Sun May 5 22:51:50 UTC 2024 I: starting to build raxml/trixie/amd64 on jenkins on '2024-05-05 22:51' Sun May 5 22:51:50 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_14/5771/console.log Sun May 5 22:51:50 UTC 2024 I: Downloading source for trixie/raxml=8.2.13+dfsg-1 --2024-05-05 22:51:51-- http://deb.debian.org/debian/pool/main/r/raxml/raxml_8.2.13%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2014 (2.0K) [text/prs.lines.tag] Saving to: ‘raxml_8.2.13+dfsg-1.dsc’ 0K . 100% 279M=0s 2024-05-05 22:51:51 (279 MB/s) - ‘raxml_8.2.13+dfsg-1.dsc’ saved [2014/2014] Sun May 5 22:51:51 UTC 2024 I: raxml_8.2.13+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: raxml Binary: raxml Architecture: any Version: 8.2.13+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://cme.h-its.org/exelixis/web/software/raxml/index.html Standards-Version: 4.6.2 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 f65c4f8e68e691abc8398c96fcdb3f2c69159b3c 20016 raxml_8.2.13+dfsg-1.debian.tar.xz Checksums-Sha256: 34b11973d306240275287e7b3c43b59de6707880840d93a34086c7bdb58bb2ed 1006760 raxml_8.2.13+dfsg.orig.tar.xz 2ec90cc3c96c04a05f57eea941052ef8601408d5c3591f4f20bfc9f3c67b7220 20016 raxml_8.2.13+dfsg-1.debian.tar.xz Files: 73f896a05f9bd8185cd449300764c89c 1006760 raxml_8.2.13+dfsg.orig.tar.xz e752e72f51701a78a2096a009ca2b705 20016 raxml_8.2.13+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmVlxVURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtE4vw/+M8S9CtkJaMTsUSFfs8Emt/rIP7YHstl3 EQ5vlecmjLwRpCwu/SCnYAlZKumegNx3dKOFQKfI1wLJ0SyOi4ZToyPdmIit7t+V 9pToKC8W0+FYLETqQLvsJl6ERFFsar2TTGLXVs9ZihHu15YRxL784eR+Q+goBSJ0 n33rEA28S4RaSajabIgRG87iUkVY2CIOC6+BXHTRGKNwK5MwqJF8/Zk1lL6GsG8l 6seTY+L/cW82FhKhQVAtjbBf4DdcrumsD0BaeFJiNiwTFaKrsl5QTvc/IeyAaCYA VlnScjWXzHd0l4pyTp5HYj3iL5LKOI0SQiY0An+EZnBDqdL+fLi8VM/rKwMnpg6D fKK5JIZ6b+3L/4BDTuxj4YVd5iwyDtkXlJ8CfeRa7QIdQeilyeb8olQqZqNnFqiI A1mN2vJl0KlqL9HbQMCZmAmD1h/Yx2pKr3PUdfRIz6bLpVGdQ91emOoc1SflS8wP EGeiRX33Xw7Gsvwy62hLzQc4mf4sIyffmP+fz8vjRIhkYfA4/qRe6m8SQ4oCQjyx gj1ai1pPRicMXFrVnh0AVv8Ongn88F2wGmZUpBOpdhL2zN/FNyt7n+3pXyQusFCL i83TUVxIAGCrtB2NLxfNq49m4qrjA4oVrs/ocDZ2wMPoqkAkUoqG8N4zCMStwjPv OKetnQru288= =GR6c -----END PGP SIGNATURE----- Sun May 5 22:51:51 UTC 2024 I: Checking whether the package is not for us Sun May 5 22:51:51 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Sun May 5 22:51:51 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Sun May 5 22:54:18 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Jun 7 17:14:52 -12 2025 I: pbuilder-time-stamp: 1749359692 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [raxml_8.2.13+dfsg-1.dsc] I: copying [./raxml_8.2.13+dfsg.orig.tar.xz] I: copying [./raxml_8.2.13+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Nov 28 10:47:49 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./raxml_8.2.13+dfsg-1.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-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying simde dpkg-source: info: applying hardening I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/612385/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='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='a4d941eb5e9f4483b7b4abdd0773b6e1' 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='612385' 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.mnOa2EgP/pbuilderrc_fqo1 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mnOa2EgP/b1 --logfile b1/build.log raxml_8.2.13+dfsg-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 7 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/612385/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 ... 19694 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} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsimde-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 19.5 MB of archives. After unpacking 82.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-1 [465 kB] Fetched 19.5 MB in 0s (39.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19694 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../22-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../30-libsimde-dev_0.8.2-1_all.deb ... Unpacking libsimde-dev (0.8.2-1) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libsimde-dev (0.8.2-1) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.37-19) ... 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-1_source.changes dpkg-buildpackage: info: source package raxml dpkg-buildpackage: info: source version 8.2.13+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean 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 (= 0.8.2-1), " 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-1_amd64.deb'. dpkg-deb: building package 'raxml-dbgsym' in '../raxml-dbgsym_8.2.13+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../raxml_8.2.13+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../raxml_8.2.13+dfsg-1_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: including full 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/612385 and its subdirectories I: Current time: Sat Jun 7 17:17:16 -12 2025 I: pbuilder-time-stamp: 1749359836 Sun May 5 22:54:19 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Sun May 5 22:54:19 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Sun May 5 22:56:32 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Sun May 5 22:56:33 UTC 2024 I: raxml_8.2.13+dfsg-1_amd64.changes: Format: 1.8 Date: Tue, 28 Nov 2023 11:44:47 +0100 Source: raxml Binary: raxml raxml-dbgsym Architecture: amd64 Version: 8.2.13+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: raxml - Randomized Axelerated Maximum Likelihood of phylogenetic trees Changes: raxml (8.2.13+dfsg-1) unstable; urgency=medium . * New upstream version * Revert: Add missing build dependency on dh addon. * Standards-Version: 4.6.2 (routine-update) * d/watch: Fix download name * README -> README.md Checksums-Sha1: e852329939d75f8f31a945a8adf5b2edd7b53289 3082520 raxml-dbgsym_8.2.13+dfsg-1_amd64.deb 3195731e128eaa3b11443e5fe95fa9546a5f6b9e 5190 raxml_8.2.13+dfsg-1_amd64.buildinfo 4fb4111c2bb33efc72108532a3b42690a0cc0cb5 1480352 raxml_8.2.13+dfsg-1_amd64.deb Checksums-Sha256: 7d87262c3f65b42f373d8ea61c1632adb64e9d172c184e15c4572faa38a0cb20 3082520 raxml-dbgsym_8.2.13+dfsg-1_amd64.deb c35d35eb639d164ab01edd9a9e16f33c949d792fbbce25927688fa3240ff4cf5 5190 raxml_8.2.13+dfsg-1_amd64.buildinfo 4653bcb4e762cf1944413cc04b0eeb6dd7f9e26dc49418ea68050d2b630e20a3 1480352 raxml_8.2.13+dfsg-1_amd64.deb Files: e0cb399ac652cfd4877cb35796a070cb 3082520 debug optional raxml-dbgsym_8.2.13+dfsg-1_amd64.deb 416189bd8a550e596e60cec6a026da35 5190 science optional raxml_8.2.13+dfsg-1_amd64.buildinfo aba5dae806128d6854e3a4faf39230cb 1480352 science optional raxml_8.2.13+dfsg-1_amd64.deb Sun May 5 22:56:34 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_14-5771.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.mnOa2EgP/raxml_8.2.13+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.mnOa2EgP/raxml_8.2.13+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.mnOa2EgP/raxml_8.2.13+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.mnOa2EgP/b1/raxml_8.2.13+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.mnOa2EgP/b2/raxml_8.2.13+dfsg-1_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 abc.DotChangesFile ## main (total time: 0.496s) 0.496s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.079s) 0.079s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 891ms CPU time consumed: 891ms Sun May 5 22:56:35 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Sun May 5 22:56:35 UTC 2024 I: raxml from trixie built successfully and reproducibly on amd64. Sun May 5 22:56:36 UTC 2024 I: Submitting .buildinfo files to external archives: Sun May 5 22:56:36 UTC 2024 I: Submitting 8.0K b1/raxml_8.2.13+dfsg-1_amd64.buildinfo.asc Sun May 5 22:56:38 UTC 2024 I: Submitting 8.0K b2/raxml_8.2.13+dfsg-1_amd64.buildinfo.asc Sun May 5 22:56:39 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun May 5 22:56:39 UTC 2024 I: Done submitting .buildinfo files. Sun May 5 22:56:39 UTC 2024 I: Removing signed raxml_8.2.13+dfsg-1_amd64.buildinfo.asc files: removed './b1/raxml_8.2.13+dfsg-1_amd64.buildinfo.asc' removed './b2/raxml_8.2.13+dfsg-1_amd64.buildinfo.asc'