Wed Apr 19 12:51:12 UTC 2023 I: starting to build raxml/bookworm/amd64 on jenkins on '2023-04-19 12:51' Wed Apr 19 12:51:12 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_12/31566/console.log Wed Apr 19 12:51:12 UTC 2023 I: Downloading source for bookworm/raxml=8.2.12+dfsg-8 --2023-04-19 12:51:12-- http://cdn-fastly.deb.debian.org/debian/pool/main/r/raxml/raxml_8.2.12%2bdfsg-8.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2022 (2.0K) [text/prs.lines.tag] Saving to: ‘raxml_8.2.12+dfsg-8.dsc’ 0K . 100% 181M=0s 2023-04-19 12:51:12 (181 MB/s) - ‘raxml_8.2.12+dfsg-8.dsc’ saved [2022/2022] Wed Apr 19 12:51:12 UTC 2023 I: raxml_8.2.12+dfsg-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: raxml Binary: raxml Architecture: any Version: 8.2.12+dfsg-8 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://cme.h-its.org/exelixis/web/software/raxml/index.html Standards-Version: 4.6.0 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, debhelper Package-List: raxml deb science optional arch=any Checksums-Sha1: 6edd346413be6cc1fd31863e3cb39d0a52e52473 959232 raxml_8.2.12+dfsg.orig.tar.xz 77ec9323ed2906d3e2ae7fa665bde24137a0be96 19604 raxml_8.2.12+dfsg-8.debian.tar.xz Checksums-Sha256: ac42bd6e3aef6d5c1671a813bab8ce1faab3d86153688144d332e11ca01c6515 959232 raxml_8.2.12+dfsg.orig.tar.xz e621f7b5bb98f165c4441568c4a8469cf77987b4ec1426ad20c57404f1a37649 19604 raxml_8.2.12+dfsg-8.debian.tar.xz Files: 74a6cdbd23618eb599fc07587aba948a 959232 raxml_8.2.12+dfsg.orig.tar.xz 91b5bb62f58a8eaa99e73b8f63d2b728 19604 raxml_8.2.12+dfsg-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmHlhfkRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFDzhAAhC5p0wtHiUQeCAe0+T4ZpMrMc0OfCaUi vMCdCBfzHVaTV1s5PQYz7/HqvI2N9q3rA8UJfBapVC+4bqCq/nEQTp2oe8LfVfUK lA1dzXBLF2J1rll76Fm7ghrdYDFoIdcypFF8l6Awjk2qmzj6nXk/4ce13Lj05YFd ZbvIYvqubKHwtQG+1tBmO3bt8hPWMlArVpuG+kXvPy2HMN3yFUURt2qYe67Fl16k CUpUDn6FVji7ibmmmHalfeilv0HQ7yFNyfoVV0UaG8c6u7HcaF78NlNKtXBDOVGq ScZCsT/FLF02sbyQ/L8i0iEyhiVI9nkM/iNTi8qSCLzcd5h1hr4FQAw2LKeZndr0 5diXKLa0gwkY4xwNEBiHqa+LhwsV1JRucJnFLR6d2A++TMFS51iMq+GtphYwGD6N mRCLabYdunk6Lq75PhX3+Zi7IR4kxd8VkSKPAQF0k9d2GX8wyXFsT1ITRZlFBkGW RIAGnCocsnzH16XGX2OHUyaBvFxms7IYj+rMKUsr2eh65XlExeHTWbqJlwF0JXAj PPRWdMpZaJEFdn/C0uZLIK8A6Cf1SDc4KoFLcbQO99mLd1CfmcFSniLTkUDXugyF VvUHpBx6NkuviOBMPW5y2vmCANnY2vxz8X//H7UXsirAXIhR6M/wv8BUt2keG9Io GA9osWnocCM= =zCR0 -----END PGP SIGNATURE----- Wed Apr 19 12:51:12 UTC 2023 I: Checking whether the package is not for us Wed Apr 19 12:51:12 UTC 2023 I: Starting 1st build on remote node ionos15-amd64.debian.net. Wed Apr 19 12:51:12 UTC 2023 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Wed Apr 19 12:52:18 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 21 07:14:14 -12 2024 I: pbuilder-time-stamp: 1716318854 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_8.2.12+dfsg-8.dsc] I: copying [./raxml_8.2.12+dfsg.orig.tar.xz] I: copying [./raxml_8.2.12+dfsg-8.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Jan 17 03:06:33 2022 -12 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_8.2.12+dfsg-8.dsc: no acceptable signature found dpkg-source: info: extracting raxml in raxml-8.2.12+dfsg dpkg-source: info: unpacking raxml_8.2.12+dfsg.orig.tar.xz dpkg-source: info: unpacking raxml_8.2.12+dfsg-8.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/2653704/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=16' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='4fa2bbe5890e43bba68fbd0e93913b2d' 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='2653704' 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.gzGWD81a/pbuilderrc_AxnU --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gzGWD81a/b1 --logfile b1/build.log raxml_8.2.12+dfsg-8.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://85.184.249.68:3128' I: uname -a Linux ionos15-amd64 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 12 2023 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/2653704/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, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 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. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper 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} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{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 19.1 MB of archives. After unpacking 79.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libsimde-dev all 0.7.4~rc2-2 [377 kB] Fetched 19.1 MB in 0s (52.2 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 ... 19596 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... 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_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... 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 libelf1:amd64. Preparing to unpack .../22-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.1+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... 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Setting up autopoint (0.21-12) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.1+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 (0.21-12) ... Setting up libtool (2.4.7-5) ... 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 dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... 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/raxml-8.2.12+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_8.2.12+dfsg-8_source.changes dpkg-buildpackage: info: source package raxml dpkg-buildpackage: info: source version 8.2.12+dfsg-8 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/raxml-8.2.12+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/raxml-8.2.12+dfsg' rm -f *.o raxmlHPC-PTHREADS make[2]: Leaving directory '/build/raxml-8.2.12+dfsg' make[2]: Entering directory '/build/raxml-8.2.12+dfsg' rm -f *.o raxmlHPC-PTHREADS-SSE3 make[2]: Leaving directory '/build/raxml-8.2.12+dfsg' make[2]: Entering directory '/build/raxml-8.2.12+dfsg' rm -f *.o raxmlHPC-PTHREADS-AVX make[2]: Leaving directory '/build/raxml-8.2.12+dfsg' rm -rf /build/raxml-8.2.12+dfsg/debian/tmpbuild make[1]: Leaving directory '/build/raxml-8.2.12+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/raxml-8.2.12+dfsg' mkdir -p /build/raxml-8.2.12+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 ${mfile} ; \ curexe=`ls raxmlHPC* | head -n 1` ; \ if [ -e /build/raxml-8.2.12+dfsg/debian/tmpbuild/${curexe} ] ; then \ echo "**** ERROR: ${curexe} was created before!!" && false ; \ else \ mv ${curexe} /build/raxml-8.2.12+dfsg/debian/tmpbuild/${curexe} ; \ fi ; \ /usr/bin/make -f ${mfile} clean ; \ done make -j16 "INSTALL=install --strip-program=true" -f Makefile.PTHREADS.gcc make[2]: Entering directory '/build/raxml-8.2.12+dfsg' rm -f *.o raxmlHPC-PTHREADS gcc -g -O2 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/raxml-8.2.12+dfsg' make[2]: Entering directory '/build/raxml-8.2.12+dfsg' rm -f *.o raxmlHPC-PTHREADS make[2]: Leaving directory '/build/raxml-8.2.12+dfsg' make -j16 "INSTALL=install --strip-program=true" -f Makefile.SSE3.PTHREADS.gcc make[2]: Entering directory '/build/raxml-8.2.12+dfsg' rm -f *.o raxmlHPC-PTHREADS-SSE3 gcc -g -O2 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/raxml-8.2.12+dfsg' make[2]: Entering directory '/build/raxml-8.2.12+dfsg' rm -f *.o raxmlHPC-PTHREADS-SSE3 make[2]: Leaving directory '/build/raxml-8.2.12+dfsg' make -j16 "INSTALL=install --strip-program=true" -f Makefile.AVX.PTHREADS.gcc make[2]: Entering directory '/build/raxml-8.2.12+dfsg' rm -f *.o raxmlHPC-PTHREADS-AVX gcc -g -O2 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/raxml-8.2.12+dfsg' make[2]: Entering directory '/build/raxml-8.2.12+dfsg' rm -f *.o raxmlHPC-PTHREADS-AVX make[2]: Leaving directory '/build/raxml-8.2.12+dfsg' make[1]: Leaving directory '/build/raxml-8.2.12+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/raxml-8.2.12+dfsg' dh_install dh_install debian/bin/raxmlHPC usr/bin make[1]: Leaving directory '/build/raxml-8.2.12+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/raxml-8.2.12+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/raxml-8.2.12+dfsg/debian/raxml/usr/share/doc/raxml/examples/`basename ${pscript}` ; \ done make[1]: Leaving directory '/build/raxml-8.2.12+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/raxml-8.2.12+dfsg' dh_installman for cexe in `ls /build/raxml-8.2.12+dfsg/debian/tmpbuild/raxmlHPC*` ; do \ curexe=`basename ${cexe}` ; \ if [ ${curexe} != raxmlHPC ] ; then \ ln -s raxmlHPC.1.gz /build/raxml-8.2.12+dfsg/debian/raxml/usr/share/man/man1/${curexe}.1.gz ; \ fi ; \ done make[1]: Leaving directory '/build/raxml-8.2.12+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/raxml-8.2.12+dfsg' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.4~rc2-2), " make[1]: Leaving directory '/build/raxml-8.2.12+dfsg' dh_md5sums dh_builddeb dpkg-deb: building package 'raxml' in '../raxml_8.2.12+dfsg-8_amd64.deb'. dpkg-deb: building package 'raxml-dbgsym' in '../raxml-dbgsym_8.2.12+dfsg-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../raxml_8.2.12+dfsg-8_amd64.buildinfo dpkg-genchanges --build=binary -O../raxml_8.2.12+dfsg-8_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/2653704 and its subdirectories I: Current time: Tue May 21 07:15:18 -12 2024 I: pbuilder-time-stamp: 1716318918 Wed Apr 19 12:52:18 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Wed Apr 19 12:52:18 UTC 2023 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Wed Apr 19 12:58:37 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Wed Apr 19 12:58:37 UTC 2023 I: raxml_8.2.12+dfsg-8_amd64.changes: Format: 1.8 Date: Mon, 17 Jan 2022 16:01:38 +0100 Source: raxml Binary: raxml raxml-dbgsym Architecture: amd64 Version: 8.2.12+dfsg-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: raxml - Randomized Axelerated Maximum Likelihood of phylogenetic trees Changes: raxml (8.2.12+dfsg-8) unstable; urgency=medium . * Really fix watch file * Add missing build dependency on dh addon. Checksums-Sha1: 67a260f3cb97960ae37f2b3bb1bb091d9ddda1b0 3055912 raxml-dbgsym_8.2.12+dfsg-8_amd64.deb 9ed5fc7d03dd7ae9e736a1cd9cddd3358f78782e 5182 raxml_8.2.12+dfsg-8_amd64.buildinfo 6a7972257a71c3a2b264611e15611af7e1fa2664 1480280 raxml_8.2.12+dfsg-8_amd64.deb Checksums-Sha256: 7ad279023876c0c94556a94d356bae0d35b64316cfd331fe5f6e234e67fdf8fa 3055912 raxml-dbgsym_8.2.12+dfsg-8_amd64.deb 2b3d4fc0f654fbf51b8afda17866aad66dcd15c15262849f2128b2fd7cea055e 5182 raxml_8.2.12+dfsg-8_amd64.buildinfo 1f673c24d225a457e2da74de7a0f6df4a8d6c9c1e0170728c104c54408c765df 1480280 raxml_8.2.12+dfsg-8_amd64.deb Files: 09953a61e41d97a1e2d771a1e8e75aee 3055912 debug optional raxml-dbgsym_8.2.12+dfsg-8_amd64.deb 4610cd669332841ec89b3938f59dfae0 5182 science optional raxml_8.2.12+dfsg-8_amd64.buildinfo 680e593d3ff0ad8d16393009b59a67cf 1480280 science optional raxml_8.2.12+dfsg-8_amd64.deb Wed Apr 19 12:58:38 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.gzGWD81a/raxml_8.2.12+dfsg-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.gzGWD81a/raxml_8.2.12+dfsg-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.gzGWD81a/raxml_8.2.12+dfsg-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.gzGWD81a/b1/raxml_8.2.12+dfsg-8_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.gzGWD81a/b2/raxml_8.2.12+dfsg-8_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: 0.508s) 0.508s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.080s) 0.079s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Wed Apr 19 12:58:39 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Wed Apr 19 12:58:39 UTC 2023 I: raxml from bookworm built successfully and reproducibly on amd64. Wed Apr 19 12:58:41 UTC 2023 I: Submitting .buildinfo files to external archives: Wed Apr 19 12:58:41 UTC 2023 I: Submitting 8.0K b1/raxml_8.2.12+dfsg-8_amd64.buildinfo.asc Wed Apr 19 12:58:42 UTC 2023 I: Submitting 8.0K b2/raxml_8.2.12+dfsg-8_amd64.buildinfo.asc Wed Apr 19 12:58:43 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Apr 19 12:58:43 UTC 2023 I: Done submitting .buildinfo files. Wed Apr 19 12:58:43 UTC 2023 I: Removing signed raxml_8.2.12+dfsg-8_amd64.buildinfo.asc files: removed './b1/raxml_8.2.12+dfsg-8_amd64.buildinfo.asc' removed './b2/raxml_8.2.12+dfsg-8_amd64.buildinfo.asc'