/baitfisher didn't produce a buildlog, even though it has been built. [2024-11-22 17:39:40] INFO: Finished at 2024-11-22 17:39:40.415663, took: 0:00:00.424825 Fri Nov 22 17:39:40 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/i386/baitfisher.html Fri Nov 22 17:39:40 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Nov 22 17:39:40 UTC 2024 I: Submitting 8.0K b1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo.asc https://buildinfo.debian.net/8b99dda21abfce894d2624afcaa2d71079050417/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386 Fri Nov 22 17:39:41 UTC 2024 I: Submitting 8.0K b2/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo.asc https://buildinfo.debian.net/806f81fdb19d628d7618283676b2a60ba2506ca7/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386 Fri Nov 22 17:39:41 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Nov 22 17:39:41 UTC 2024 I: Done submitting .buildinfo files. Fri Nov 22 17:39:41 UTC 2024 I: Removing signed baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo.asc files: removed './b1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo.asc' removed './b2/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_i386.buildinfo.asc' 1732297181 i386 trixie baitfisher Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.rbuild.log: 84.0% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1.rbuild.log.gz [2024-11-22 17:39:42] INFO: Starting at 2024-11-22 17:39:42.243451 [2024-11-22 17:39:42] INFO: Generating the pages of 1 package(s) [2024-11-22 17:39:42] INFO: Finished at 2024-11-22 17:39:42.653555, took: 0:00:00.410110 All cleanup done. Fri Nov 22 17:39:42 UTC 2024 - total duration: 0h 2m 7s. Fri Nov 22 17:39:42 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-H7TIpOVg, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 2min 10.360s CPU time consumed: 6.961s