Running as unit: rb-build-amd64_12-64367.service ==================================================================================== Thu Jul 31 23:52:38 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_12) on jenkins, called using "ionos15-amd64 ionos1-amd64" as arguments. Thu Jul 31 23:52:38 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-BwfQ1Q0g" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Jul 31 23:52:38 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Thu Jul 31 23:52:38 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-IuVQae' Thu Jul 31 23:52:39 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Thu Jul 31 23:52:39 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Ft4gtz' ok, let's check if raxml is building anywhere yet… ok, raxml is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of raxml in unstable on amd64 on jenkins now. 1st build will be done on ionos15-amd64.debian.net. 2nd build will be done on ionos1-amd64.debian.net. ============================================================================= Thu Jul 31 23:52:53 UTC 2025 I: starting to build raxml/unstable/amd64 on jenkins on '2025-07-31 23:52' Thu Jul 31 23:52:53 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_12/64367/console.log 1754005973 amd64 unstable raxml Thu Jul 31 23:52:53 UTC 2025 I: Downloading source for unstable/raxml=8.2.13+dfsg-2 --2025-07-31 23:52:53-- 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% 197M=0s 2025-07-31 23:52:53 (197 MB/s) - ‘raxml_8.2.13+dfsg-2.dsc’ saved [2177/2177] --2025-07-31 23:52:53-- 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% 197M=0s 2025-07-31 23:52:53 (197 MB/s) - ‘raxml_8.2.13+dfsg-2.dsc’ saved [2177/2177] Thu Jul 31 23:52:53 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----- Thu Jul 31 23:52:53 UTC 2025 I: Checking whether the package is not for us Thu Jul 31 23:52:53 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Thu Jul 31 23:52:53 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Thu Jul 31 23:52:53 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Thu Jul 31 23:52:53 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-0dAKrI' ==================================================================================== Thu Sep 3 06:15:53 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "1 raxml unstable /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb 8.2.13+dfsg-2" as arguments. Thu Sep 3 06:15:53 UTC 2026 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-GKmtyOSz" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 3 06:15:53 UTC 2026 I: Downloading source for unstable/raxml=8.2.13+dfsg-2 Reading package lists... NOTICE: 'raxml' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/raxml.git Please use: git clone https://salsa.debian.org/med-team/raxml.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1031 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main raxml 8.2.13+dfsg-2 (dsc) [2177 B] Get:2 http://deb.debian.org/debian unstable/main raxml 8.2.13+dfsg-2 (tar) [1007 kB] Get:3 http://deb.debian.org/debian unstable/main raxml 8.2.13+dfsg-2 (diff) [22.1 kB] Fetched 1031 kB in 0s (16.0 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'raxml' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/raxml.git Please use: git clone https://salsa.debian.org/med-team/raxml.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1031 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main raxml 8.2.13+dfsg-2 (dsc) [2177 B] Get:2 http://deb.debian.org/debian unstable/main raxml 8.2.13+dfsg-2 (tar) [1007 kB] Get:3 http://deb.debian.org/debian unstable/main raxml 8.2.13+dfsg-2 (diff) [22.1 kB] Fetched 1031 kB in 0s (16.0 MB/s) Download complete and in download only mode ============================================================================= Building raxml in unstable on amd64 on ionos15-amd64 now. Date: Thu Sep 3 06:15:53 UTC 2026 Date UTC: Thu Sep 3 06:15:53 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 2 18:15:54 -12 2026 I: pbuilder-time-stamp: 1788416154 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: no acceptable signature found 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/55742/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='3c5158fa417e4f8caa93b3dac4ca1540' 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='55742' 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.hPCPFxXb/pbuilderrc_Ol4o --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.hPCPFxXb/b1 --logfile b1/build.log raxml_8.2.13+dfsg-2.dsc' SUDO_GID='111' SUDO_UID='106' 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 ionos15-amd64 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/55742/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19850 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 11.7 MB of archives. After unpacking 51.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Fetched 11.7 MB in 3s (3724 kB/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 ... 19850 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... 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_13.24.2_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:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-2.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2_amd64.deb ... Unpacking gettext (0.23.1-2) ... 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_13.24.2_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:amd64 (1.5.8-1) ... Setting up libsimde-dev (0.8.2-3) ... Setting up bsdextrautils (2.41-5) ... 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:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... 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 (1.23.0-9) ... 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 (13.24.2) ... Processing triggers for libc-bin (2.41-11) ... 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 amd64 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.PTHREADS.gcc Makefile.SSE3.PTHREADS.gcc 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 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-SSE3 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' 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.PTHREADS.gcc Makefile.SSE3.PTHREADS.gcc Makefile.AVX.PTHREADS.gcc; do \ dh_auto_build --buildsystem=makefile -- -f ${mfile} ; \ curexe=`ls raxmlHPC* | head -n 1` ; \ if [ -e /build/reproducible-path/raxml-8.2.13+dfsg/debian/tmpbuild/${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 -j42 "INSTALL=install --strip-program=true" -f Makefile.PTHREADS.gcc make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' rm -f *.o raxmlHPC-PTHREADS 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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -Wdate-time -D_FORTIFY_SOURCE=2 -c -o classify.o classify.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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ancestralStates.o ancestralStates.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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mem_alloc.o mem_alloc.c gcc -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -c -o eigen.o eigen.c gcc -o raxmlHPC-PTHREADS 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 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 make[2]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' make -j42 "INSTALL=install --strip-program=true" -f Makefile.SSE3.PTHREADS.gcc make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' rm -f *.o raxmlHPC-PTHREADS-SSE3 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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -c -o classify.o classify.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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ancestralStates.o ancestralStates.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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mem_alloc.o mem_alloc.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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigen.o eigen.c gcc -o raxmlHPC-PTHREADS-SSE3 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 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-SSE3 make[2]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' make -j42 "INSTALL=install --strip-program=true" -f Makefile.AVX.PTHREADS.gcc 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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o classify.o classify.c gcc -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ancestralStates.o ancestralStates.c gcc -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mem_alloc.o mem_alloc.c gcc -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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_install debian/bin/raxmlHPC usr/bin 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 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_amd64.deb'. dpkg-deb: building package 'raxml-dbgsym' in '../raxml-dbgsym_8.2.13+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../raxml_8.2.13+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../raxml_8.2.13+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/55742 and its subdirectories I: Current time: Wed Sep 2 18:17:06 -12 2026 I: pbuilder-time-stamp: 1788416226 Thu Sep 3 06:17:06 UTC 2026 I: Signing ./b1/raxml_8.2.13+dfsg-2_amd64.buildinfo as raxml_8.2.13+dfsg-2_amd64.buildinfo.asc Thu Sep 3 06:17:06 UTC 2026 I: Signed ./b1/raxml_8.2.13+dfsg-2_amd64.buildinfo as ./b1/raxml_8.2.13+dfsg-2_amd64.buildinfo.asc Thu Sep 3 06:17:06 UTC 2026 - build #1 for raxml/unstable/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Thu Sep 3 06:17:06 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-GKmtyOSz, removing. /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Jul 31 23:54 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jul 31 23:52 b2 -rw-r--r-- 1 jenkins jenkins 2177 Mar 2 13:03 raxml_8.2.13+dfsg-2.dsc -rw------- 1 jenkins jenkins 3297 Jul 31 23:52 rbuildlog.MoCF6Ux /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/b1: total 4656 -rw-r--r-- 1 jenkins jenkins 49565 Jul 31 23:54 build.log -rw-r--r-- 1 jenkins jenkins 3143724 Jul 31 23:54 raxml-dbgsym_8.2.13+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 22096 Jul 31 23:54 raxml_8.2.13+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2177 Jul 31 23:54 raxml_8.2.13+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 4940 Jul 31 23:54 raxml_8.2.13+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5822 Jul 31 23:54 raxml_8.2.13+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1738 Jul 31 23:54 raxml_8.2.13+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 1514008 Jul 31 23:54 raxml_8.2.13+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1582 Jul 31 23:54 raxml_8.2.13+dfsg-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/b2: total 0 Thu Jul 31 23:54:07 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 2 18:15:54 -12 2026 I: pbuilder-time-stamp: 1788416154 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: no acceptable signature found 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/55742/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='3c5158fa417e4f8caa93b3dac4ca1540' 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='55742' 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.hPCPFxXb/pbuilderrc_Ol4o --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.hPCPFxXb/b1 --logfile b1/build.log raxml_8.2.13+dfsg-2.dsc' SUDO_GID='111' SUDO_UID='106' 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 ionos15-amd64 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/55742/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19850 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 11.7 MB of archives. After unpacking 51.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Fetched 11.7 MB in 3s (3724 kB/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 ... 19850 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... 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_13.24.2_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:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-2.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2_amd64.deb ... Unpacking gettext (0.23.1-2) ... 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_13.24.2_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:amd64 (1.5.8-1) ... Setting up libsimde-dev (0.8.2-3) ... Setting up bsdextrautils (2.41-5) ... 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:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... 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 (1.23.0-9) ... 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 (13.24.2) ... Processing triggers for libc-bin (2.41-11) ... 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 amd64 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.PTHREADS.gcc Makefile.SSE3.PTHREADS.gcc 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 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-SSE3 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' 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.PTHREADS.gcc Makefile.SSE3.PTHREADS.gcc Makefile.AVX.PTHREADS.gcc; do \ dh_auto_build --buildsystem=makefile -- -f ${mfile} ; \ curexe=`ls raxmlHPC* | head -n 1` ; \ if [ -e /build/reproducible-path/raxml-8.2.13+dfsg/debian/tmpbuild/${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 -j42 "INSTALL=install --strip-program=true" -f Makefile.PTHREADS.gcc make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' rm -f *.o raxmlHPC-PTHREADS 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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -Wdate-time -D_FORTIFY_SOURCE=2 -c -o classify.o classify.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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ancestralStates.o ancestralStates.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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mem_alloc.o mem_alloc.c gcc -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -c -o eigen.o eigen.c gcc -o raxmlHPC-PTHREADS 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 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 make[2]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' make -j42 "INSTALL=install --strip-program=true" -f Makefile.SSE3.PTHREADS.gcc make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' rm -f *.o raxmlHPC-PTHREADS-SSE3 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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -c -o classify.o classify.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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ancestralStates.o ancestralStates.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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mem_alloc.o mem_alloc.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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigen.o eigen.c gcc -o raxmlHPC-PTHREADS-SSE3 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 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-SSE3 make[2]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' make -j42 "INSTALL=install --strip-program=true" -f Makefile.AVX.PTHREADS.gcc 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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o classify.o classify.c gcc -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ancestralStates.o ancestralStates.c gcc -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mem_alloc.o mem_alloc.c gcc -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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_install debian/bin/raxmlHPC usr/bin 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 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_amd64.deb'. dpkg-deb: building package 'raxml-dbgsym' in '../raxml-dbgsym_8.2.13+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../raxml_8.2.13+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../raxml_8.2.13+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/55742 and its subdirectories I: Current time: Wed Sep 2 18:17:06 -12 2026 I: pbuilder-time-stamp: 1788416226 Thu Jul 31 23:54:08 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Thu Jul 31 23:54:08 UTC 2025 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Thu Jul 31 23:54:08 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Thu Jul 31 23:54:08 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-5wce1I' ==================================================================================== Thu Jul 31 23:54:09 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "2 raxml unstable /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb 8.2.13+dfsg-2" as arguments. Thu Jul 31 23:54:09 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-ZLPv2zWS" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Jul 31 23:54:09 UTC 2025 I: Downloading source for unstable/raxml=8.2.13+dfsg-2 Reading package lists... NOTICE: 'raxml' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/raxml.git Please use: git clone https://salsa.debian.org/med-team/raxml.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1031 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main raxml 8.2.13+dfsg-2 (dsc) [2177 B] Get:2 http://deb.debian.org/debian unstable/main raxml 8.2.13+dfsg-2 (tar) [1007 kB] Get:3 http://deb.debian.org/debian unstable/main raxml 8.2.13+dfsg-2 (diff) [22.1 kB] Fetched 1031 kB in 0s (35.3 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'raxml' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/raxml.git Please use: git clone https://salsa.debian.org/med-team/raxml.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1031 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main raxml 8.2.13+dfsg-2 (dsc) [2177 B] Get:2 http://deb.debian.org/debian unstable/main raxml 8.2.13+dfsg-2 (tar) [1007 kB] Get:3 http://deb.debian.org/debian unstable/main raxml 8.2.13+dfsg-2 (diff) [22.1 kB] Fetched 1031 kB in 0s (35.3 MB/s) Download complete and in download only mode ============================================================================= Re-Building raxml in unstable on amd64 on ionos1-amd64 now. Date: Thu Jul 31 23:54:10 UTC 2025 Date UTC: Thu Jul 31 23:54:10 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/pbuilderrc_nQqI + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' raxml = debian-installer -o raxml = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' raxml = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/pbuilderrc_nQqI --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/b2 --logfile b2/build.log raxml_8.2.13+dfsg-2.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Aug 1 13:54:10 +14 2025 I: pbuilder-time-stamp: 1754006050 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: no acceptable signature found 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/3441382/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jul 31 23:54 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3441382/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3441382/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=9804fc533e1e4164beb09e2b6a3bdff1 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3441382 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/pbuilderrc_nQqI --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/b2 --logfile b2/build.log raxml_8.2.13+dfsg-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3441382/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19850 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 11.7 MB of archives. After unpacking 51.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Fetched 11.7 MB in 2s (6140 kB/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 ... 19850 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... 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_13.24.2_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:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-2.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2_amd64.deb ... Unpacking gettext (0.23.1-2) ... 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_13.24.2_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:amd64 (1.5.8-1) ... Setting up libsimde-dev (0.8.2-3) ... Setting up bsdextrautils (2.41-5) ... 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:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... 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 (1.23.0-9) ... 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 (13.24.2) ... Processing triggers for libc-bin (2.41-11) ... 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: user script /srv/workspace/pbuilder/3441382/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3441382/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/raxml-8.2.13+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../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 amd64 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.PTHREADS.gcc Makefile.SSE3.PTHREADS.gcc 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 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-SSE3 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' 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.PTHREADS.gcc Makefile.SSE3.PTHREADS.gcc Makefile.AVX.PTHREADS.gcc; do \ dh_auto_build --buildsystem=makefile -- -f ${mfile} ; \ curexe=`ls raxmlHPC* | head -n 1` ; \ if [ -e /build/reproducible-path/raxml-8.2.13+dfsg/debian/tmpbuild/${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 -j40 "INSTALL=install --strip-program=true" -f Makefile.PTHREADS.gcc make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' rm -f *.o raxmlHPC-PTHREADS 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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -Wdate-time -D_FORTIFY_SOURCE=2 -c -o classify.o classify.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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ancestralStates.o ancestralStates.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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mem_alloc.o mem_alloc.c gcc -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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -c -o eigen.o eigen.c gcc -o raxmlHPC-PTHREADS 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 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 make[2]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' make -j40 "INSTALL=install --strip-program=true" -f Makefile.SSE3.PTHREADS.gcc make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' rm -f *.o raxmlHPC-PTHREADS-SSE3 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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -c -o classify.o classify.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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ancestralStates.o ancestralStates.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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mem_alloc.o mem_alloc.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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eigen.o eigen.c gcc -o raxmlHPC-PTHREADS-SSE3 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 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-SSE3 make[2]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' make -j40 "INSTALL=install --strip-program=true" -f Makefile.AVX.PTHREADS.gcc 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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o classify.o classify.c gcc -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ancestralStates.o ancestralStates.c gcc -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mem_alloc.o mem_alloc.c gcc -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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -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_install debian/bin/raxmlHPC usr/bin 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 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_amd64.deb'. dpkg-deb: building package 'raxml-dbgsym' in '../raxml-dbgsym_8.2.13+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../raxml_8.2.13+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../raxml_8.2.13+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3441382/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3441382/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3441382 and its subdirectories I: Current time: Fri Aug 1 13:57:20 +14 2025 I: pbuilder-time-stamp: 1754006240 + false + set +x Thu Jul 31 23:57:20 UTC 2025 I: Signing ./b2/raxml_8.2.13+dfsg-2_amd64.buildinfo as raxml_8.2.13+dfsg-2_amd64.buildinfo.asc Thu Jul 31 23:57:20 UTC 2025 I: Signed ./b2/raxml_8.2.13+dfsg-2_amd64.buildinfo as ./b2/raxml_8.2.13+dfsg-2_amd64.buildinfo.asc Thu Jul 31 23:57:20 UTC 2025 - build #2 for raxml/unstable/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Thu Jul 31 23:57:20 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-ZLPv2zWS, removing. /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb: total 68 drwxr-xr-x 2 jenkins jenkins 4096 Jul 31 23:54 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jul 31 23:57 b2 -rw-r--r-- 1 jenkins jenkins 2177 Mar 2 13:03 raxml_8.2.13+dfsg-2.dsc -rw------- 1 jenkins jenkins 53149 Jul 31 23:54 rbuildlog.MoCF6Ux /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/b1: total 4668 -rw-r--r-- 1 jenkins jenkins 49565 Jul 31 23:54 build.log -rw-r--r-- 1 jenkins jenkins 3143724 Jul 31 23:54 raxml-dbgsym_8.2.13+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 22096 Jul 31 23:54 raxml_8.2.13+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2177 Jul 31 23:54 raxml_8.2.13+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 4940 Jul 31 23:54 raxml_8.2.13+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5822 Jul 31 23:54 raxml_8.2.13+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1738 Jul 31 23:54 raxml_8.2.13+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 1514008 Jul 31 23:54 raxml_8.2.13+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1582 Jul 31 23:54 raxml_8.2.13+dfsg-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/b2: total 4656 -rw-r--r-- 1 jenkins jenkins 51489 Jul 31 23:57 build.log -rw-r--r-- 1 jenkins jenkins 3143724 Jul 31 23:57 raxml-dbgsym_8.2.13+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 22096 Jul 31 23:57 raxml_8.2.13+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2177 Jul 31 23:57 raxml_8.2.13+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 4927 Jul 31 23:57 raxml_8.2.13+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5809 Jul 31 23:57 raxml_8.2.13+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1738 Jul 31 23:57 raxml_8.2.13+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 1514008 Jul 31 23:57 raxml_8.2.13+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1582 Jul 31 23:57 raxml_8.2.13+dfsg-2_source.changes Thu Jul 31 23:57:21 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Thu Jul 31 23:57:21 UTC 2025 I: raxml_8.2.13+dfsg-2_amd64.changes: Format: 1.8 Date: Sun, 02 Mar 2025 13:38:42 +0100 Source: raxml Binary: raxml raxml-dbgsym Architecture: amd64 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: 92597b21186dd448c1d8853022e2d7de445616e7 3143724 raxml-dbgsym_8.2.13+dfsg-2_amd64.deb 0cbdb46791ccb5b42d3de108d50b93104cea1bc0 4940 raxml_8.2.13+dfsg-2_amd64.buildinfo 9d4f0bec4c257899134f54a63822dc2b652b0f12 1514008 raxml_8.2.13+dfsg-2_amd64.deb Checksums-Sha256: 11b5d9a8596736b7f800ef451a4219bebc11aebadf3b224e4aa30eb569dcf743 3143724 raxml-dbgsym_8.2.13+dfsg-2_amd64.deb fbacc63b8b496644f3159758557f6d42e1ade4349adc23af00fc0ba0b00883bb 4940 raxml_8.2.13+dfsg-2_amd64.buildinfo 01b04e6e1520ffbea3ac38aa3fb70938b940fd7a95177aa491e5a7424c3f38c5 1514008 raxml_8.2.13+dfsg-2_amd64.deb Files: 1d341a84f7f4af74a3ef112d95de606a 3143724 debug optional raxml-dbgsym_8.2.13+dfsg-2_amd64.deb dc3356674c008ec209f4ea482f23d5ac 4940 science optional raxml_8.2.13+dfsg-2_amd64.buildinfo 1ec05b558d04aebb534f8eb98df60840 1514008 science optional raxml_8.2.13+dfsg-2_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/raxml_8.2.13+dfsg-2.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/raxml_8.2.13+dfsg-2.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/raxml_8.2.13+dfsg-2.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/raxml_8.2.13+dfsg-2.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/raxml_8.2.13+dfsg-2_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/raxml_8.2.13+dfsg-2.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-07-31 23:54:07.817321388 +0000 +++ b2/build.log 2025-07-31 23:57:21.217564303 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Sep 2 18:15:54 -12 2026 -I: pbuilder-time-stamp: 1788416154 +I: Current time: Fri Aug 1 13:54:10 +14 2025 +I: pbuilder-time-stamp: 1754006050 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ 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/55742/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3441382/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jul 31 23:54 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3441382/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3441382/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='3c5158fa417e4f8caa93b3dac4ca1540' - 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='55742' - PS1='# ' - PS2='> ' + INVOCATION_ID=9804fc533e1e4164beb09e2b6a3bdff1 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3441382 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.hPCPFxXb/pbuilderrc_Ol4o --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.hPCPFxXb/b1 --logfile b1/build.log raxml_8.2.13+dfsg-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - 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' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/pbuilderrc_nQqI --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/b2 --logfile b2/build.log raxml_8.2.13+dfsg-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/55742/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3441382/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -141,7 +173,7 @@ Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-3 [467 kB] -Fetched 11.7 MB in 3s (3724 kB/s) +Fetched 11.7 MB in 2s (6140 kB/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 ... 19850 files and directories currently installed.) @@ -276,7 +308,11 @@ 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 +I: user script /srv/workspace/pbuilder/3441382/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3441382/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/raxml-8.2.13+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../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 @@ -317,7 +353,7 @@ fi ; \ /usr/bin/make -f ${mfile} clean ; \ done - make -j42 "INSTALL=install --strip-program=true" -f Makefile.PTHREADS.gcc + make -j40 "INSTALL=install --strip-program=true" -f Makefile.PTHREADS.gcc make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' rm -f *.o raxmlHPC-PTHREADS 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 -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -D_USE_PTHREADS -msse -Wdate-time -D_FORTIFY_SOURCE=2 -c -o axml.o axml.c @@ -348,7 +384,7 @@ make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' rm -f *.o raxmlHPC-PTHREADS make[2]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' - make -j42 "INSTALL=install --strip-program=true" -f Makefile.SSE3.PTHREADS.gcc + make -j40 "INSTALL=install --strip-program=true" -f Makefile.SSE3.PTHREADS.gcc make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' rm -f *.o raxmlHPC-PTHREADS-SSE3 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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -c -o axml.o axml.c @@ -379,7 +415,7 @@ make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg' rm -f *.o raxmlHPC-PTHREADS-SSE3 make[2]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg' - make -j42 "INSTALL=install --strip-program=true" -f Makefile.AVX.PTHREADS.gcc + make -j40 "INSTALL=install --strip-program=true" -f Makefile.AVX.PTHREADS.gcc 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 -fcf-protection -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX -mavx -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o axml.o axml.c @@ -467,12 +503,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3441382/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3441382/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/55742 and its subdirectories -I: Current time: Wed Sep 2 18:17:06 -12 2026 -I: pbuilder-time-stamp: 1788416226 +I: removing directory /srv/workspace/pbuilder/3441382 and its subdirectories +I: Current time: Fri Aug 1 13:57:20 +14 2025 +I: pbuilder-time-stamp: 1754006240 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/raxml_8.2.13+dfsg-2.diff: 69.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/raxml_8.2.13+dfsg-2.diff.gz b2/build.log: 86.4% -- replaced with stdout Compressing the 1st log... b1/build.log: 87.2% -- replaced with stdout Thu Jul 31 23:57:22 UTC 2025 I: diffoscope 302 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_raxml_unstable_amd64_1754006242 + touch /var/log/reproducible-builds/diffoscope_stamp_raxml_unstable_amd64_1754006242 + RESULT=0 + systemd-run '--description=diffoscope on raxml/8.2.13+dfsg-2 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_12-64367 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb --run-session -c jenkins-reproducible-unstable-diffoscope-1717fef2-34da-426f-bb06-a2b61631af1e -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/dbd-tmp-k5wfoTb ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/raxml_8.2.13+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/raxml_8.2.13+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/raxml_8.2.13+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/b1/raxml_8.2.13+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/b2/raxml_8.2.13+dfsg-2_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_12-64367.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/raxml_8.2.13+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/raxml_8.2.13+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/raxml_8.2.13+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/b1/raxml_8.2.13+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.hPCPFxXb/b2/raxml_8.2.13+dfsg-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 161ms CPU time consumed: 163ms _ _ __ __ ___ ___ __ ___ | | | '__/ _` \ \/ / '_ ` _ \| | | | | (_| |> <| | | | | | | |_| \__,_/_/\_\_| |_| |_|_| Thu Jul 31 23:57:23 UTC 2025 I: diffoscope 302 found no differences in the changes files, and a .buildinfo file also exists. Thu Jul 31 23:57:23 UTC 2025 I: raxml from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-07-31 23:57:23] INFO: Starting at 2025-07-31 23:57:23.514103 [2025-07-31 23:57:23] INFO: Generating the pages of 1 package(s) [2025-07-31 23:57:23] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/raxml didn't produce a buildlog, even though it has been built. [2025-07-31 23:57:23] INFO: Finished at 2025-07-31 23:57:23.751082, took: 0:00:00.236982 Thu Jul 31 23:57:23 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/raxml.html Thu Jul 31 23:57:23 UTC 2025 I: Removing signed raxml_8.2.13+dfsg-2_amd64.buildinfo.asc files: removed './b1/raxml_8.2.13+dfsg-2_amd64.buildinfo.asc' removed './b2/raxml_8.2.13+dfsg-2_amd64.buildinfo.asc' 1754006243 amd64 unstable raxml Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/raxml_8.2.13+dfsg-2.rbuild.log: 83.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/raxml_8.2.13+dfsg-2.rbuild.log.gz [2025-07-31 23:57:24] INFO: Starting at 2025-07-31 23:57:24.001490 [2025-07-31 23:57:24] INFO: Generating the pages of 1 package(s) [2025-07-31 23:57:24] INFO: Finished at 2025-07-31 23:57:24.227145, took: 0:00:00.225659 All cleanup done. Thu Jul 31 23:57:24 UTC 2025 - total duration: 0h 4m 45s. Thu Jul 31 23:57:24 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-BwfQ1Q0g, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 4min 45.756s CPU time consumed: 4.491s