Running as unit: rb-build-amd64_29-58984.service; invocation ID: 94d0d055f32d4b78bff55eb4bc1df7ac ==================================================================================== Fri Oct 31 12:56:50 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_29) on jenkins, called using "ionos1-amd64 ionos15-amd64" as arguments. Fri Oct 31 12:56:50 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-WuUYQqOj" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Oct 31 12:56:50 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Fri Oct 31 12:56:50 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-1U7BQZ' Fri Oct 31 12:56:51 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Fri Oct 31 12:56:51 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-LAthsl' ok, let's check if baitfisher is building anywhere yet… ok, baitfisher is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of baitfisher in unstable on amd64 on jenkins now. 1st build will be done on ionos1-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Fri Oct 31 12:57:10 UTC 2025 I: starting to build baitfisher/unstable/amd64 on jenkins on '2025-10-31 12:56' Fri Oct 31 12:57:10 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_29/58984/console.log 1761915430 amd64 unstable baitfisher Fri Oct 31 12:57:10 UTC 2025 I: Downloading source for unstable/baitfisher=1.2.7+git20211020.de26d5c+dfsg-2 --2025-10-31 12:57:10-- http://deb.debian.org/debian/pool/main/b/baitfisher/baitfisher_1.2.7%2bgit20211020.de26d5c%2bdfsg-2.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-2.dsc’ 0K .. 100% 255M=0s 2025-10-31 12:57:10 (255 MB/s) - ‘baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.dsc’ saved [2207/2207] --2025-10-31 12:57:10-- http://deb.debian.org/debian/pool/main/b/baitfisher/baitfisher_1.2.7%2bgit20211020.de26d5c%2bdfsg-2.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-2.dsc’ 0K .. 100% 255M=0s 2025-10-31 12:57:10 (255 MB/s) - ‘baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.dsc’ saved [2207/2207] Fri Oct 31 12:57:10 UTC 2025 I: baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: baitfisher Binary: baitfisher Architecture: any Version: 1.2.7+git20211020.de26d5c+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou Homepage: https://github.com/cmayer/BaitFisher-package Standards-Version: 4.7.0 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 6a4f00c75c712c3b2011ddba7ace3f1d031da7f1 4980 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.debian.tar.xz Checksums-Sha256: 18173901d19d48a42d2f73d43f20fcbe7e9a7bc7be0d085cf396b9e06dae8103 3454988 baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz d1cb5b08e3042552127f2c226f48ff3334c49032d89770a44003787f5c520fbf 4980 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.debian.tar.xz Files: ea5113239392acc66501bb398a69a45d 3454988 baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz b18d7700fc12c0e558791d764da890ea 4980 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmdco1ARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGRJA/+P1GMEfJm6uKtPjqKml50n7utsi7rR0OI PGx+rI4kt0B6cXHka2q6o5wA0cc9JvU6hCm4AqalLruvbd0NIXgKa2q63FWTWZil YAN9a3UwmhOxB5Lf0bu3absoq3zBHOr2Ymd79Am7FpSOMn91w7DBM1VNd4txh0hf sx0vNgtS5PLnOeIGcp//9kkDY7Sbn/+86mO//HWFQ/EvvFjoM1TXRYwdGSeALdXU NbjsOQLYvr9/PQC8/IJwabAr8m7RYNkVqruWsVqPaXpxlsYXuBq/uAdy9gca5m7b dPBisJpfz4gZ9Ul984sTTBoxWJbFeDc7QeVRyx5LHvPJGc6GR3JV48XzADI10ysa AJB9kzpYa6IOHQpnAdR3+nCPLK8ozGd3+n5wGgA7BohOItvu/bXKL/Rz/PbVaTOA 6Cbm8Az4ef5HFI8SM+DsOU24RXfU6k0DlkbtTmQsAu3VQUYAwZjBrpx0+TNXFsma ErbtdVpbXvSE6JzPf2afRnk1zcPeYqtZGSpelglfsY8crECzU4fr8uOAuBQJ/nZW tWf8V/aSp6YyRnm29tIvVJ6uwNbKakUb3EY3vsByvuxt4OVSEaAjh607v98NGjLM rsl7syx6+tzcvo5UXyC1X8raUIa8MGVZZaU19TxQ9Zm0AjBeGMcgSjr0KvWE7n8h wFcEO791HjU= =JXgM -----END PGP SIGNATURE----- Fri Oct 31 12:57:10 UTC 2025 I: Checking whether the package is not for us Fri Oct 31 12:57:10 UTC 2025 I: Starting 1st build on remote node ionos1-amd64.debian.net. Fri Oct 31 12:57:10 UTC 2025 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Fri Oct 31 12:57:10 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Fri Oct 31 12:57:10 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-clyQbK' ==================================================================================== Fri Oct 31 12:57:11 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "1 baitfisher unstable /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K 1.2.7+git20211020.de26d5c+dfsg-2" as arguments. Fri Oct 31 12:57:11 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-ZBUCkN4l" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Oct 31 12:57:11 UTC 2025 I: Downloading source for unstable/baitfisher=1.2.7+git20211020.de26d5c+dfsg-2 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 unstable/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-2 (dsc) [2207 B] Get:2 http://deb.debian.org/debian unstable/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-2 (tar) [3455 kB] Get:3 http://deb.debian.org/debian unstable/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-2 (diff) [4980 B] Fetched 3462 kB in 0s (122 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 unstable/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-2 (dsc) [2207 B] Get:2 http://deb.debian.org/debian unstable/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-2 (tar) [3455 kB] Get:3 http://deb.debian.org/debian unstable/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-2 (diff) [4980 B] Fetched 3462 kB in 0s (122 MB/s) Download complete and in download only mode ============================================================================= Building baitfisher in unstable on amd64 on ionos1-amd64 now. Date: Fri Oct 31 12:57:11 UTC 2025 Date UTC: Fri Oct 31 12:57:11 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: Fri Oct 31 00:57:11 -12 2025 I: pbuilder-time-stamp: 1761915431 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.dsc] I: copying [./baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz] I: copying [./baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.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-2.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/851012/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='6736552dd588420b9c186f6f51bb739c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='851012' 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.wkcVqB1K/pbuilderrc_XPIm --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/b1 --logfile b1/build.log baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/851012/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: amd64 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 ... 19862 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} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtclap-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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 14.8 MB of archives. After unpacking 58.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.2-4 [98.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-2 [325 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-2 [877 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-7 [540 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.194-1 [185 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.1+dfsg-0.3 [640 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.28 [941 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libtclap-dev amd64 1.2.5-1+b2 [3359 kB] Fetched 14.8 MB in 2s (6074 kB/s) Preconfiguring packages ... 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 ... 19862 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... 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-2_source.changes dpkg-buildpackage: info: source package baitfisher dpkg-buildpackage: info: source version 1.2.7+git20211020.de26d5c+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j40 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 -j40 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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); // | ^~~~~~~~~~~~~~~~ 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 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::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: 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: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::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::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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2_amd64.deb'. dpkg-deb: building package 'baitfisher-dbgsym' in '../baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/851012 and its subdirectories I: Current time: Fri Oct 31 00:57:56 -12 2025 I: pbuilder-time-stamp: 1761915476 Fri Oct 31 12:57:56 UTC 2025 I: Signing ./b1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo as baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo.asc Fri Oct 31 12:57:56 UTC 2025 I: Signed ./b1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo as ./b1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo.asc Fri Oct 31 12:57:56 UTC 2025 - build #1 for baitfisher/unstable/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Fri Oct 31 12:57:56 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-ZBUCkN4l, removing. /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Oct 31 12:57 b1 drwxrwxr-x 2 jenkins jenkins 4096 Oct 31 12:57 b2 -rw-rw-r-- 1 jenkins jenkins 2207 Dec 13 2024 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.dsc -rw------- 1 jenkins jenkins 3457 Oct 31 12:57 rbuildlog.rzFPQ3l /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/b1: total 2216 -rw-r--r-- 1 jenkins jenkins 1957736 Oct 31 12:57 baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 4980 Oct 31 12:57 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2207 Oct 31 12:57 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 5083 Oct 31 12:57 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5965 Oct 31 12:57 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1730 Oct 31 12:57 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 217568 Oct 31 12:57 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1571 Oct 31 12:57 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_source.changes -rw-r--r-- 1 jenkins jenkins 53002 Oct 31 12:57 build.log /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/b2: total 0 Fri Oct 31 12:57:56 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Oct 31 00:57:11 -12 2025 I: pbuilder-time-stamp: 1761915431 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.dsc] I: copying [./baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz] I: copying [./baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.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-2.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/851012/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='6736552dd588420b9c186f6f51bb739c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='851012' 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.wkcVqB1K/pbuilderrc_XPIm --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/b1 --logfile b1/build.log baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/851012/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: amd64 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 ... 19862 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} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtclap-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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 14.8 MB of archives. After unpacking 58.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.2-4 [98.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-2 [325 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-2 [877 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-7 [540 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.194-1 [185 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.1+dfsg-0.3 [640 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.28 [941 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libtclap-dev amd64 1.2.5-1+b2 [3359 kB] Fetched 14.8 MB in 2s (6074 kB/s) Preconfiguring packages ... 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 ... 19862 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... 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Setting up libdebhelper-perl (13.28) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-2) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.194-1) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up libtclap-dev (1.2.5-1+b2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.18.1-2) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (21) ... 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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-2_source.changes dpkg-buildpackage: info: source package baitfisher dpkg-buildpackage: info: source version 1.2.7+git20211020.de26d5c+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j40 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 -j40 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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); // | ^~~~~~~~~~~~~~~~ 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 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::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: 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: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::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::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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2_amd64.deb'. dpkg-deb: building package 'baitfisher-dbgsym' in '../baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/851012 and its subdirectories I: Current time: Fri Oct 31 00:57:56 -12 2025 I: pbuilder-time-stamp: 1761915476 Fri Oct 31 12:57:56 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Fri Oct 31 12:57:56 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Fri Oct 31 12:57:56 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Fri Oct 31 12:57:56 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-TiM810' ==================================================================================== Thu Dec 3 19:20:59 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "2 baitfisher unstable /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K 1.2.7+git20211020.de26d5c+dfsg-2" as arguments. Thu Dec 3 19:20:59 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-py2SdgSN" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Dec 3 19:20:59 UTC 2026 I: Downloading source for unstable/baitfisher=1.2.7+git20211020.de26d5c+dfsg-2 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 unstable/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-2 (dsc) [2207 B] Get:2 http://deb.debian.org/debian unstable/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-2 (tar) [3455 kB] Get:3 http://deb.debian.org/debian unstable/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-2 (diff) [4980 B] Fetched 3462 kB in 0s (81.2 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 unstable/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-2 (dsc) [2207 B] Get:2 http://deb.debian.org/debian unstable/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-2 (tar) [3455 kB] Get:3 http://deb.debian.org/debian unstable/main baitfisher 1.2.7+git20211020.de26d5c+dfsg-2 (diff) [4980 B] Fetched 3462 kB in 0s (81.2 MB/s) Download complete and in download only mode ============================================================================= Re-Building baitfisher in unstable on amd64 on ionos15-amd64 now. Date: Thu Dec 3 19:20:59 UTC 2026 Date UTC: Thu Dec 3 19:20:59 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/pbuilderrc_RF9l + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${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.wkcVqB1K/pbuilderrc_RF9l --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/b2 --logfile b2/build.log baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.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: Fri Dec 4 09:21:00 +14 2026 I: pbuilder-time-stamp: 1796325660 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.dsc] I: copying [./baitfisher_1.2.7+git20211020.de26d5c+dfsg.orig.tar.xz] I: copying [./baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.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-2.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/2597991/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. 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 Dec 3 19:21 /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/2597991/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2597991/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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=7405d5660fa84f239ee8a2574522ab5a LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-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=2597991 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.wkcVqB1K/pbuilderrc_RF9l --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/b2 --logfile b2/build.log baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.dsc' SUDO_GID=111 SUDO_HOME=/var/lib/jenkins SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2597991/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: amd64 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 ... 19862 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} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtclap-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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 14.8 MB of archives. After unpacking 58.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.2-4 [98.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-2 [325 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-2 [877 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-7 [540 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.194-1 [185 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.1+dfsg-0.3 [640 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.28 [941 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libtclap-dev amd64 1.2.5-1+b2 [3359 kB] Fetched 14.8 MB in 0s (37.5 MB/s) Preconfiguring packages ... 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 ... 19862 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.41.2-4_amd64.deb ... Unpacking bsdextrautils (2.41.2-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.20-2_amd64.deb ... Unpacking m4 (1.4.20-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.18.1-2_all.deb ... Unpacking automake (1:1.18.1-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.28_all.deb ... Unpacking libdebhelper-perl (13.28) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-7_all.deb ... Unpacking libtool (2.5.4-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... 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_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../22-libelf1t64_0.194-1_amd64.deb ... Unpacking libelf1t64:amd64 (0.194-1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../24-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../25-libxml2-16_2.15.1+dfsg-0.3_amd64.deb ... Unpacking libxml2-16:amd64 (2.15.1+dfsg-0.3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... 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_13.28_all.deb ... Unpacking debhelper (13.28) ... Selecting previously unselected package help2man. Preparing to unpack .../30-help2man_1.49.3_amd64.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package libtclap-dev. Preparing to unpack .../31-libtclap-dev_1.2.5-1+b2_amd64.deb ... Unpacking libtclap-dev (1.2.5-1+b2) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41.2-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.15.1+dfsg-0.3) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2597991/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2597991/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-2_source.changes dpkg-buildpackage: info: source package baitfisher dpkg-buildpackage: info: source version 1.2.7+git20211020.de26d5c+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j42 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 -j42 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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; | ^ 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::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 | ^~~~~~~~~~~~~~~~~~~~ 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: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::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 | ^~~~~~~~~~~~~~~~~~ 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; | ^ 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 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; | ^ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-2_amd64.deb'. dpkg-deb: building package 'baitfisher-dbgsym' in '../baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2597991/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2597991/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/2597991 and its subdirectories I: Current time: Fri Dec 4 09:22:43 +14 2026 I: pbuilder-time-stamp: 1796325763 + false + set +x Thu Dec 3 19:22:43 UTC 2026 I: Signing ./b2/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo as baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo.asc Thu Dec 3 19:22:43 UTC 2026 I: Signed ./b2/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo as ./b2/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo.asc Thu Dec 3 19:22:43 UTC 2026 - build #2 for baitfisher/unstable/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Thu Dec 3 19:22:43 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-py2SdgSN, removing. /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K: total 72 drwxrwxr-x 2 jenkins jenkins 4096 Oct 31 12:57 b1 drwxrwxr-x 2 jenkins jenkins 4096 Oct 31 12:59 b2 -rw-rw-r-- 1 jenkins jenkins 2207 Dec 13 2024 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.dsc -rw------- 1 jenkins jenkins 56747 Oct 31 12:57 rbuildlog.rzFPQ3l /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/b1: total 2228 -rw-r--r-- 1 jenkins jenkins 1957736 Oct 31 12:57 baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 4980 Oct 31 12:57 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2207 Oct 31 12:57 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 5083 Oct 31 12:57 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5965 Oct 31 12:57 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1730 Oct 31 12:57 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 217568 Oct 31 12:57 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1571 Oct 31 12:57 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_source.changes -rw-r--r-- 1 jenkins jenkins 53002 Oct 31 12:57 build.log /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/b2: total 2220 -rw-r--r-- 1 jenkins jenkins 1957736 Oct 31 12:59 baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 4980 Oct 31 12:59 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2207 Oct 31 12:59 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.dsc -rw-rw-r-- 1 jenkins jenkins 5083 Oct 31 12:59 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5965 Oct 31 12:59 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1730 Oct 31 12:59 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 217568 Oct 31 12:59 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb -rw-rw-r-- 1 jenkins jenkins 1571 Oct 31 12:59 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_source.changes -rw-rw-r-- 1 jenkins jenkins 54937 Oct 31 12:59 build.log Fri Oct 31 12:59:49 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Fri Oct 31 12:59:50 UTC 2025 I: baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.changes: Format: 1.8 Date: Fri, 13 Dec 2024 21:24:05 +0100 Source: baitfisher Binary: baitfisher baitfisher-dbgsym Architecture: amd64 Version: 1.2.7+git20211020.de26d5c+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: baitfisher - software package for designing hybrid enrichment probes Closes: 1043995 Changes: baitfisher (1.2.7+git20211020.de26d5c+dfsg-2) unstable; urgency=medium . * Team upload. * Fix clean target Closes: #1043995 * Standards-Version: 4.7.0 (routine-update) Checksums-Sha1: 34627b54f29b7d7794869695e22e1e69302c05c8 1957736 baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb 8eead59349a6460f4abd500f318143dfba7c6c4a 5083 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo 599bf37fd585ef742cadfd45735335298abef840 217568 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb Checksums-Sha256: fd7cc06e351b6b0f8e5dc846540b08bb89f77ed8e37ca2de61b5ee187447c880 1957736 baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb af928d984694be16b26c9e211a05b94884994c3351b80592f58cc60c5157ecf5 5083 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo 13ed9d9400c51a7850e44c050390e390540dbaf18f28611e269c33a1da742fa5 217568 baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb Files: 9fc8f43925c9f9a127623010dccc5174 1957736 debug optional baitfisher-dbgsym_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb 3390d6ec92fab65f5d545d17d3a4ee09 5083 science optional baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo 2137570c5db7fd9a38b924f862ef9a74 217568 science optional baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-10-31 12:57:56.666853467 +0000 +++ b2/build.log 2025-10-31 12:59:49.510992827 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Oct 31 00:57:11 -12 2025 -I: pbuilder-time-stamp: 1761915431 +I: Current time: Fri Dec 4 09:21:00 +14 2026 +I: pbuilder-time-stamp: 1796325660 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -24,53 +24,85 @@ 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/851012/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2597991/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +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 Dec 3 19:21 /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/2597991/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2597991/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='6736552dd588420b9c186f6f51bb739c' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='851012' - PS1='# ' - PS2='> ' + INVOCATION_ID=7405d5660fa84f239ee8a2574522ab5a + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=2597991 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.wkcVqB1K/pbuilderrc_XPIm --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/b1 --logfile b1/build.log baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.wkcVqB1K/pbuilderrc_RF9l --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/b2 --logfile b2/build.log baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/851012/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2597991/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -144,7 +176,7 @@ Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.28 [941 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libtclap-dev amd64 1.2.5-1+b2 [3359 kB] -Fetched 14.8 MB in 2s (6074 kB/s) +Fetched 14.8 MB in 0s (37.5 MB/s) Preconfiguring packages ... 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 ... 19862 files and directories currently installed.) @@ -287,7 +319,11 @@ 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-2_source.changes +I: user script /srv/workspace/pbuilder/2597991/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2597991/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-2_source.changes dpkg-buildpackage: info: source package baitfisher dpkg-buildpackage: info: source version 1.2.7+git20211020.de26d5c+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -297,7 +333,7 @@ debian/rules clean dh clean dh_auto_clean - make -j40 clean + make -j42 clean make[1]: Entering directory '/build/reproducible-path/baitfisher-1.2.7+git20211020.de26d5c+dfsg' rm -f *.o rm -f BaitFisher-v1.2.8 @@ -310,7 +346,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j40 INSTALL="install --strip-program=true" + make -j42 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c bait-fisher.cpp -o bait-fisher.o @@ -318,11 +354,6 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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: @@ -330,8 +361,8 @@ 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: +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; @@ -410,8 +441,26 @@ 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: +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::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; @@ -447,6 +496,14 @@ 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 | ^~~~~~~~~~~~~~~~~~~~ +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:431:30: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 431 | register bool removegaps_bool = (pflag & removegaps); // handled | ^~~~~~~~~~~~~~~ @@ -490,34 +547,6 @@ 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 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; @@ -562,6 +591,11 @@ 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 | ^~~~~~~~~~~~~~~~~~ +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; + | ^ 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; @@ -588,14 +622,18 @@ 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::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: 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); // | ^~~~~~~~~~~~~~~~~~~~ @@ -605,10 +643,21 @@ 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::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 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; @@ -700,19 +749,6 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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' @@ -763,12 +799,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2597991/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2597991/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/851012 and its subdirectories -I: Current time: Fri Oct 31 00:57:56 -12 2025 -I: pbuilder-time-stamp: 1761915476 +I: removing directory /srv/workspace/pbuilder/2597991 and its subdirectories +I: Current time: Fri Dec 4 09:22:43 +14 2026 +I: pbuilder-time-stamp: 1796325763 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.diff: 81.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.diff.gz b2/build.log: 86.9% -- replaced with stdout Compressing the 1st log... b1/build.log: 87.7% -- replaced with stdout Fri Oct 31 12:59:51 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_baitfisher_unstable_amd64_1761915591 + touch /var/log/reproducible-builds/diffoscope_stamp_baitfisher_unstable_amd64_1761915591 + RESULT=0 + systemd-run '--description=diffoscope on baitfisher/1.2.7+git20211020.de26d5c+dfsg-2 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_29-58984 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K --run-session -c jenkins-reproducible-unstable-diffoscope-8d46e85e-e966-4c2c-bf57-cc69570f8682 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/dbd-tmp-yxE1UP4 ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/b1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/b2/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_29-58984.service; invocation ID: c69e25dbdc474bc38bef66f838f8eb9b # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/b1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.wkcVqB1K/b2/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 198ms CPU time consumed: 169ms Memory peak: 18M (swap: 0B) _ _ _ __ _ _ | |__ __ _(_) |_ / _(_)___| |__ ___ _ __ | '_ \ / _` | | __| |_| / __| '_ \ / _ \ '__| | |_) | (_| | | |_| _| \__ \ | | | __/ | |_.__/ \__,_|_|\__|_| |_|___/_| |_|\___|_| Fri Oct 31 12:59:51 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Fri Oct 31 12:59:51 UTC 2025 I: baitfisher from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-10-31 12:59:52] INFO: Starting at 2025-10-31 12:59:52.003914 [2025-10-31 12:59:52] INFO: Generating the pages of 1 package(s) [2025-10-31 12:59:52] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/baitfisher didn't produce a buildlog, even though it has been built. [2025-10-31 12:59:52] INFO: Finished at 2025-10-31 12:59:52.266463, took: 0:00:00.262553 Fri Oct 31 12:59:52 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/baitfisher.html Fri Oct 31 12:59:52 UTC 2025 I: Removing signed baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo.asc files: removed './b1/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo.asc' removed './b2/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.buildinfo.asc' 1761915592 amd64 unstable baitfisher Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.rbuild.log: 84.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2.rbuild.log.gz [2025-10-31 12:59:52] INFO: Starting at 2025-10-31 12:59:52.596661 [2025-10-31 12:59:52] INFO: Generating the pages of 1 package(s) [2025-10-31 12:59:52] INFO: Finished at 2025-10-31 12:59:52.858240, took: 0:00:00.261584 All cleanup done. Fri Oct 31 12:59:52 UTC 2025 - total duration: 0h 3m 1s. Fri Oct 31 12:59:52 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-WuUYQqOj, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 3min 2.211s CPU time consumed: 3.098s Memory peak: 44.7M (swap: 0B)