Sun Oct 13 13:59:22 UTC 2024 I: starting to build probcons/trixie/i386 on jenkins on '2024-10-13 13:59' Sun Oct 13 13:59:22 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_2/40263/console.log Sun Oct 13 13:59:22 UTC 2024 I: Downloading source for trixie/probcons=1.12-14 --2024-10-13 13:59:22-- http://deb.debian.org/debian/pool/main/p/probcons/probcons_1.12-14.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2049 (2.0K) [text/prs.lines.tag] Saving to: ‘probcons_1.12-14.dsc’ 0K .. 100% 150M=0s 2024-10-13 13:59:22 (150 MB/s) - ‘probcons_1.12-14.dsc’ saved [2049/2049] Sun Oct 13 13:59:22 UTC 2024 I: probcons_1.12-14.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: probcons Binary: probcons, probcons-extra Architecture: any Version: 1.12-14 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: http://probcons.stanford.edu/ Standards-Version: 4.6.0 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 07968801e65b5f82622bbd32fb20c4c750d95689 13236 probcons_1.12-14.debian.tar.xz Checksums-Sha256: ecf3f9ab9ad47e14787c76d1c64aeea5533d4038c4be0236c00cdd79104cf383 43200 probcons_1.12.orig.tar.gz 1b2bc5be50ed89589074a47eb107b2f339bad83ef8fccbf9ab2959e754bb2fe9 13236 probcons_1.12-14.debian.tar.xz Files: a658e24b07aaa9e8194317345133ac9d 43200 probcons_1.12.orig.tar.gz ef21598c91ea670f7725728a7ee29c86 13236 probcons_1.12-14.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmEnVBsRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF2BxAAhAhVjXFOIReqExzDERNoIAutuviXoXa7 Fz61vADED/5xOqYexCq6vUgrsp2NK5JkzH4KLxVUN8x6KFbD4OfgLxd9XWr/Naut cvJoFPfyDJh6mSIIF33qFNy1Bv4+WV4SLQFx3KplmqkHYdYtXffAOotM5pkwMWs1 C316vaw2PgbNTc5snaeYxlTs1JFADkk4qpIVK9cBqeiJiU1f9PFLKKz8QFV+QNPB rf7rbrWRZm4F/KEmMW3DrehiPTI5kOiXuv3zjAjUAd4xa7sO2QzfdGC2pYtLpJCl j9cMKNivUiZPOOGlzZnXxme25cKJK5TsLc2Qck1PH4j5X5h8IWQCJmZV5oW15S5r oHimHJ9n2SvjaCVgFonaRpyAFdHxiWobt8iwC5QCc8CtuqlS4inJV6D7RNx7oDxF QiBWrcpwgvtynEAQxhVstBhygbefW8ZyAq765YOyOO+XmEACDBl0Ci/YWJMGbLIz hlG+wjnKEaB0fAhmtb5ysdtepaVN/xl0jytn4WGOgHxwUy9R2dYvNXNeknkJ5D5N 6bbXwrT2FHLCzMJD9p0Nozu/nI1oluFtkf8NaSBAOx1iyby6nD1uqZtC62zJGnc2 wEnkvzGovSr64+eQ+nS97mvRVOGK4cBFT/ark/DU457NY3E75h4q0JuHTOdcdb70 gHPDk20zDCs= =xEjt -----END PGP SIGNATURE----- Sun Oct 13 13:59:22 UTC 2024 I: Checking whether the package is not for us Sun Oct 13 13:59:22 UTC 2024 I: Starting 1st build on remote node ionos6-i386.debian.net. Sun Oct 13 13:59:22 UTC 2024 I: Preparing to do remote build '1' on ionos6-i386.debian.net. Sun Oct 13 13:59:56 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 15 08:22:20 -12 2025 I: pbuilder-time-stamp: 1763238140 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [probcons_1.12-14.dsc] I: copying [./probcons_1.12.orig.tar.gz] I: copying [./probcons_1.12-14.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Aug 26 08:43:07 2021 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./probcons_1.12-14.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_1.12-14.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/27819/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='02cd4763dcf84779836be0b4c3a4a237' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='27819' 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.HU7lYVh8/pbuilderrc_Y4qi --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HU7lYVh8/b1 --logfile b1/build.log probcons_1.12-14.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos6-i386 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/27819/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19774 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} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 20.1 MB of archives. After unpacking 75.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-9 [102 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.191-2 [194 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5 [9550 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.1 [733 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Fetched 20.1 MB in 0s (85.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19774 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_i386.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_i386.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_i386.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_i386.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-9_i386.deb ... Unpacking bsdextrautils (2.40.2-9) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../08-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... 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_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../21-libelf1t64_0.191-2_i386.deb ... Unpacking libelf1t64:i386 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../23-libicu72_72.1-5_i386.deb ... Unpacking libicu72:i386 (72.1-5) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.1_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_i386.deb ... Unpacking gettext (0.22.5-2) ... 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_13.20_all.deb ... Unpacking debhelper (13.20) ... Setting up libpipeline1:i386 (1.5.8-1) ... Setting up libicu72:i386 (72.1-5) ... Setting up bsdextrautils (2.40.2-9) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:i386 (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:i386 (0.191-2) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:i386 (0.0.8-1+b1) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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_1.12-14_source.changes dpkg-buildpackage: info: source package probcons dpkg-buildpackage: info: source version 1.12-14 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_auto_clean make -j22 clean make[1]: Entering directory '/build/reproducible-path/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 -j22 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/probcons-1.12' g++ -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 -Wformat -Werror=format-security -lm -o probcons Main.cc -Wl,-z,relro -Wl,-z,now g++ -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 -Wformat -Werror=format-security -lm -o probcons-RNA Main-RNA.cc -Wl,-z,relro -Wl,-z,now g++ -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 -Wformat -Werror=format-security -o pc-compare CompareToRef.cc -Wl,-z,relro -Wl,-z,now g++ -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 -Wformat -Werror=format-security -o pc-project ProjectPairwise.cc -Wl,-z,relro -Wl,-z,now g++ -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 -Wformat -Werror=format-security -o pc-makegnuplot MakeGnuPlot.cc -Wl,-z,relro -Wl,-z,now 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 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 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) {} | ^~~~~~~~~~ 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){ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 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(); | ^~~~~~~ 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-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.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-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.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-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) {} | ^~~~~~~~~~ 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'probcons-dbgsym' in '../probcons-dbgsym_1.12-14_i386.deb'. dpkg-deb: building package 'probcons' in '../probcons_1.12-14_i386.deb'. dpkg-deb: building package 'probcons-extra-dbgsym' in '../probcons-extra-dbgsym_1.12-14_i386.deb'. dpkg-deb: building package 'probcons-extra' in '../probcons-extra_1.12-14_i386.deb'. dpkg-genbuildinfo --build=binary -O../probcons_1.12-14_i386.buildinfo dpkg-genchanges --build=binary -O../probcons_1.12-14_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: 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/27819 and its subdirectories I: Current time: Sat Nov 15 08:22:51 -12 2025 I: pbuilder-time-stamp: 1763238171 Sun Oct 13 13:59:57 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net. Sun Oct 13 13:59:57 UTC 2024 I: Preparing to do remote build '2' on ionos2-i386.debian.net. Sun Oct 13 14:00:58 UTC 2024 I: Deleting $TMPDIR on ionos2-i386.debian.net. Sun Oct 13 14:00:59 UTC 2024 I: probcons_1.12-14_i386.changes: Format: 1.8 Date: Thu, 26 Aug 2021 10:37:09 +0200 Source: probcons Binary: probcons probcons-dbgsym probcons-extra probcons-extra-dbgsym Architecture: i386 Version: 1.12-14 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: probcons - PROBabilistic CONSistency-based multiple sequence alignment probcons-extra - Extra programs from the probcons package Changes: probcons (1.12-14) unstable; urgency=medium . * Remove outdated copyright file * Standards-Version: 4.6.0 (routine-update) Checksums-Sha1: 2580d847b49e0eb0eca0a776390bab41c5a80df7 1085632 probcons-dbgsym_1.12-14_i386.deb 6ac72214b017c84305e5a3b9194e1544f93c00d5 410192 probcons-extra-dbgsym_1.12-14_i386.deb 8587e017a0cf2c288e8263bc96760d690735ccc1 38876 probcons-extra_1.12-14_i386.deb bef866059af77d876e2557bc6f6ff9606cb04827 5415 probcons_1.12-14_i386.buildinfo 503fd460ff31d94a48a220a53b5ea1129596baa1 116228 probcons_1.12-14_i386.deb Checksums-Sha256: 78e985909da5c9df9bdffcc2176887ac35123053a29d80bf17c0bc35727f0516 1085632 probcons-dbgsym_1.12-14_i386.deb a6b6f5b92e14bc6cd42682bce5bf76ae518bef0b4500c8f1acfd254d61426a11 410192 probcons-extra-dbgsym_1.12-14_i386.deb 42fcb5fb21085a14f76ca8236790da4ab25aaf411e46411ef93b4355c9b6b607 38876 probcons-extra_1.12-14_i386.deb 3fdc1f7314df3696e046e497bdc6be26cc5719cf781e7b2331cdb9f86e228c2d 5415 probcons_1.12-14_i386.buildinfo acfd3b19dbb47ff3db0e51a0225e207760c272271bbc5c653d099bf7a310d9bf 116228 probcons_1.12-14_i386.deb Files: 687b1e6068a0e79a35a69e53348b39b4 1085632 debug optional probcons-dbgsym_1.12-14_i386.deb a914459d9aa5e638fc1647b1d0808046 410192 debug optional probcons-extra-dbgsym_1.12-14_i386.deb bde3de2d13c42e24738c76d900c1e590 38876 science optional probcons-extra_1.12-14_i386.deb bbd46ec22b6c38f5a57ecfa7aac4d868 5415 science optional probcons_1.12-14_i386.buildinfo 5eaeda57590d9575eb62b60eb01ce21b 116228 science optional probcons_1.12-14_i386.deb Sun Oct 13 14:01:00 UTC 2024 I: diffoscope 280 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_2-40263.service Warning: program compiled against libxml 212 using older 209 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.HU7lYVh8/probcons_1.12-14.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.HU7lYVh8/probcons_1.12-14.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.HU7lYVh8/probcons_1.12-14.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.HU7lYVh8/b1/probcons_1.12-14_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.HU7lYVh8/b2/probcons_1.12-14_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.403s) 0.403s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.035s) 0.035s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 739ms CPU time consumed: 740ms Sun Oct 13 14:01:01 UTC 2024 I: diffoscope 280 found no differences in the changes files, and a .buildinfo file also exists. Sun Oct 13 14:01:01 UTC 2024 I: probcons from trixie built successfully and reproducibly on i386. Sun Oct 13 14:01:02 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Oct 13 14:01:02 UTC 2024 I: Submitting 8.0K b1/probcons_1.12-14_i386.buildinfo.asc Sun Oct 13 14:01:03 UTC 2024 I: Submitting 8.0K b2/probcons_1.12-14_i386.buildinfo.asc Sun Oct 13 14:01:04 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Oct 13 14:01:04 UTC 2024 I: Done submitting .buildinfo files. Sun Oct 13 14:01:04 UTC 2024 I: Removing signed probcons_1.12-14_i386.buildinfo.asc files: removed './b1/probcons_1.12-14_i386.buildinfo.asc' removed './b2/probcons_1.12-14_i386.buildinfo.asc'