Thu Sep 11 22:42:54 UTC 2025 I: starting to build probcons/forky/arm64 on jenkins on '2025-09-11 22:42' Thu Sep 11 22:42:54 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_10/96499/console.log Thu Sep 11 22:42:54 UTC 2025 I: Downloading source for forky/probcons=1.12-15 --2025-09-11 22:42:54-- http://deb.debian.org/debian/pool/main/p/probcons/probcons_1.12-15.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2167 (2.1K) [text/prs.lines.tag] Saving to: ‘probcons_1.12-15.dsc’ 0K .. 100% 214M=0s 2025-09-11 22:42:54 (214 MB/s) - ‘probcons_1.12-15.dsc’ saved [2167/2167] Thu Sep 11 22:42:54 UTC 2025 I: probcons_1.12-15.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: probcons Binary: probcons, probcons-extra Architecture: any Version: 1.12-15 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: http://probcons.stanford.edu/ Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/probcons Vcs-Git: https://salsa.debian.org/med-team/probcons.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: probcons deb science optional arch=any probcons-extra deb science optional arch=any Checksums-Sha1: ee6ce81777c9ce366f575ab4096ff07f39af9829 43200 probcons_1.12.orig.tar.gz 2dd1a9bf4927229dbfec6b4ae384cbde1c5b9db4 13388 probcons_1.12-15.debian.tar.xz Checksums-Sha256: ecf3f9ab9ad47e14787c76d1c64aeea5533d4038c4be0236c00cdd79104cf383 43200 probcons_1.12.orig.tar.gz 02b93a44c6e8af98757804de60cc85239b771a84a4b2c876daab7c2922e66eaa 13388 probcons_1.12-15.debian.tar.xz Files: a658e24b07aaa9e8194317345133ac9d 43200 probcons_1.12.orig.tar.gz 9f3cb48056a7fbf677158c6974b41390 13388 probcons_1.12-15.debian.tar.xz Dgit: 33fa077b566dcec26db13d71d0ccdeb579d40fe0 debian archive/debian/1.12-15 https://git.dgit.debian.org/probcons -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmi/Q8sUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdp7ERAAlbC3g8uGSdPl1F5cKAD6zALr9IBA m/Me17wcLcBj0GIBQ2gDPVnQe4QEp2G1Fl6QN9sFRAvBZdS1hrgiIrU+ZyT2PpwN l7Ydi2y7UxzDpbCLSilOhRYu/dM4AbpLWVM+cWbs633e5r1+wsz5YkJaOKHx1uqF MScVmTWEJqs6u8hB2zBJPPtA1cQ7kBMqjyN0zateROgrdlUoXHrmTU4utX3C3pwp v0mQmshV6W59W2iXfPWtWbNSiYQ2Wz0C+cIkaE2WP/8se+NXYrWmlpM9j7A12XNz 5hfrMUcdsP8hZTiTFwiMocc3ftzDflLEvBOSz9KCuObcPLz/1Lqrezv5CBLys/3B wHWb8YzHcbrBjyX4cAurFRTIdfkma/BcXsvx4BjkjI/Z+oBJtO1tpWEznHxsgGQE Rs0Xs4896nTnkhFyqZg7DTKI5xVnLPdLIPN0RUEbZZzYd7Nmo0z4j+F2GHdYd5Qr glKU+rTOeu506Qznxwz2PrKVnOZ1IrV6LqR45TO8UeNnFQHWGNLr8678DcE2q6RK 1XyzP27GJ+elHpYckJucZ0W8V7XKdvQVpZKbyDYpULzQvCP2hVfH1M1KkY6fwcDX a2KYy4p+LTv0f1ihn5XkCqAa0MEpYd9joBwc+LT96pECd7U12T1nBRByDBS1FGcb ETXqZ9MGz4kdmcE= =6PXt -----END PGP SIGNATURE----- Thu Sep 11 22:42:54 UTC 2025 I: Checking whether the package is not for us Thu Sep 11 22:42:54 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Thu Sep 11 22:42:54 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Thu Sep 11 22:44:33 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 11 10:42:56 -12 2025 I: pbuilder-time-stamp: 1757630576 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 [probcons_1.12-15.dsc] I: copying [./probcons_1.12.orig.tar.gz] I: copying [./probcons_1.12-15.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./probcons_1.12-15.dsc: no acceptable signature found dpkg-source: info: extracting probcons in probcons-1.12 dpkg-source: info: unpacking probcons_1.12.orig.tar.gz dpkg-source: info: unpacking probcons_1.12-15.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 10_add-RNA-in-Makefile.patch dpkg-source: info: applying 11-Rename-programs-in-Makefile.patch dpkg-source: info: applying fix-gcc-4.5-headers 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/768226/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='e330f556e1444dd6bf4bd0eb373d6705' 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='768226' 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.CoPq9Ju6/pbuilderrc_VLK8 --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.CoPq9Ju6/b1 --logfile b1/build.log probcons_1.12-15.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.12.43+deb13-cloud-arm64 #1 SMP Debian 6.12.43-1 (2025-08-27) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/768226/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 21045 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. 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} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 11.0 MB of archives. After unpacking 44.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.1-2 [93.9 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-1 [316 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.26 [91.8 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-5 [540 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.16-2 [100 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.5+dfsg-0.2 [582 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 debhelper all 13.26 [939 kB] Fetched 11.0 MB in 0s (65.4 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21045 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_arm64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-2_arm64.deb ... Unpacking bsdextrautils (2.41.1-2) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-1_arm64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-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 .../19-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 .../20-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-2_arm64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2-16:arm64. Preparing to unpack .../24-libxml2-16_2.14.5+dfsg-0.2_arm64.deb ... Unpacking libxml2-16:arm64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_arm64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-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 .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41.1-2) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-2) ... 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 (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... 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 (13.26) ... 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/probcons-1.12/ && 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 > ../probcons_1.12-15_source.changes dpkg-buildpackage: info: source package probcons dpkg-buildpackage: info: source version 1.12-15 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/probcons-1.12' rm -f probcons probcons-RNA pc-compare pc-project pc-makegnuplot make[1]: Leaving directory '/build/reproducible-path/probcons-1.12' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/probcons-1.12' dh_clean probcons probcons-RNA pc-project pc-compare pc-makegnuplot Main-RNA.cc Defaults-RNA.h make[1]: Leaving directory '/build/reproducible-path/probcons-1.12' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/probcons-1.12' cp Main.cc Main-RNA.cc sed -i s/Defaults.h/Defaults-RNA.h/ Main-RNA.cc cp debian/Defaults-RNA.h Defaults-RNA.h dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/probcons-1.12' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -ffile-prefix-map=/build/reproducible-path/probcons-1.12=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -lm -o probcons Main.cc -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=1 -DVERSION="1.12" -funroll-loops -g -O2 -ffile-prefix-map=/build/reproducible-path/probcons-1.12=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -lm -o probcons-RNA Main-RNA.cc -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -ffile-prefix-map=/build/reproducible-path/probcons-1.12=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -o pc-compare CompareToRef.cc -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -ffile-prefix-map=/build/reproducible-path/probcons-1.12=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -o pc-project ProjectPairwise.cc -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -ffile-prefix-map=/build/reproducible-path/probcons-1.12=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -o pc-makegnuplot MakeGnuPlot.cc -Wl,-z,relro -Wl,-z,now In file included from MultiSequence.h:18, from Main-RNA.cc:8: 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-RNA.cc:7: 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) {} | ^~~~~~~~~~ In file included from MultiSequence.h:18, from ProjectPairwise.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 ProjectPairwise.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) {} | ^~~~~~~~~~ In file included from MultiSequence.h:18, from CompareToRef.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 CompareToRef.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) {} | ^~~~~~~~~~ In file included from Main-RNA.cc:11: ProbabilisticModel.h: In member function 'void ProbabilisticModel::ComputeNewParameters(Sequence*, Sequence*, const VF&, const VF&, VF&, VF&, VF&, VVF&, VF&, bool) const': ProbabilisticModel.h:493:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 493 | if (enableTrainEmissions && i != 1 || j != 1){ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ ProbabilisticModel.h: In member function 'VF* ProbabilisticModel::BuildPosterior(MultiSequence*, MultiSequence*, const SafeVector >&, float) const': ProbabilisticModel.h:1027:18: warning: variable 'postPtr' set but not used [-Wunused-but-set-variable] 1027 | VF::iterator postPtr = posterior.begin(); | ^~~~~~~ In file included from MultiSequence.h:18, from Main.cc:8: 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:7: 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) {} | ^~~~~~~~~~ Main-RNA.cc: In function 'void PrintParameters(const char*, const VF&, const VF&, const VF&, const VVF&, const VF&, const char*)': Main-RNA.cc:282:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~ Main-RNA.cc:282:88: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~~~~~ Main-RNA.cc:283:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~ Main-RNA.cc:283:87: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~~~~~ Main-RNA.cc:284:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~ Main-RNA.cc:284:89: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~~~~~ Main-RNA.cc: In function 'MultiSequence* DoAlign(MultiSequence*, const ProbabilisticModel&, VF&, VF&, VF&, VVF&, VF&)': Main-RNA.cc:400:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 400 | if (enableVerbose) | ^~ Main-RNA.cc:403:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 403 | delete alignment.first; | ^~~~~~ Main-RNA.cc: In function 'void ReadParameters()': Main-RNA.cc:893:40: warning: implicitly-declared 'SafeVector >& SafeVector >::operator=(const SafeVector >&)' is deprecated [-Wdeprecated-copy] 893 | emitPairs = VVF (256, VF (256, 1e-10)); | ^ SafeVector.h:29:3: note: because 'SafeVector >' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ Main-RNA.cc:894:29: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 894 | emitSingle = VF (256, 1e-5); | ^ SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = float]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ In file included from Main.cc:11: ProbabilisticModel.h: In member function 'void ProbabilisticModel::ComputeNewParameters(Sequence*, Sequence*, const VF&, const VF&, VF&, VF&, VF&, VVF&, VF&, bool) const': ProbabilisticModel.h:493:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 493 | if (enableTrainEmissions && i != 1 || j != 1){ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ ProbabilisticModel.h: In member function 'VF* ProbabilisticModel::BuildPosterior(MultiSequence*, MultiSequence*, const SafeVector >&, float) const': ProbabilisticModel.h:1027:18: warning: variable 'postPtr' set but not used [-Wunused-but-set-variable] 1027 | VF::iterator postPtr = posterior.begin(); | ^~~~~~~ Main.cc: In function 'void PrintParameters(const char*, const VF&, const VF&, const VF&, const VVF&, const VF&, const char*)': Main.cc:282:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~ Main.cc:282:88: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~~~~~ Main.cc:283:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~ Main.cc:283:87: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~~~~~ Main.cc:284:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~ Main.cc:284:89: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~~~~~ Main.cc: In function 'MultiSequence* DoAlign(MultiSequence*, const ProbabilisticModel&, VF&, VF&, VF&, VVF&, VF&)': Main.cc:400:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 400 | if (enableVerbose) | ^~ Main.cc:403:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 403 | delete alignment.first; | ^~~~~~ Main.cc: In function 'void ReadParameters()': Main.cc:893:40: warning: implicitly-declared 'SafeVector >& SafeVector >::operator=(const SafeVector >&)' is deprecated [-Wdeprecated-copy] 893 | emitPairs = VVF (256, VF (256, 1e-10)); | ^ SafeVector.h:29:3: note: because 'SafeVector >' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ Main.cc:894:29: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 894 | emitSingle = VF (256, 1e-5); | ^ SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = float]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ make[2]: Leaving directory '/build/reproducible-path/probcons-1.12' make[1]: Leaving directory '/build/reproducible-path/probcons-1.12' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl debian/rules override_dh_link make[1]: Entering directory '/build/reproducible-path/probcons-1.12' rm -rf /build/reproducible-path/probcons-1.12/debian/probcons-extra/usr/share/doc/probcons-extra dh_link -p probcons-extra usr/share/doc/probcons usr/share/doc/probcons-extra make[1]: Leaving directory '/build/reproducible-path/probcons-1.12' dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'probcons-dbgsym' in '../probcons-dbgsym_1.12-15_arm64.deb'. dpkg-deb: building package 'probcons-extra' in '../probcons-extra_1.12-15_arm64.deb'. dpkg-deb: building package 'probcons' in '../probcons_1.12-15_arm64.deb'. dpkg-deb: building package 'probcons-extra-dbgsym' in '../probcons-extra-dbgsym_1.12-15_arm64.deb'. dpkg-genbuildinfo --build=binary -O../probcons_1.12-15_arm64.buildinfo dpkg-genchanges --build=binary -O../probcons_1.12-15_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/768226 and its subdirectories I: Current time: Thu Sep 11 10:44:32 -12 2025 I: pbuilder-time-stamp: 1757630672 Thu Sep 11 22:44:34 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Thu Sep 11 22:44:34 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Thu Sep 11 22:45:18 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Thu Sep 11 22:45:19 UTC 2025 I: probcons_1.12-15_arm64.changes: Format: 1.8 Date: Mon, 08 Sep 2025 22:47:06 +0200 Source: probcons Binary: probcons probcons-dbgsym probcons-extra probcons-extra-dbgsym Architecture: arm64 Version: 1.12-15 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: probcons - PROBabilistic CONSistency-based multiple sequence alignment probcons-extra - Extra programs from the probcons package Changes: probcons (1.12-15) unstable; urgency=medium . * Team upload. * hardening.patch: also inject CPPFLAGS. * d/patches/*: refresh dep3 headers. * d/control: declare compliance to standards version 4.7.2. Checksums-Sha1: a2c6b6162329a38b2969cd59fd462cfb8960d3cf 1091484 probcons-dbgsym_1.12-15_arm64.deb d0c0c69c470cee0423cd011bbe52dbf56578cb15 408552 probcons-extra-dbgsym_1.12-15_arm64.deb f23ffa17cc495ec128dfcc69c5a02422cc01d4c8 37792 probcons-extra_1.12-15_arm64.deb bc63bf676ec6b4298057de941e8f5d359887ca1d 5599 probcons_1.12-15_arm64.buildinfo 8fb9702a987ef5c37f8212a3ccd5ab27f569f4ab 126116 probcons_1.12-15_arm64.deb Checksums-Sha256: be5bde1c0256b25419c8b1c83d60c8f27bb2485182603a7b9a93f8a72dd3e736 1091484 probcons-dbgsym_1.12-15_arm64.deb a224346f9ebc8dca5ddc5cfa44ab479075d4476878c5000164b399fc1040df4c 408552 probcons-extra-dbgsym_1.12-15_arm64.deb 1729a39a9dc681a8bbea9d7dfb0e4d4d0cf3bf6c2c10f9de781d5d4cf28e9f98 37792 probcons-extra_1.12-15_arm64.deb 2758413d99ffc4a065fa6bdfb55a4264426fdba8bb3dffff1fbe448311fd315c 5599 probcons_1.12-15_arm64.buildinfo 69e6ad25741b35f3f7bb7ae6408410499b05ca2bc3b67726368f82260f193d9a 126116 probcons_1.12-15_arm64.deb Files: 3b81c1ceaa5846bcbf4947fa507d8c4c 1091484 debug optional probcons-dbgsym_1.12-15_arm64.deb b9f2f843b85753bd3c5e4a41bc6e2906 408552 debug optional probcons-extra-dbgsym_1.12-15_arm64.deb 6b07be0362e9cb4fd2919a483eb5d1e1 37792 science optional probcons-extra_1.12-15_arm64.deb a79374c3eb65299197c3f3ee0d710562 5599 science optional probcons_1.12-15_arm64.buildinfo 5891fc9aaa9e9bdf1fbfe6075b9047d9 126116 science optional probcons_1.12-15_arm64.deb Thu Sep 11 22:45:20 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_10-96499.service; invocation ID: 010444d1cf724d91bcc36a458bad81cb # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.CoPq9Ju6/probcons_1.12-15.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.CoPq9Ju6/probcons_1.12-15.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.CoPq9Ju6/probcons_1.12-15.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.CoPq9Ju6/b1/probcons_1.12-15_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.CoPq9Ju6/b2/probcons_1.12-15_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 232ms CPU time consumed: 182ms Memory peak: 18.4M (swap: 0B) Thu Sep 11 22:55:04 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Thu Sep 11 22:55:04 UTC 2025 I: probcons from forky built successfully and reproducibly on arm64. Thu Sep 11 22:55:05 UTC 2025 I: Removing signed probcons_1.12-15_arm64.buildinfo.asc files: removed './b1/probcons_1.12-15_arm64.buildinfo.asc' removed './b2/probcons_1.12-15_arm64.buildinfo.asc'