Sun Feb 9 03:06:50 UTC 2025 I: starting to build phyml/trixie/arm64 on jenkins on '2025-02-09 03:06' Sun Feb 9 03:06:50 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_6/78762/console.log Sun Feb 9 03:06:50 UTC 2025 I: Downloading source for trixie/phyml=3:3.3.20220408-4 --2025-02-09 03:06:50-- 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% 368M=0s 2025-02-09 03:06:50 (368 MB/s) - ‘phyml_3.3.20220408-4.dsc’ saved [2256/2256] Sun Feb 9 03:06:50 UTC 2025 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----- Sun Feb 9 03:06:50 UTC 2025 I: Checking whether the package is not for us Sun Feb 9 03:06:50 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Sun Feb 9 03:06:50 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Sun Feb 9 03:08:30 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Mar 13 21:29:52 -12 2026 I: pbuilder-time-stamp: 1773480592 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [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 dpkg-source: warning: cannot verify inline signature for ./phyml_3.3.20220408-4.dsc: unsupported subcommand 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/1643570/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='7a72cf7fa1e54d0aa4fd5b519419088a' 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='1643570' 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.1mvcnE4P/pbuilderrc_QHSs --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.1mvcnE4P/b1 --logfile b1/build.log phyml_3.3.20220408-4.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1643570/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: arm64 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} ca-certificates{a} chrpath{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-14{a} gfortran-14-aarch64-linux-gnu{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libcbor0.10{a} libcom-err2{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libfabric1{a} libffi8{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libllvm17t64{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmunge2{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi40{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} librdmacm1t64{a} libreadline8t64{a} libtool{a} libuchardet0{a} libucx0{a} libunistring5{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libz3-4{a} m4{a} man-db{a} media-types{a} mpi-default-dev{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-snowballstemmer{a} python3-sphinx{a} python3-urllib3{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libjson-xs-perl libmail-sendmail-perl libpaper-utils lynx python3-pil wget xauth 0 packages upgraded, 144 newly installed, 0 to remove and 0 not upgraded. Need to get 116 MB of archives. After unpacking 505 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.13-minimal arm64 3.13.1-3+b1 [852 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.13-minimal arm64 3.13.1-3+b1 [1987 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-6 [257 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libpython3.13-stdlib arm64 3.13.1-3+b1 [1913 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 python3.13 arm64 3.13.1-3+b1 [740 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B] Get: 14 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.13.1-2 [28.0 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.4.0-2 [1385 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20241223 [164 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-2 [91.5 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libcbor0.10 arm64 0.10.2-2 [27.4 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libfido2-1 arm64 1.15.0-1+b1 [74.3 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 35 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 openssh-client arm64 1:9.9p1-3 [928 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 chrpath arm64 0.18-1 [13.2 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 50 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-12 [361 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libgfortran-14-dev arm64 14.2.0-12 [427 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-12 [9791 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 gfortran-14 arm64 14.2.0-12 [13.4 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libnl-3-200 arm64 3.7.0-0.3+b1 [57.0 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libnl-route-3-200 arm64 3.7.0-0.3+b1 [167 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libibverbs1 arm64 55.0-1 [58.6 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 ibverbs-providers arm64 55.0-1 [328 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libllvm17t64 arm64 1:17.0.6-20+b2 [21.3 MB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b2 [12.1 MB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libdrm-common all 2.4.123-1 [8084 B] Get: 73 http://deb.debian.org/debian trixie/main arm64 libdrm2 arm64 2.4.123-1 [38.0 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libdrm-amdgpu1 arm64 2.4.123-1 [21.6 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libnuma1 arm64 2.0.18-1+b1 [21.8 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libhsakmt1 arm64 6.1.2+ds-1 [56.9 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libhsa-runtime64-1 arm64 5.7.1-3 [278 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libamdhip64-5 arm64 5.7.1-5 [8823 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10+b1 [126 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-10+b1 [102 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10+b1 [54.4 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-10+b1 [60.4 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libevent-dev arm64 2.1.12-stable-10+b1 [304 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 librdmacm1t64 arm64 55.0-1 [67.0 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libfabric1 arm64 1.17.0-3.1 [480 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libhwloc15 arm64 2.11.2-1 [141 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libnuma-dev arm64 2.0.18-1+b1 [37.8 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libltdl7 arm64 2.5.4-3 [415 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libltdl-dev arm64 2.5.4-3 [168 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libhwloc-dev arm64 2.11.2-1 [237 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libpciaccess0 arm64 0.17-3+b3 [51.2 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libxnvctrl0 arm64 535.171.04-1+b2 [14.0 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b2 [39.3 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libhwloc-plugins arm64 2.11.2-1 [17.9 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libibumad3 arm64 55.0-1 [27.2 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libibmad5 arm64 55.0-1 [41.3 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libnl-3-dev arm64 3.7.0-0.3+b1 [101 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libnl-route-3-dev arm64 3.7.0-0.3+b1 [198 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libibverbs-dev arm64 55.0-1 [637 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libmunge2 arm64 0.5.16-1 [19.2 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libpmix2t64 arm64 5.0.6-1 [577 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libucx0 arm64 1.17.0+ds-3 [959 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libopenmpi40 arm64 5.0.6-3 [2087 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 openmpi-common all 5.0.6-3 [97.0 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 sphinx-common all 8.1.3-4 [616 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 python3-babel all 2.17.0-1 [117 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 python3-roman all 5.0-1 [10.6 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 126 http://deb.debian.org/debian trixie/main arm64 python3-markupsafe arm64 2.1.5-1+b3 [14.0 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 python3-jinja2 all 3.1.5-2 [107 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 python3-certifi all 2024.12.14+ds-1 [9624 B] Get: 131 http://deb.debian.org/debian trixie/main arm64 python3-charset-normalizer arm64 3.4.0-1+b1 [129 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 python3-idna all 3.8-2 [41.6 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 python3-urllib3 all 2.3.0-1 [114 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 python3-sphinx all 8.1.3-4 [468 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 libpmix-dev arm64 5.0.6-1 [3933 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 openmpi-bin arm64 5.0.6-3 [180 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libopenmpi-dev arm64 5.0.6-3 [1088 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 mpi-default-dev arm64 1.18 [3372 B] Get: 143 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Fetched 116 MB in 1s (202 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (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 .../libpython3.13-minimal_3.13.1-3+b1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.1-3+b1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... 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Preparing to unpack .../0-python3-minimal_3.13.1-2_arm64.deb ... Unpacking python3-minimal (3.13.1-2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024b-6_all.deb ... Unpacking tzdata (2024b-6) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.4.6-1_arm64.deb ... Unpacking libffi8:arm64 (3.4.6-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.1-3+b1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.1-3+b1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.1-3+b1_arm64.deb ... Unpacking python3.13 (3.13.1-3+b1) ... 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Selecting previously unselected package dh-autoreconf. Preparing to unpack .../032-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../033-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 .../034-libfile-stripnondeterminism-perl_1.14.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../035-dh-strip-nondeterminism_1.14.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../036-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../037-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../038-libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../039-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../040-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../041-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../042-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../043-po-debconf_1.0.21+nmu1_all.deb ... 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Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up libibumad3:arm64 (55.0-1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libibmad5:arm64 (55.0-1) ... Setting up libcom-err2:arm64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up python-babel-localedata (2.17.0-1) ... Setting up libkrb5support0:arm64 (1.21.3-4) ... Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Mar 14 09:30:20 UTC 2026. Universal Time is now: Sat Mar 14 09:30:20 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.13.3-1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libmunge2:arm64 (0.5.16-1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up libhwloc15:arm64 (2.11.2-1) ... 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Setting up openssl (3.4.0-2) ... Setting up libdrm-common (2.4.123-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up chrpath (0.18-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:arm64 (14.2.0-12) ... Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-3) ... Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libevent-openssl-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libxext6:arm64 (2:1.3.4-1+b3) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:arm64 (2.0.18-1+b1) ... Setting up libnl-route-3-200:arm64 (3.7.0-0.3+b1) ... Setting up libxnvctrl0:arm64 (535.171.04-1+b2) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:arm64 (2.5.4-3) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:arm64 (1:17.0.6-20+b2) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-4) ... Setting up libjs-sphinxdoc (8.1.3-4) ... Setting up libevent-extra-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... Setting up libdrm2:arm64 (2.4.123-1) ... Setting up libnl-3-dev:arm64 (3.7.0-0.3+b1) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up gfortran-14-aarch64-linux-gnu (14.2.0-12) ... Setting up libhwloc-dev:arm64 (2.11.2-1) ... Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up gfortran-14 (14.2.0-12) ... Setting up libpython3.13-stdlib:arm64 (3.13.1-3+b1) ... Setting up libpython3-stdlib:arm64 (3.13.1-2) ... Setting up libdrm-amdgpu1:arm64 (2.4.123-1) ... Setting up libibverbs1:arm64 (55.0-1) ... Setting up ibverbs-providers:arm64 (55.0-1) ... Setting up python3.13 (3.13.1-3+b1) ... Setting up openssh-client (1:9.9p1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.1-2) ... Setting up libhwloc-plugins:arm64 (2.11.2-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (2.1.5-1+b3) ... Setting up libnl-route-3-dev:arm64 (3.7.0-0.3+b1) ... Setting up python3-roman (5.0-1) ... Setting up python3-jinja2 (3.1.5-2) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-certifi (2024.12.14+ds-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up sphinx-common (8.1.3-4) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up python3-idna (3.8-2) ... Setting up libpmix2t64:arm64 (5.0.6-1) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up librdmacm1t64:arm64 (55.0-1) ... Setting up libhsakmt1:arm64 (6.1.2+ds-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up libfabric1:arm64 (1.17.0-3.1) ... Setting up python3-babel (2.17.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up debhelper (13.24.1) ... Setting up libibverbs-dev:arm64 (55.0-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up libhsa-runtime64-1:arm64 (5.7.1-3) ... Setting up libamdhip64-5 (5.7.1-5) ... Setting up libucx0:arm64 (1.17.0+ds-3) ... Setting up libopenmpi40:arm64 (5.0.6-3) ... Setting up openmpi-bin (5.0.6-3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Processing triggers for libc-bin (2.40-6) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-4) ... Setting up libpmix-dev:arm64 (5.0.6-1) ... Setting up libopenmpi-dev:arm64 (5.0.6-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode Setting up mpi-default-dev (1.18) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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 arm64 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=aarch64-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/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-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 aarch64-unknown-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 -j12 "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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o bionj.o bionj.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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o models.o models.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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o sse.o sse.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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o ancestral.o ancestral.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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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' rm -f phyml rm -f *.o rm -f *.tab.c rm -f test . = "." || 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' rm -f test . = "." || 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=aarch64-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/aarch64-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 sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 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 xargs -n works... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-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 aarch64-unknown-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 -j12 "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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o bionj.o bionj.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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o free.o free.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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mixt.o mixt.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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mpi_boot.o mpi_boot.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 -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -j12 check "TESTSUITEFLAGS=-j12 --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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -j12 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phyml' in '../phyml_3.3.20220408-4_arm64.deb'. dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.3.20220408-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../phyml_3.3.20220408-4_arm64.buildinfo dpkg-genchanges --build=binary -O../phyml_3.3.20220408-4_arm64.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/1643570 and its subdirectories I: Current time: Fri Mar 13 21:31:29 -12 2026 I: pbuilder-time-stamp: 1773480689 Sun Feb 9 03:08:31 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Sun Feb 9 03:08:31 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Sun Feb 9 03:10:16 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Sun Feb 9 03:10:16 UTC 2025 I: phyml_3.3.20220408-4_arm64.changes: Format: 1.8 Date: Sat, 09 Nov 2024 19:50:59 +0100 Source: phyml Binary: phyml phyml-dbgsym Architecture: arm64 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: 0cb038d6a47dfa4dc297cafbc7dcf4b581d27363 2050620 phyml-dbgsym_3.3.20220408-4_arm64.deb 7d336c7c035ad07e06e764eb05146bafba04db5e 8793 phyml_3.3.20220408-4_arm64.buildinfo 5da4c3394bc93a63431d20a94dd467bc01c450f5 1083544 phyml_3.3.20220408-4_arm64.deb Checksums-Sha256: 34c346050484803418bab46f0c335b2f467ea7eead5bf6bf93ae25d25423434e 2050620 phyml-dbgsym_3.3.20220408-4_arm64.deb ce74c23acdf93ed3d33f5ddfa2cadf96f60d4852bd6f5ec6c77c4cab49161ff4 8793 phyml_3.3.20220408-4_arm64.buildinfo ac2b08610a05bc9ed207111c0afc51d7f1cb2ff7f7b1e9c680af8300be25cce8 1083544 phyml_3.3.20220408-4_arm64.deb Files: 7417fb04bc68726f1290e120d81fac1a 2050620 debug optional phyml-dbgsym_3.3.20220408-4_arm64.deb d630673d956b4a25a830754c0e8c652a 8793 science optional phyml_3.3.20220408-4_arm64.buildinfo 806ba25c7c6a96f23a14711524e6e0b2 1083544 science optional phyml_3.3.20220408-4_arm64.deb Sun Feb 9 03:10:17 UTC 2025 I: diffoscope 288 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_6-78762.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.1mvcnE4P/phyml_3.3.20220408-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.1mvcnE4P/phyml_3.3.20220408-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.1mvcnE4P/phyml_3.3.20220408-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.1mvcnE4P/b1/phyml_3.3.20220408-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.1mvcnE4P/b2/phyml_3.3.20220408-4_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.005s) 0.005s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 322ms CPU time consumed: 323ms Sun Feb 9 03:10:19 UTC 2025 I: diffoscope 288 found no differences in the changes files, and a .buildinfo file also exists. Sun Feb 9 03:10:19 UTC 2025 I: phyml from trixie built successfully and reproducibly on arm64. Sun Feb 9 03:10:20 UTC 2025 I: Submitting .buildinfo files to external archives: Sun Feb 9 03:10:20 UTC 2025 I: Submitting 12K b1/phyml_3.3.20220408-4_arm64.buildinfo.asc Sun Feb 9 03:10:21 UTC 2025 I: Submitting 12K b2/phyml_3.3.20220408-4_arm64.buildinfo.asc Sun Feb 9 03:10:21 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Feb 9 03:10:21 UTC 2025 I: Done submitting .buildinfo files. Sun Feb 9 03:10:21 UTC 2025 I: Removing signed phyml_3.3.20220408-4_arm64.buildinfo.asc files: removed './b1/phyml_3.3.20220408-4_arm64.buildinfo.asc' removed './b2/phyml_3.3.20220408-4_arm64.buildinfo.asc'