Mon Aug 25 01:40:18 UTC 2025 I: starting to build probalign/forky/amd64 on jenkins on '2025-08-25 01:40' Mon Aug 25 01:40:18 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_26/53734/console.log Mon Aug 25 01:40:18 UTC 2025 I: Downloading source for forky/probalign=1.4-10 --2025-08-25 01:40:18-- http://deb.debian.org/debian/pool/main/p/probalign/probalign_1.4-10.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1971 (1.9K) [text/prs.lines.tag] Saving to: ‘probalign_1.4-10.dsc’ 0K . 100% 262M=0s 2025-08-25 01:40:18 (262 MB/s) - ‘probalign_1.4-10.dsc’ saved [1971/1971] Mon Aug 25 01:40:18 UTC 2025 I: probalign_1.4-10.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: probalign Binary: probalign Architecture: any Version: 1.4-10 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://web.njit.edu/~usman/probalign/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/probalign Vcs-Git: https://salsa.debian.org/med-team/probalign.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), help2man Package-List: probalign deb science optional arch=any Checksums-Sha1: b03b52e084da024780dfe051213c11e664592aeb 30060 probalign_1.4.orig.tar.gz a9bf04ea52818bfd737645c96f4235b813e15fad 4916 probalign_1.4-10.debian.tar.xz Checksums-Sha256: b221a27c5cbc3e5c707b0514c71301806074a2bf54047b57bd2d40497b663c29 30060 probalign_1.4.orig.tar.gz c28a26c9c36682e17dfd5da67b29058ba750b6d1dcb694003ee8cf52f141cfc3 4916 probalign_1.4-10.debian.tar.xz Files: 255d6ab775867a54d3727764b8dff561 30060 probalign_1.4.orig.tar.gz 37ad63fb22faa20345333dd9a2e6c6e6 4916 probalign_1.4-10.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmPJQxERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGh/w//d9nUAzZDMLKfSmVCj0MGGKCxs7AJiBYa 1r219oAiSyFT0vO+NlRu1bgMRdkrJ5K31KZP0riZQLhmwtdJCqet0ucvfaftaAzD SHeeigdFCijW7HMY7CjdVt8VW0jsV7TgonbGB9BPZjYr9gu/zZlmLnV6rL6IKGl/ QhXgVPP3akG11afV+yG+n4vb0hMd31sh/I1ZJz242DNhqYUHXsr2i1BBptTrji9i RMw/wMdrIBq2bU1Wilctum7Jk/FpxaqOWO93GhRQFyOaduO7ZS5zb6YSyQfUwIsy YIgW92NLd0+qGLzRyp8N8974a5wewydiMVQiyE5HFkT2OkOcf/pKeS0PML8F09p3 811Of+Pc/3YaVnn2EV8ypBJbKygyG94M9Oei9Msj9Wgr8c3OkagqEDCde27HCQAB DgUs8DktA9Zh9x3jysRLLMdFqM0cZu+BLNeDS8iCyD4KI9QqG39GbzEk1UfTF1z+ 50z40fIuPdLY+P+h+7Dl/kpvf0ynoFQYcpRSmerlk0U9tbUaRfeEYyvJ0AkId0dA sRa6RUUC3ElgqYnWCcbCUd+ukcSzhsEXIPAm+4PAZl4vGAaxbA812oAUrTuBSeNa /RbpPyho9Ly9Fe7LNheD54Mz0FUE1X4Nmxdwv+cDNL0dxN3LkxARneXO+CdnifvP lui2mPieYXA= =8del -----END PGP SIGNATURE----- Mon Aug 25 01:40:18 UTC 2025 I: Checking whether the package is not for us Mon Aug 25 01:40:18 UTC 2025 I: Starting 1st build on remote node ionos5-amd64.debian.net. Mon Aug 25 01:40:18 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Mon Aug 25 01:42:01 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Sep 26 20:03:19 -12 2026 I: pbuilder-time-stamp: 1790496199 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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 [probalign_1.4-10.dsc] I: copying [./probalign_1.4.orig.tar.gz] I: copying [./probalign_1.4-10.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./probalign_1.4-10.dsc: no acceptable signature found dpkg-source: info: extracting probalign in probalign-1.4 dpkg-source: info: unpacking probalign_1.4.orig.tar.gz dpkg-source: info: unpacking probalign_1.4-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc_fixes.patch dpkg-source: info: applying fix-gcc-4.6.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying mayhem.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2493688/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=42 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='7eafc05d587b4535ab6650b4e09add5a' 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='2493688' 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.QsF2X1Ay/pbuilderrc_Ht9r --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QsF2X1Ay/b1 --logfile b1/build.log probalign_1.4-10.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://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) 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/2493688/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 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19855 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. 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} 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, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 11.4 MB of archives. After unpacking 43.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-1 [94.7 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.25 [91.6 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-4 [539 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 23 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.1 [640 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 debhelper all 13.25 [937 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 help2man amd64 1.49.3 [198 kB] Fetched 11.4 MB in 5s (2076 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 ... 19855 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_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... 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_2.41.1-1_amd64.deb ... Unpacking bsdextrautils (2.41.1-1) ... 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_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... 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%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... 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_13.25_all.deb ... Unpacking libdebhelper-perl (13.25) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../22-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... 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_2.14.5+dfsg-0.1_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.1) ... 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_13.25_all.deb ... Unpacking debhelper (13.25) ... Selecting previously unselected package help2man. Preparing to unpack .../30-help2man_1.49.3_amd64.deb ... Unpacking help2man (1.49.3) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41.1-1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.1) ... Setting up libdebhelper-perl (13.25) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... 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 dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.25) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/probalign-1.4/ && 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 > ../probalign_1.4-10_source.changes dpkg-buildpackage: info: source package probalign dpkg-buildpackage: info: source version 1.4-10 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/probalign-1.4' rm -f probalign make[1]: Leaving directory '/build/reproducible-path/probalign-1.4' 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/probalign-1.4' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/probalign-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -W -Wall -funroll-loops -lm -o probalign Main.cc PostProbs.cc ComputeAlignment.cc ReadMatrix.cc -Wl,-z,relro -Wl,-z,now In file included from MultiSequence.h:18, from Main.cc:9: Sequence.h: In member function 'Sequence* Sequence::Clone() const': Sequence.h:293:21: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 293 | *(ret->data) = *data; | ^~~~ In file included from Main.cc:8: SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = char]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ PostProbs.cc: In function 'VF* revers_partf(long double**, float, float, float)': PostProbs.cc:312:17: warning: variable 'zz' set but not used [-Wunused-but-set-variable] 312 | long double zz = 0; | ^~ PostProbs.cc: In function 'VF* ComputePostProbs(int, int, std::string, std::string)': PostProbs.cc:892:9: warning: variable 'stock_loop' set but not used [-Wunused-but-set-variable] 892 | int stock_loop = 1; | ^~~~~~~~~~ PostProbs.cc: In function 'VF* revers_partf(long double**, float, float, float)': PostProbs.cc:508:18: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 508 | delete(Zf); | ^ PostProbs.cc:180:33: note: returned from 'void* operator new [](std::size_t)' 180 | Zf = new long double *[2]; | ^ PostProbs.cc:511:18: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 511 | delete(Ze); | ^ PostProbs.cc:179:33: note: returned from 'void* operator new [](std::size_t)' 179 | Ze = new long double *[2]; | ^ PostProbs.cc:515:18: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 515 | delete(Zm); | ^ PostProbs.cc:178:33: note: returned from 'void* operator new [](std::size_t)' 178 | Zm = new long double *[2]; | ^ PostProbs.cc:508:18: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 508 | delete(Zf); | ^ PostProbs.cc:180:33: note: returned from 'void* operator new [](std::size_t)' 180 | Zf = new long double *[2]; | ^ PostProbs.cc:511:18: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 511 | delete(Ze); | ^ PostProbs.cc:179:33: note: returned from 'void* operator new [](std::size_t)' 179 | Ze = new long double *[2]; | ^ PostProbs.cc:515:18: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 515 | delete(Zm); | ^ PostProbs.cc:178:33: note: returned from 'void* operator new [](std::size_t)' 178 | Zm = new long double *[2]; | ^ PostProbs.cc: In function 'long double** partf(float, float, float)': PostProbs.cc:871:21: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 871 | delete(Zf[0]); | ^ PostProbs.cc:590:56: note: returned from 'void* operator new [](std::size_t)' 590 | Zf[0] = new long double[sequences[0].length + 1]; | ^ PostProbs.cc:872:21: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 872 | delete(Ze[0]); | ^ PostProbs.cc:589:56: note: returned from 'void* operator new [](std::size_t)' 589 | Ze[0] = new long double[sequences[0].length + 1]; | ^ PostProbs.cc:873:21: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 873 | delete(Zf[1]); | ^ PostProbs.cc:592:56: note: returned from 'void* operator new [](std::size_t)' 592 | Zf[1] = new long double[sequences[0].length + 1]; | ^ PostProbs.cc:874:21: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 874 | delete(Ze[1]); | ^ PostProbs.cc:591:56: note: returned from 'void* operator new [](std::size_t)' 591 | Ze[1] = new long double[sequences[0].length + 1]; | ^ PostProbs.cc:877:14: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 877 | delete(Zf); | ^ PostProbs.cc:584:33: note: returned from 'void* operator new [](std::size_t)' 584 | Zf = new long double *[2]; | ^ PostProbs.cc:878:14: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 878 | delete(Ze); | ^ PostProbs.cc:583:33: note: returned from 'void* operator new [](std::size_t)' 583 | Ze = new long double *[2]; | ^ In file included from MultiSequence.h:18, from ComputeAlignment.cc:12: Sequence.h: In member function 'Sequence* Sequence::Clone() const': Sequence.h:293:21: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 293 | *(ret->data) = *data; | ^~~~ In file included from ComputeAlignment.cc:10: SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = char]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ ReadMatrix.cc: In function 'void read_matrix(score_matrix)': ReadMatrix.cc:100:10: warning: storing the address of local variable 'matrx' in 'bases' [-Wdangling-pointer=] 100 | bases=(char *)matrx.monomers; | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ ReadMatrix.cc:96:38: note: 'matrx' declared here 96 | inline void read_matrix(score_matrix matrx) | ~~~~~~~~~~~~~^~~~~ ReadMatrix.cc:19:23: note: 'bases' declared here 19 | extern char *aminos, *bases, matrixtype[20]; | ^~~~~ make[1]: Leaving directory '/build/reproducible-path/probalign-1.4' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/probalign-1.4' help2man --name="Align sequences in MFAFILE(s) and print result to standard output" \ --no-discard-stderr \ --version-string=1.4 \ --help-option=" " \ --no-info \ /build/reproducible-path/probalign-1.4/probalign > /build/reproducible-path/probalign-1.4/debian/probalign/usr/share/man/man1/probalign.1 make[1]: Leaving directory '/build/reproducible-path/probalign-1.4' dh_install dh_installdocs dh_installchangelogs dh_installman 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 'probalign' in '../probalign_1.4-10_amd64.deb'. dpkg-deb: building package 'probalign-dbgsym' in '../probalign-dbgsym_1.4-10_amd64.deb'. dpkg-genbuildinfo --build=binary -O../probalign_1.4-10_amd64.buildinfo dpkg-genchanges --build=binary -O../probalign_1.4-10_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/2493688 and its subdirectories I: Current time: Sat Sep 26 20:05:00 -12 2026 I: pbuilder-time-stamp: 1790496300 Mon Aug 25 01:42:02 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Mon Aug 25 01:42:02 UTC 2025 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Mon Aug 25 01:42:45 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Mon Aug 25 01:42:46 UTC 2025 I: probalign_1.4-10_amd64.changes: Format: 1.8 Date: Thu, 19 Jan 2023 14:15:16 +0100 Source: probalign Binary: probalign probalign-dbgsym Architecture: amd64 Version: 1.4-10 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: probalign - multiple sequence alignment using partition function posterior pr Changes: probalign (1.4-10) unstable; urgency=medium . * Fix Homepage and download location * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 92bea6e13ab9e3a34b9c5bfe3e1d423acf266890 601164 probalign-dbgsym_1.4-10_amd64.deb 66efca2f783d6b7c82661228fc59f0087fbc5c49 4952 probalign_1.4-10_amd64.buildinfo eaeead82200dce66ccd7bc76aaeb9177e63093a8 73172 probalign_1.4-10_amd64.deb Checksums-Sha256: ede19f5bac1c75615de54a546eee7b66b3f432d9866fed39050c45e39bff5905 601164 probalign-dbgsym_1.4-10_amd64.deb 236c1887c6063296ed3f880f8339a1ca68a5e9f562673bdfb1fb080e70bbb067 4952 probalign_1.4-10_amd64.buildinfo 04cde963781bd7334a766c22de3ede4e6a419a11eff6fdbfab90255522f35521 73172 probalign_1.4-10_amd64.deb Files: c512b214e6729fe242db4ce604de8b37 601164 debug optional probalign-dbgsym_1.4-10_amd64.deb c27e2c6520ac65464a811b75ee4af5a8 4952 science optional probalign_1.4-10_amd64.buildinfo 6a17f23efa54ad3df4cd8cc6d234d3e3 73172 science optional probalign_1.4-10_amd64.deb Mon Aug 25 01:42:46 UTC 2025 I: diffoscope 305 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_26-53734.service; invocation ID: e4966660f3534851a88b22d6b407b644 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.QsF2X1Ay/probalign_1.4-10.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.QsF2X1Ay/probalign_1.4-10.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.QsF2X1Ay/probalign_1.4-10.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.QsF2X1Ay/b1/probalign_1.4-10_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.QsF2X1Ay/b2/probalign_1.4-10_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: 232ms CPU time consumed: 178ms Memory peak: 18.7M (swap: 0B) Mon Aug 25 01:54:51 UTC 2025 I: diffoscope 305 found no differences in the changes files, and a .buildinfo file also exists. Mon Aug 25 01:54:51 UTC 2025 I: probalign from forky built successfully and reproducibly on amd64. Mon Aug 25 01:54:52 UTC 2025 I: Removing signed probalign_1.4-10_amd64.buildinfo.asc files: removed './b1/probalign_1.4-10_amd64.buildinfo.asc' removed './b2/probalign_1.4-10_amd64.buildinfo.asc'