Thu Dec 5 07:01:17 UTC 2024 I: starting to build phyml/trixie/i386 on jenkins on '2024-12-05 07:00' Thu Dec 5 07:01:17 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_18/34773/console.log Thu Dec 5 07:01:17 UTC 2024 I: Downloading source for trixie/phyml=3:3.3.20220408-4 --2024-12-05 07:01:17-- http://deb.debian.org/debian/pool/main/p/phyml/phyml_3.3.20220408-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2256 (2.2K) [text/prs.lines.tag] Saving to: ‘phyml_3.3.20220408-4.dsc’ 0K .. 100% 331M=0s 2024-12-05 07:01:17 (331 MB/s) - ‘phyml_3.3.20220408-4.dsc’ saved [2256/2256] Thu Dec 5 07:01:17 UTC 2024 I: phyml_3.3.20220408-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phyml Binary: phyml Architecture: any Version: 3:3.3.20220408-4 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Kevin Murray , Étienne Mollier Homepage: http://www.atgc-montpellier.fr/phyml Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/phyml Vcs-Git: https://salsa.debian.org/med-team/phyml.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), pkgconf, mpi-default-dev, chrpath Package-List: phyml deb science optional arch=any Checksums-Sha1: 1dd5067ba9094eb54ff9f9c2c39c1c35ee750944 1803950 phyml_3.3.20220408.orig.tar.gz 4ca11e948f0e7e8585f0daad5f709e2be3170331 27020 phyml_3.3.20220408-4.debian.tar.xz Checksums-Sha256: 9cef375c0186e8a8d4db72ac02148707624c97174ffac244167a138ceb9f65bd 1803950 phyml_3.3.20220408.orig.tar.gz a76294e8f8b118a105217755ea67701870ffed751c8940b54168f3b578ff1fad 27020 phyml_3.3.20220408-4.debian.tar.xz Files: b35e641af77d7f058cf1ddc73be5e0b7 1803950 phyml_3.3.20220408.orig.tar.gz 48050b4235d2e54572c398938a25a5e4 27020 phyml_3.3.20220408-4.debian.tar.xz Dgit: c34b7a51c3c1b3dedfd37ab64fe7ee062fb94633 debian archive/debian/3%3.3.20220408-4 https://git.dgit.debian.org/phyml -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmcvtLQUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdobew/6Anprva8MJNpL/ScGgyqU5HGqZpSG WAeG7rfbMwAAWbhsJfec1I9QgB+Usrrio+t8Pf8Hfp2khAWeAN7UBPjkGr8CAlm2 7LKnMdqhFMdSiQrEHsG51Ad1aVi5UV8kEzApUjYjgLTaLn/DqHFqn3r80Q5/HIYD MLL/LFqN/IlyYfhpe8TZ1z3u/bcvZIStdKkUcVFHERSZfn5oyKwNTqdIgryqoWlI WtmiAE49EfH0Q9oJJtawe6ipE+QUMpU1kdRMTjGBM9uZ9Razx8dSicpQDJx18KgR 9rm0FEIDnW2tLzJrtVcG0MU2OXSBA3D+bBlfZ7Uizgixj/y9doAGMzC2sgxqfMFY X7coENXQ29I/IWAOhMpEbFRXMuLuXYGLN+T8CDZibPzrIRqpKBV5t7fEhPS5revs EUWUBfhvNXpGG3nKLCggkrZaFQMM6TgcIjWR5pzfeU9haGWzSwp6ik4mLdMn5oXU YjorPvzno1qbfY4dFK6PCGgaEggbCjif9y6OvlEu/QrjuZpDpFMyLzb+VXrwr+5n Ki44HSd5tJtVeFBZ541TIReT25+Jx0yATCloc6uEN8f6UZz2HBI/4XNsgQ5EMwIN 5ei7+OiwxIZmBeyG2xGv4n4eL0A7kCO8YrNXgC4IdPfHJ59KzX/y28gpuSVv3SjH 8tbh3nnDI9TaOws= =0W3Z -----END PGP SIGNATURE----- Thu Dec 5 07:01:17 UTC 2024 I: Checking whether the package is not for us Thu Dec 5 07:01:17 UTC 2024 I: Starting 1st build on remote node infom08-i386.debian.net. Thu Dec 5 07:01:17 UTC 2024 I: Preparing to do remote build '1' on infom08-i386.debian.net. Thu Dec 5 07:02:09 UTC 2024 I: Deleting $TMPDIR on infom08-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jan 7 01:24:17 -12 2026 I: pbuilder-time-stamp: 1767792257 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [phyml_3.3.20220408-4.dsc] I: copying [./phyml_3.3.20220408.orig.tar.gz] I: copying [./phyml_3.3.20220408-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 9 19:15:00 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phyml_3.3.20220408-4.dsc: no acceptable signature found dpkg-source: info: extracting phyml in phyml-3.3.20220408 dpkg-source: info: unpacking phyml_3.3.20220408.orig.tar.gz dpkg-source: info: unpacking phyml_3.3.20220408-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying sse_only_if_supported.patch dpkg-source: info: applying no-configure-ac-date.patch dpkg-source: info: applying fix_declaration_of_temp.patch dpkg-source: info: applying fix_wrong_initialisation_of_array.patch dpkg-source: info: applying no-march-native.patch dpkg-source: info: applying apply-cflags.patch dpkg-source: info: applying filter-sse3-intrinsics.patch dpkg-source: info: applying apply-ldflags.patch dpkg-source: info: applying typos.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/32431/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='bf4f29b4e3184a34be4594b3d6684473' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='32431' 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.BubMAQwh/pbuilderrc_pwvh --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.BubMAQwh/b1 --logfile b1/build.log phyml_3.3.20220408-4.dsc' SUDO_GID='111' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom08-i386 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/32431/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), pkgconf, mpi-default-dev, chrpath dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19956 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 pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath 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} chrpath{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-14{a} gfortran-14-i686-linux-gnu{a} groff-base{a} hwloc-nox{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libhwloc-dev{a} libhwloc15{a} libicu72{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmpich-dev{a} libmpich12{a} libnuma-dev{a} libnuma1{a} libpipeline1{a} libpkgconf3{a} libslurm41t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mpi-default-dev{a} mpich{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libhwloc-plugins libmail-sendmail-perl lynx wget 0 packages upgraded, 49 newly installed, 0 to remove and 0 not upgraded. Need to get 40.6 MB of archives. After unpacking 153 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-11 [95.6 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 chrpath i386 0.18-1 [14.0 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14.2.0-8 [735 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libgfortran-14-dev i386 14.2.0-8 [800 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 gfortran-14-i686-linux-gnu i386 14.2.0-8 [12.5 MB] Get: 34 http://deb.debian.org/debian trixie/main i386 gfortran-14 i386 14.2.0-8 [12.2 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libhwloc15 i386 2.11.2-1 [177 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 hwloc-nox i386 2.11.2-1 [229 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libnuma1 i386 2.0.18-1+b1 [23.9 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 libnuma-dev i386 2.0.18-1+b1 [38.8 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libltdl7 i386 2.4.7-8 [395 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libltdl-dev i386 2.4.7-8 [167 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libhwloc-dev i386 2.11.2-1 [271 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 libmpich12 i386 4.2.0-14 [1518 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 libslurm41t64 i386 24.05.4-1 [739 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 mpich i386 4.2.0-14 [235 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libmpich-dev i386 4.2.0-14 [2494 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 mpi-default-dev i386 1.17 [3144 B] Get: 48 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-4 [26.2 kB] Fetched 40.6 MB in 0s (108 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 ... 19956 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_i386.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_i386.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_i386.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_i386.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../08-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package chrpath. Preparing to unpack .../15-chrpath_0.18-1_i386.deb ... Unpacking chrpath (0.18-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../22-libelf1t64_0.192-4_i386.deb ... Unpacking libelf1t64:i386 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../24-libicu72_72.1-5+b1_i386.deb ... Unpacking libicu72:i386 (72.1-5+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.22.5-2_i386.deb ... Unpacking gettext (0.22.5-2) ... 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 dh-autoreconf (20) ... Setting up libltdl-dev:i386 (2.4.7-8) ... Setting up gfortran-14-i686-linux-gnu (14.2.0-8) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libhwloc-dev:i386 (2.11.2-1) ... Setting up gfortran-14 (14.2.0-8) ... Setting up mpich (4.2.0-14) ... update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libmpich-dev:i386 (4.2.0-14) ... update-alternatives: using /usr/include/i386-linux-gnu/mpich to provide /usr/include/i386-linux-gnu/mpi (mpi-i386-linux-gnu) in auto mode Setting up mpi-default-dev (1.17) ... Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/phyml-3.3.20220408/ && 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 > ../phyml_3.3.20220408-4_source.changes dpkg-buildpackage: info: source package phyml dpkg-buildpackage: info: source version 3:3.3.20220408-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' # save pdf from cleaning mv doc/phyml-manual.pdf . dh_auto_clean mv phyml-manual.pdf doc # remove temporary bin dir for phyml (see above hack) rm -rf debian/bin rm -rf doc/Makefile make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' dh_autoreconf --as-needed configure.ac:31: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:31: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:31: the top level configure.ac:52: warning: The macro 'AC_FUNC_SETVBUF_REVERSED' is obsolete. Remove it and all references to SETVBUF_REVERSED. ./lib/autoconf/functions.m4:1785: AC_FUNC_SETVBUF_REVERSED is expanded from... configure.ac:52: the top level configure.ac:14: installing './compile' configure.ac:12: installing './config.guess' configure.ac:12: installing './config.sub' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' src/Makefile.am: installing './depcomp' make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' # According to README you need different configure options to get different executables # Here we hack in a full build process for phyml executable # The hack includes saving the documentation from beeing cleaned up mv doc/phyml-manual.pdf . dh_auto_configure ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none configure: "Do not use MSSE = because not available on arch i686-pc-linux-gnu" checking for log in -lm... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for float.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for pdflatex... no checking for latex... no configure: WARNING: Documentation will not be built! checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now" make -j6 "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' make all-recursive make[3]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' Making all in src make[4]: Entering directory '/build/reproducible-path/phyml-3.3.20220408/src' gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utilities.o utilities.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o optimiz.o optimiz.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o lk.o lk.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bionj.o bionj.c .: Building [phyml]. Version 3.3.3:3.3.20220408-4 :. gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o models.o models.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o free.o free.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o help.o help.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simu.o simu.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o eigen.o eigen.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pars.o pars.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alrt.o alrt.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o interface.o interface.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cl.o cl.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o spr.o spr.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o draw.o draw.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stats.o stats.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o make.o make.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o nexus.o nexus.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o init.o init.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o xml.o xml.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sse.o sse.c io.c: In function 'Sub_Trees': io.c:511:25: warning: 'subs' may be used uninitialized [-Wmaybe-uninitialized] 511 | subs = (char **)mRealloc(subs,*degree+1,sizeof(char *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c:479:10: note: 'subs' was declared here 479 | char **subs; | ^~~~ gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o avx.o avx.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tbe.o tbe.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ancestral.o ancestral.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mixt.o mixt.c gcc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o io.o make.o nexus.o init.o xml.o sse.o avx.o tbe.o ancestral.o mixt.o -lm -lm Done. make[4]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408/src' make[4]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' make[4]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' make[3]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' make[2]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' # move phyml binary to temporary dir inside debian/ mkdir -p /build/reproducible-path/phyml-3.3.20220408/debian/bin mv src/phyml /build/reproducible-path/phyml-3.3.20220408/debian/bin/phyml /usr/bin/make distclean make[2]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' Making distclean in src make[3]: Entering directory '/build/reproducible-path/phyml-3.3.20220408/src' test -z "phyml" || rm -f phyml rm -f *.o rm -f *.tab.c test -z "" || rm -f test . = "." || test -z "" || rm -f rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f ./.deps/alrt.Po rm -f ./.deps/ancestral.Po rm -f ./.deps/avx.Po rm -f ./.deps/bionj.Po rm -f ./.deps/cl.Po rm -f ./.deps/date.Po rm -f ./.deps/draw.Po rm -f ./.deps/eigen.Po rm -f ./.deps/free.Po rm -f ./.deps/help.Po rm -f ./.deps/init.Po rm -f ./.deps/interface.Po rm -f ./.deps/io.Po rm -f ./.deps/lk.Po rm -f ./.deps/location.Po rm -f ./.deps/main.Po rm -f ./.deps/make.Po rm -f ./.deps/mcmc.Po rm -f ./.deps/mg.Po rm -f ./.deps/mixt.Po rm -f ./.deps/models.Po rm -f ./.deps/mpi_boot.Po rm -f ./.deps/nexus.Po rm -f ./.deps/optimiz.Po rm -f ./.deps/pars.Po rm -f ./.deps/phyrex.Po rm -f ./.deps/rates.Po rm -f ./.deps/rrw.Po rm -f ./.deps/rw.Po rm -f ./.deps/simu.Po rm -f ./.deps/slfv.Po rm -f ./.deps/spr.Po rm -f ./.deps/sse.Po rm -f ./.deps/stats.Po rm -f ./.deps/tbe.Po rm -f ./.deps/times.Po rm -f ./.deps/utilities.Po rm -f ./.deps/xml.Po rm -f Makefile make[3]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408/src' make[3]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' test -z "" || rm -f test . = "." || test -z "" || rm -f rm -f config.h stamp-h1 rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f cscope.out cscope.in.out cscope.po.out cscope.files make[3]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' rm -f config.status config.cache config.log configure.lineno config.status.lineno rm -f Makefile make[2]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' dh_auto_configure -- --enable-phyml-mpi ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-phyml-mpi checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none configure: "Do not use MSSE = because not available on arch i686-pc-linux-gnu" checking for log in -lm... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for float.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for pdflatex... no checking for latex... no configure: WARNING: Documentation will not be built! checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now" make -j6 "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' make all-recursive make[3]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' Making all in src make[4]: Entering directory '/build/reproducible-path/phyml-3.3.20220408/src' mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utilities.o utilities.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o optimiz.o optimiz.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o lk.o lk.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bionj.o bionj.c .: Building [phyml-mpi]. Version 3.3.3:3.3.20220408-4 :. mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o models.o models.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o free.o free.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o help.o help.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simu.o simu.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o eigen.o eigen.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pars.o pars.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alrt.o alrt.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o interface.o interface.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cl.o cl.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o spr.o spr.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o draw.o draw.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stats.o stats.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o make.o make.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o nexus.o nexus.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o init.o init.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o xml.o xml.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mixt.o mixt.c io.c: In function 'Sub_Trees': io.c:511:25: warning: 'subs' may be used uninitialized [-Wmaybe-uninitialized] 511 | subs = (char **)mRealloc(subs,*degree+1,sizeof(char *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c:479:10: note: 'subs' was declared here 479 | char **subs; | ^~~~ mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tbe.o tbe.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sse.o sse.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o avx.o avx.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ancestral.o ancestral.c mpicc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mpi_boot.o mpi_boot.c mpicc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o phyml-mpi main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o io.o make.o nexus.o init.o xml.o mixt.o tbe.o sse.o avx.o ancestral.o mpi_boot.o -lm -lm Done. make[4]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408/src' make[4]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' make[4]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' make[3]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' make[2]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' # move phyml binary to temporary dir inside debian/ # mkdir -p /build/reproducible-path/phyml-3.3.20220408/debian/bin mv src/phyml-mpi /build/reproducible-path/phyml-3.3.20220408/debian/bin/phyml-mpi mv phyml-manual.pdf doc make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' dh_auto_test make -j6 check "TESTSUITEFLAGS=-j6 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' Making check in src make[2]: Entering directory '/build/reproducible-path/phyml-3.3.20220408/src' mpicc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phyml-3.3.20220408=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o phyml-mpi main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o io.o make.o nexus.o init.o xml.o mixt.o tbe.o sse.o avx.o ancestral.o mpi_boot.o -lm -lm .: Building [phyml-mpi]. Version 3.3.3:3.3.20220408-4 :. Done. make[2]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408/src' make[2]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' make[2]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' dh_auto_install make -j6 install DESTDIR=/build/reproducible-path/phyml-3.3.20220408/debian/phyml AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' Making install in src make[3]: Entering directory '/build/reproducible-path/phyml-3.3.20220408/src' .: Building [phyml-mpi]. Version 3.3.3:3.3.20220408-4 :. Done. make[4]: Entering directory '/build/reproducible-path/phyml-3.3.20220408/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/bin' /usr/bin/install -c phyml-mpi '/build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/bin' make[4]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408/src' make[3]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408/src' make[3]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' make[4]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' make[3]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' make[2]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' # install phyml binary we have kept safe above mkdir -p /build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/lib/phyml/bin mv /build/reproducible-path/phyml-3.3.20220408/debian/bin/* /build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/lib/phyml/bin chrpath --delete debian/phyml/usr/lib/phyml/bin/phyml* make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' dh_install debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' dh_installdocs mv /build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf /build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' dh_fixperms find debian/*/usr/share/doc -name "*.nxs" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.xml" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.mat" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.txt" -exec chmod -x \{\} \; chmod -x debian/*/usr/share/doc/phyml/examples/nucleic chmod -x debian/*/usr/share/doc/phyml/examples/proteic make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' dh_missing debian/rules override_dh_dwz make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' echo "Do not run dh_dwz" Do not run dh_dwz make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phyml' in '../phyml_3.3.20220408-4_i386.deb'. dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.3.20220408-4_i386.deb'. dpkg-genbuildinfo --build=binary -O../phyml_3.3.20220408-4_i386.buildinfo dpkg-genchanges --build=binary -O../phyml_3.3.20220408-4_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/32431 and its subdirectories I: Current time: Wed Jan 7 01:25:05 -12 2026 I: pbuilder-time-stamp: 1767792305 Thu Dec 5 07:02:09 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom07-i386.debian.net. Thu Dec 5 07:02:09 UTC 2024 I: Preparing to do remote build '2' on infom07-i386.debian.net. Thu Dec 5 07:05:06 UTC 2024 I: Deleting $TMPDIR on infom07-i386.debian.net. Thu Dec 5 07:05:07 UTC 2024 I: phyml_3.3.20220408-4_i386.changes: Format: 1.8 Date: Sat, 09 Nov 2024 19:50:59 +0100 Source: phyml Binary: phyml phyml-dbgsym Architecture: i386 Version: 3:3.3.20220408-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: phyml - Phylogenetic estimation using Maximum Likelihood Closes: 1086912 Changes: phyml (3:3.3.20220408-4) unstable; urgency=medium . * d/p/series: disable cross.patch. The cross compilation procedure relies on mpi-c.pc to operate properly, but mpich misses it for the moment. * d/control: migrate to mpi-default-*. (Closes: #1086912) * d/control: declare compliance to standards version 4.7.0. * d/control: migrate to pkgconf. * d/patches/*: normalise header, notably Last-Update format. Checksums-Sha1: 50540e4975decd909d1b110c8d4638c4e80eb2e7 1693156 phyml-dbgsym_3.3.20220408-4_i386.deb 64c7dced0773804a06588ce9dba2afcee86ffeee 5554 phyml_3.3.20220408-4_i386.buildinfo 703bea45b8b1e99b0554ccbf2c8860e64f84c1d3 1057852 phyml_3.3.20220408-4_i386.deb Checksums-Sha256: 3745414983db8314adb62129682a7b6c955c04cec02df3664cd9e21a9924a6e2 1693156 phyml-dbgsym_3.3.20220408-4_i386.deb 01c727e3812676e1f1fa69c234e4ea6cd3b3455d3a792badd38dbd25f180adaf 5554 phyml_3.3.20220408-4_i386.buildinfo c7e42bb585c207fa8b66fb3d64bb5115c0b0ecbf30b28276a03991cdbf824351 1057852 phyml_3.3.20220408-4_i386.deb Files: 53727f7f722b7e3b62d86de12e65a67d 1693156 debug optional phyml-dbgsym_3.3.20220408-4_i386.deb ecf36f67ba4d4d337ae911d35f082c2d 5554 science optional phyml_3.3.20220408-4_i386.buildinfo 16bc1d6bac3c8d36d7a3cc1a66069f46 1057852 science optional phyml_3.3.20220408-4_i386.deb Thu Dec 5 07:05:08 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_18-34773.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.BubMAQwh/phyml_3.3.20220408-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.BubMAQwh/phyml_3.3.20220408-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.BubMAQwh/phyml_3.3.20220408-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.BubMAQwh/b1/phyml_3.3.20220408-4_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.BubMAQwh/b2/phyml_3.3.20220408-4_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.386s) 0.386s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.040s) 0.040s 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: 715ms CPU time consumed: 711ms Thu Dec 5 07:05:09 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Thu Dec 5 07:05:09 UTC 2024 I: phyml from trixie built successfully and reproducibly on i386. Thu Dec 5 07:05:10 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Dec 5 07:05:10 UTC 2024 I: Submitting 8.0K b1/phyml_3.3.20220408-4_i386.buildinfo.asc Thu Dec 5 07:05:11 UTC 2024 I: Submitting 8.0K b2/phyml_3.3.20220408-4_i386.buildinfo.asc Thu Dec 5 07:05:12 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Dec 5 07:05:12 UTC 2024 I: Done submitting .buildinfo files. Thu Dec 5 07:05:12 UTC 2024 I: Removing signed phyml_3.3.20220408-4_i386.buildinfo.asc files: removed './b1/phyml_3.3.20220408-4_i386.buildinfo.asc' removed './b2/phyml_3.3.20220408-4_i386.buildinfo.asc'