Mon Apr 14 21:53:28 UTC 2025 I: starting to build raxml/unstable/armhf on jenkins on '2025-04-14 21:53' Mon Apr 14 21:53:28 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_27/14315/console.log Mon Apr 14 21:53:28 UTC 2025 I: Downloading source for unstable/raxml=8.2.13+dfsg-2 --2025-04-14 21:53:29-- http://deb.debian.org/debian/pool/main/r/raxml/raxml_8.2.13%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2177 (2.1K) [text/prs.lines.tag] Saving to: ‘raxml_8.2.13+dfsg-2.dsc’ 0K .. 100% 328M=0s 2025-04-14 21:53:29 (328 MB/s) - ‘raxml_8.2.13+dfsg-2.dsc’ saved [2177/2177] Mon Apr 14 21:53:29 UTC 2025 I: raxml_8.2.13+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: raxml Binary: raxml Architecture: any Version: 8.2.13+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://cme.h-its.org/exelixis/web/software/raxml/index.html Standards-Version: 4.7.2. Vcs-Browser: https://salsa.debian.org/med-team/raxml Vcs-Git: https://salsa.debian.org/med-team/raxml.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libsimde-dev Package-List: raxml deb science optional arch=any Checksums-Sha1: ba0c08918b0157959d085745ea7bdcc0afb094e7 1006760 raxml_8.2.13+dfsg.orig.tar.xz ac5d107bb56704df478719a3206c6a48731557f4 22096 raxml_8.2.13+dfsg-2.debian.tar.xz Checksums-Sha256: 34b11973d306240275287e7b3c43b59de6707880840d93a34086c7bdb58bb2ed 1006760 raxml_8.2.13+dfsg.orig.tar.xz d11e6c3a75aed097a52d5f4b227f575cd30d2a265157272b2e0ef104317f8b0e 22096 raxml_8.2.13+dfsg-2.debian.tar.xz Files: 73f896a05f9bd8185cd449300764c89c 1006760 raxml_8.2.13+dfsg.orig.tar.xz 507472979d3e960cba8b0831ddba015b 22096 raxml_8.2.13+dfsg-2.debian.tar.xz Dgit: f750b041995701c17d1d04ee51d5e3bf61bbd661 debian archive/debian/8.2.13+dfsg-2 https://git.dgit.debian.org/raxml -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmfEVKIUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqJGg/7BNfDbWn4cx3qLkp8kj06xXH0tVkV MqNgFxyt5zkbXCGPjA26eQ24irs5PDbD5g25RigVYtB7n3S4+gnr+/SXfoQqQf4v J4SxdpxuMHSfUpUPiL//rBjo/poiZBifsp4a+c7aTgkVqkdOHKM8NFfm1hX2xGad luf1X7rH7mMnsJp+480JY8g4s8Os1BaRVtxt6UVC5TyJdFQF8M6AbMhEdxpWNQ+6 twWRfk7brDeiGNIqXCwtoa013jBRGuj9bCgTZEoLionMSLIjSkCFD5jor1rwF5y0 l5SFLr0BlipF+2Xq0+w/Euz7yqkCfCp9hLGoqqSoKkCl6toM2RZB7FvB7aaE5mD7 6fkhYS8hZOSNN8SKiYHLqsAdpH3EIDSmBhSIjm/8z6frgTcwm53neBx+aTln1zLP 2yjunKM+tlCNGOhmPdPuBkxDgY8ap4wvmjJ2NCk2sekzAHF+Dq9Z1zDdzmC53bts +TTvXYeDxlN6efvVzQTTOaJ+PpL2DZdF3wcZ0MK/ie3SLPP+Z4OOqJpjWfwHB/Ak i92S4YkBrwdP3p7XT/5RM1jAwSi0+XuAgh5qamo1EcODEugjbzhy7h74kxExyjYF i3Y/7bucoOxBhORFP5b4OlMxClhthEdKrA94pyiEolORxaOyzE2MKifMRrAwjxOj Ai6lH2yMnYt3q8k= =SdIR -----END PGP SIGNATURE----- Mon Apr 14 21:53:29 UTC 2025 I: Checking whether the package is not for us Mon Apr 14 21:53:29 UTC 2025 I: Starting 1st build on remote node virt64z-armhf-rb.debian.net. Mon Apr 14 21:53:29 UTC 2025 I: Preparing to do remote build '1' on virt64z-armhf-rb.debian.net. Mon Apr 14 21:55:47 UTC 2025 I: Deleting $TMPDIR on virt64z-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Apr 14 09:53:35 -12 2025 I: pbuilder-time-stamp: 1744667615 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [raxml_8.2.13+dfsg-2.dsc] I: copying [./raxml_8.2.13+dfsg.orig.tar.xz] I: copying [./raxml_8.2.13+dfsg-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./raxml_8.2.13+dfsg-2.dsc: unsupported subcommand dpkg-source: info: extracting raxml in raxml-8.2.13+dfsg dpkg-source: info: unpacking raxml_8.2.13+dfsg.orig.tar.xz dpkg-source: info: unpacking raxml_8.2.13+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying simde dpkg-source: info: applying hardening dpkg-source: info: applying c23.patch dpkg-source: info: applying typos.patch dpkg-source: info: applying interpreter-path.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/31252/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='77244372a5ed4f9a8d17d128770f25de' 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='31252' 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.KhLp2ZvH/pbuilderrc_mqdQ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.KhLp2ZvH/b1 --logfile b1/build.log raxml_8.2.13+dfsg-2.dsc' SUDO_GID='110' SUDO_UID='103' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64z 6.1.0-33-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/31252/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: armhf 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), libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19566 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 libsimde-dev; however: Package libsimde-dev 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} libsimde-dev{a} libtool{a} libuchardet0{a} libunistring5{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, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 11.2 MB of archives. After unpacking 49.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.46-5 [100 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.46-5 [42.8 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.23.1-1 [238 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-7 [1095 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.41-4 [86.5 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-7 [272 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.24.2 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf libunistring5 armhf 1.3-2 [441 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.4 [604 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.23.1-1 [1560 kB] Get: 27 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf debhelper all 13.24.2 [919 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf libsimde-dev all 0.8.2-3 [467 kB] Fetched 11.2 MB in 1s (11.4 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 ... 19566 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%3a5.46-5_armhf.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_armhf.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_armhf.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_armhf.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-4_armhf.deb ... Unpacking bsdextrautils (2.41-4) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-7_armhf.deb ... Unpacking m4 (1.4.19-7) ... 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_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_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... 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_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../21-libelf1t64_0.192-4_armhf.deb ... Unpacking libelf1t64:armhf (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libunistring5:armhf. Preparing to unpack .../23-libunistring5_1.3-2_armhf.deb ... Unpacking libunistring5:armhf (1.3-2) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.4_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.4) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-1_armhf.deb ... Unpacking gettext (0.23.1-1) ... 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_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../29-libsimde-dev_0.8.2-3_all.deb ... Unpacking libsimde-dev (0.8.2-3) ... Setting up libpipeline1:armhf (1.5.8-1) ... Setting up libsimde-dev (0.8.2-3) ... Setting up bsdextrautils (2.41-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:armhf (1:5.46-5) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-7) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:armhf (1.3-2) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.4) ... 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 (0.23.1-1) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... 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 (13.24.2) ... Processing triggers for libc-bin (2.41-7) ... 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/raxml-8.2.13+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../raxml_8.2.13+dfsg-2_source.changes dpkg-buildpackage: info: source package raxml dpkg-buildpackage: info: source version 8.2.13+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' for mfile in Makefile.AVX.PTHREADS.gcc; do /usr/bin/make -f ${mfile} clean ; done make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' rm -f *.o raxmlHPC-PTHREADS-AVX make[2]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' rm -rf /build/reproducible-path/raxml-8.2.13+dfsg/debian/tmpbuild make[1]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' mkdir -p /build/reproducible-path/raxml-8.2.13+dfsg/debian/tmpbuild set -e ; for mfile in Makefile.AVX.PTHREADS.gcc; do \ dh_auto_build --buildsystem=makefile -- -f ${mfile} CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3"; \ curexe=`ls raxmlHPC* | head -n 1` ; \ if [ -e /build/reproducible-path/raxml-8.2.13+dfsg/debian/tmpbuild/${curexe} ] ; then \ echo "**** ERROR: ${curexe} was created before!!" && false ; \ else \ mv ${curexe} /build/reproducible-path/raxml-8.2.13+dfsg/debian/tmpbuild/${curexe} ; \ fi ; \ /usr/bin/make -f ${mfile} clean ; \ done make -j3 "INSTALL=install --strip-program=true" -f Makefile.AVX.PTHREADS.gcc "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3" make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' rm -f *.o raxmlHPC-PTHREADS-AVX gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o axml.o axml.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o optimizeModel.o optimizeModel.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multiple.o multiple.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o searchAlgo.o searchAlgo.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o topologies.o topologies.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o parsePartitions.o parsePartitions.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o treeIO.o treeIO.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o models.o models.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bipartitionList.o bipartitionList.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o rapidBootstrap.o rapidBootstrap.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o evaluatePartialGenericSpecial.o evaluatePartialGenericSpecial.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o evaluateGenericSpecial.o evaluateGenericSpecial.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o newviewGenericSpecial.o newviewGenericSpecial.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o makenewzGenericSpecial.o makenewzGenericSpecial.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o classify.o classify.c gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -o fastDNAparsimony.o fastDNAparsimony.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o fastSearch.o fastSearch.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o leaveDropping.o leaveDropping.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o rmqs.o rmqs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o rogueEPA.o rogueEPA.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ancestralStates.o ancestralStates.c gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -o avxLikelihood.o avxLikelihood.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mem_alloc.o mem_alloc.c gcc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -o eigen.o eigen.c gcc -o raxmlHPC-PTHREADS-AVX axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o eigen.o -lm -pthread -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' rm -f *.o raxmlHPC-PTHREADS-AVX make[2]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' make[1]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install --destdir=debian/raxml/ debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' dh_install dh_link usr/bin/raxmlHPC-PTHREADS-AVX usr/bin/raxmlHPC make[1]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' dh_installexamples # fix perl path in example scripts for pscript in `ls usefulScripts/*.pl` ; do \ sed 's?/usr/local/bin/perl?/usr/bin/perl?' ${pscript} > /build/reproducible-path/raxml-8.2.13+dfsg/debian/raxml/usr/share/doc/raxml/examples/`basename ${pscript}` ; \ done make[1]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' dh_installman for cexe in `ls /build/reproducible-path/raxml-8.2.13+dfsg/debian/tmpbuild/raxmlHPC*` ; do \ curexe=`basename ${cexe}` ; \ if [ ${curexe} != raxmlHPC ] ; then \ ln -s raxmlHPC.1.gz /build/reproducible-path/raxml-8.2.13+dfsg/debian/raxml/usr/share/man/man1/${curexe}.1.gz ; \ fi ; \ done make[1]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-3), " make[1]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' dh_md5sums dh_builddeb dpkg-deb: building package 'raxml' in '../raxml_8.2.13+dfsg-2_armhf.deb'. dpkg-deb: building package 'raxml-dbgsym' in '../raxml-dbgsym_8.2.13+dfsg-2_armhf.deb'. dpkg-genbuildinfo --build=binary -O../raxml_8.2.13+dfsg-2_armhf.buildinfo dpkg-genchanges --build=binary -O../raxml_8.2.13+dfsg-2_armhf.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/31252 and its subdirectories I: Current time: Mon Apr 14 09:55:40 -12 2025 I: pbuilder-time-stamp: 1744667740 Mon Apr 14 21:55:49 UTC 2025 I: 1st build successful. Starting 2nd build on remote node virt32a-armhf-rb.debian.net. Mon Apr 14 21:55:49 UTC 2025 I: Preparing to do remote build '2' on virt32a-armhf-rb.debian.net. Mon Apr 14 21:58:11 UTC 2025 I: Deleting $TMPDIR on virt32a-armhf-rb.debian.net. Mon Apr 14 21:58:14 UTC 2025 I: raxml_8.2.13+dfsg-2_armhf.changes: Format: 1.8 Date: Sun, 02 Mar 2025 13:38:42 +0100 Source: raxml Binary: raxml raxml-dbgsym Architecture: armhf Version: 8.2.13+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: raxml - Randomized Axelerated Maximum Likelihood of phylogenetic trees Closes: 1097774 Changes: raxml (8.2.13+dfsg-2) unstable; urgency=medium . * d/control: declare compliance to standards version 4.7.2. * c23.patch: new: fix build failure with gcc-15. (Closes: #1097774) * d/raxmlHPC.1: fix typos caught by lintian. * d/raxmlHPC.1: fix groff message. * typos.patch: fix various typos caught by lintian. * interpreter-path.patch: adjust perl interpreter path. * d/control: add myself to uploaders. Checksums-Sha1: f76efa5fdefe24a68a36bd887808294bc311495a 997896 raxml-dbgsym_8.2.13+dfsg-2_armhf.deb 9399880bb6f06ee29ebbf1d723708561664fbb88 4758 raxml_8.2.13+dfsg-2_armhf.buildinfo d108c162041494e7b895cfc79a8a23eb50b176ec 964732 raxml_8.2.13+dfsg-2_armhf.deb Checksums-Sha256: f008da6bdc10a059a3667f55559a95ca5317472992f04b436d76b07b1bdb8510 997896 raxml-dbgsym_8.2.13+dfsg-2_armhf.deb 91d4742028ac3db0049f8fa0a1d53df89b1b0805f0450a07ffef77a971cb4daa 4758 raxml_8.2.13+dfsg-2_armhf.buildinfo 38183f5e313f3c7f88143e88731fe3f78072c58de94dcee562cc2adc5cf8efd4 964732 raxml_8.2.13+dfsg-2_armhf.deb Files: 0530b1504b02ca120bb49bb65fda7cdf 997896 debug optional raxml-dbgsym_8.2.13+dfsg-2_armhf.deb 3269c64090abb352d8e534881e072fc3 4758 science optional raxml_8.2.13+dfsg-2_armhf.buildinfo bcc7871f89a01ce0a7b38413c960a009 964732 science optional raxml_8.2.13+dfsg-2_armhf.deb Mon Apr 14 21:58:16 UTC 2025 I: diffoscope 294 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_27-14315.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.KhLp2ZvH/raxml_8.2.13+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.KhLp2ZvH/raxml_8.2.13+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.KhLp2ZvH/raxml_8.2.13+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.KhLp2ZvH/b1/raxml_8.2.13+dfsg-2_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.KhLp2ZvH/b2/raxml_8.2.13+dfsg-2_armhf.changes ## command (total time: 0.156s) 0.156s 1 call cmp (internal) ## has_same_content_as (total time: 0.156s) 0.156s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.159s) 0.159s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 417ms CPU time consumed: 259ms Mon Apr 14 21:58:18 UTC 2025 I: diffoscope 294 found no differences in the changes files, and a .buildinfo file also exists. Mon Apr 14 21:58:18 UTC 2025 I: raxml from unstable built successfully and reproducibly on armhf. Mon Apr 14 21:58:20 UTC 2025 I: Submitting .buildinfo files to external archives: Mon Apr 14 21:58:20 UTC 2025 I: Submitting 8.0K b1/raxml_8.2.13+dfsg-2_armhf.buildinfo.asc Mon Apr 14 21:58:35 UTC 2025 I: Submitting 8.0K b2/raxml_8.2.13+dfsg-2_armhf.buildinfo.asc Mon Apr 14 21:58:55 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Apr 14 21:58:55 UTC 2025 I: Done submitting .buildinfo files. Mon Apr 14 21:58:55 UTC 2025 I: Removing signed raxml_8.2.13+dfsg-2_armhf.buildinfo.asc files: removed './b1/raxml_8.2.13+dfsg-2_armhf.buildinfo.asc' removed './b2/raxml_8.2.13+dfsg-2_armhf.buildinfo.asc'