Thu Dec 5 10:16:52 UTC 2024 I: starting to build phyml/trixie/arm64 on jenkins on '2024-12-05 10:16' Thu Dec 5 10:16:52 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_24/64658/console.log Thu Dec 5 10:16:52 UTC 2024 I: Downloading source for trixie/phyml=3:3.3.20220408-4 --2024-12-05 10:16:52-- 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% 333M=0s 2024-12-05 10:16:52 (333 MB/s) - ‘phyml_3.3.20220408-4.dsc’ saved [2256/2256] Thu Dec 5 10:16:52 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 10:16:52 UTC 2024 I: Checking whether the package is not for us Thu Dec 5 10:16:52 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Thu Dec 5 10:16:52 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Thu Dec 5 10:18:27 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 4 22:16:54 -12 2024 I: pbuilder-time-stamp: 1733393814 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 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/663702/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='34107a3f4eca4520bd8d61f5d354b7e6' 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='663702' 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.t0Sb80fs/pbuilderrc_VCav --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.t0Sb80fs/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 codethink04-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/663702/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 ... 20087 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} 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} libnsl2{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} libpython3.12-minimal{a} libpython3.12-stdlib{a} librdmacm1t64{a} libreadline8t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libucx0{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-autocommand{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-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-snowballstemmer{a} python3-sphinx{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3.12{a} python3.12-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, 153 newly installed, 0 to remove and 0 not upgraded. Need to get 116 MB of archives. After unpacking 504 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.7-3 [808 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 python3.12-minimal arm64 3.12.7-3 [1940 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.12.6-1 [26.7 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-4 [256 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 12 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.7-3 [1902 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libcbor0.10 arm64 0.10.2-2 [27.4 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libfido2-1 arm64 1.15.0-1+b1 [74.3 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 openssh-client arm64 1:9.9p1-3 [928 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 chrpath arm64 0.18-1 [13.2 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 52 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libgfortran-14-dev arm64 14.2.0-8 [418 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-8 [9791 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 gfortran-14 arm64 14.2.0-8 [12.2 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libnl-3-200 arm64 3.7.0-0.3+b1 [57.0 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libnl-route-3-200 arm64 3.7.0-0.3+b1 [167 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libibverbs1 arm64 52.0-2+b1 [58.8 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 ibverbs-providers arm64 52.0-2+b1 [321 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libllvm17t64 arm64 1:17.0.6-18 [21.3 MB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b2 [12.1 MB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libdrm-common all 2.4.123-1 [8084 B] Get: 74 http://deb.debian.org/debian trixie/main arm64 libdrm2 arm64 2.4.123-1 [38.0 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libdrm-amdgpu1 arm64 2.4.123-1 [21.6 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libnuma1 arm64 2.0.18-1+b1 [21.8 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libhsakmt1 arm64 5.7.0-1 [57.6 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libhsa-runtime64-1 arm64 5.7.1-3 [278 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libamdhip64-5 arm64 5.7.1-5 [8823 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10+b1 [126 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-10+b1 [102 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10+b1 [54.4 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-10+b1 [60.4 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libevent-dev arm64 2.1.12-stable-10+b1 [304 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 librdmacm1t64 arm64 52.0-2+b1 [67.4 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libfabric1 arm64 1.17.0-3.1 [480 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libhwloc15 arm64 2.11.2-1 [141 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libnuma-dev arm64 2.0.18-1+b1 [37.8 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libltdl7 arm64 2.4.7-8 [392 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libltdl-dev arm64 2.4.7-8 [165 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libhwloc-dev arm64 2.11.2-1 [237 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libpciaccess0 arm64 0.17-3+b2 [51.2 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libxnvctrl0 arm64 535.171.04-1+b1 [14.1 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b2 [39.3 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libhwloc-plugins arm64 2.11.2-1 [17.9 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libibumad3 arm64 52.0-2+b1 [27.1 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libibmad5 arm64 52.0-2+b1 [41.5 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libnl-3-dev arm64 3.7.0-0.3+b1 [101 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libnl-route-3-dev arm64 3.7.0-0.3+b1 [198 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libibverbs-dev arm64 52.0-2+b1 [625 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libmunge2 arm64 0.5.15-4+b1 [19.4 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libpmix2t64 arm64 5.0.4-1 [586 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libucx0 arm64 1.17.0+ds-3 [959 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libopenmpi40 arm64 5.0.6-3 [2087 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 openmpi-common all 5.0.6-3 [97.0 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 sphinx-common all 7.4.7-4 [731 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 129 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 python3-babel all 2.16.0-1 [114 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 python3-roman all 4.2-1 [10.4 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 135 http://deb.debian.org/debian trixie/main arm64 python3-markupsafe arm64 2.1.5-1+b3 [14.0 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 140 http://deb.debian.org/debian trixie/main arm64 python3-charset-normalizer arm64 3.4.0-1+b1 [129 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 python3-idna all 3.8-2 [41.6 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 python3-urllib3 all 2.2.3-3 [112 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 python3-sphinx all 7.4.7-4 [588 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 libpmix-dev arm64 5.0.4-1 [3942 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 openmpi-bin arm64 5.0.6-3 [180 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 libopenmpi-dev arm64 5.0.6-3 [1088 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 mpi-default-dev arm64 1.17 [3148 B] Get: 152 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Fetched 116 MB in 1s (226 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-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 ... 20087 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.7-3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_arm64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:arm64 (3.12.7-3) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (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 ... 20407 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_arm64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_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 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_arm64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (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 ... 21469 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_arm64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.3.2-2_arm64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../009-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../012-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../014-libedit2_3.1-20240808-1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20240808-1) ... Selecting previously unselected package libcbor0.10:arm64. Preparing to unpack .../015-libcbor0.10_0.10.2-2_arm64.deb ... Unpacking libcbor0.10:arm64 (0.10.2-2) ... Selecting previously unselected package libfido2-1:arm64. Preparing to unpack .../016-libfido2-1_1.15.0-1+b1_arm64.deb ... Unpacking libfido2-1:arm64 (1.15.0-1+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../017-openssh-client_1%3a9.9p1-3_arm64.deb ... Unpacking openssh-client (1:9.9p1-3) ... Selecting previously unselected package m4. Preparing to unpack .../018-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../019-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../020-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../021-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 .../022-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package chrpath. Preparing to unpack .../023-chrpath_0.18-1_arm64.deb ... Unpacking chrpath (0.18-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../024-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../025-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. 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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 (0.5.15-4+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libhwloc15:arm64 (2.11.2-1) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libltdl7:arm64 (2.4.7-8) ... Setting up libgfortran5:arm64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libnuma1:arm64 (2.0.18-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up ocl-icd-libopencl1:arm64 (2.3.2-1+b2) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libjson-perl (4.10000-1) ... Setting up libnl-3-200:arm64 (3.7.0-0.3+b1) ... Setting up openmpi-common (5.0.6-3) ... Setting up libx11-6:arm64 (2:1.8.10-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libevent-core-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:arm64 (1.15.0-1+b1) ... Setting up openssl (3.3.2-2) ... Setting up libdrm-common (2.4.123-1) ... Setting up readline-common (8.2-5) ... 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 (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:arm64 (14.2.0-8) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... 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+b2) ... 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+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:arm64 (2.4.7-8) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:arm64 (1:17.0.6-18) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libevent-extra-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libdrm2:arm64 (2.4.123-1) ... Setting up libnl-3-dev:arm64 (3.7.0-0.3+b1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up gfortran-14-aarch64-linux-gnu (14.2.0-8) ... 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 (14.2.0-8) ... Setting up libdrm-amdgpu1:arm64 (2.4.123-1) ... Setting up libibverbs1:arm64 (52.0-2+b1) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up ibverbs-providers:arm64 (52.0-2+b1) ... Setting up openssh-client (1:9.9p1-3) ... Setting up po-debconf (1.0.21+nmu1) ... 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 libnl-route-3-dev:arm64 (3.7.0-0.3+b1) ... Setting up sphinx-common (7.4.7-4) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up libpmix2t64:arm64 (5.0.4-1) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up librdmacm1t64:arm64 (52.0-2+b1) ... Setting up libhsakmt1:arm64 (5.7.0-1) ... Setting up libfabric1:arm64 (1.17.0-3.1) ... Setting up libpython3.12-stdlib:arm64 (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up libibverbs-dev:arm64 (52.0-2+b1) ... Setting up libhsa-runtime64-1:arm64 (5.7.1-3) ... Setting up libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b3) ... Setting up python3-roman (4.2-1) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.2-1) ... Setting up libamdhip64-5 (5.7.1-5) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-idna (3.8-2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-urllib3 (2.2.3-3) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libucx0:arm64 (1.17.0+ds-3) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up libopenmpi40:arm64 (5.0.6-3) ... Setting up python3-babel (2.16.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... 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 (2.40-3) ... 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 (7.4.7-4) ... Setting up libpmix-dev:arm64 (5.0.4-1) ... 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 (1.17) ... Processing triggers for ca-certificates (20240203) ... 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 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... 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 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 .: 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 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 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 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 -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' 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=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 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... 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 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 .: 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 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/663702 and its subdirectories I: Current time: Wed Dec 4 22:18:25 -12 2024 I: pbuilder-time-stamp: 1733393905 Thu Dec 5 10:18:27 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Thu Dec 5 10:18:27 UTC 2024 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Thu Dec 5 10:20:45 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Thu Dec 5 10:20:46 UTC 2024 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: e3d7fa1c0f7c67eeed649fb6493ed2e88802bcc9 2039612 phyml-dbgsym_3.3.20220408-4_arm64.deb 31e56b9e81e3f208896683a3a57bf188d623084e 9203 phyml_3.3.20220408-4_arm64.buildinfo 4e9c70c4de606b47935505f31ca2235fdfb3a63c 1086244 phyml_3.3.20220408-4_arm64.deb Checksums-Sha256: 86150a39bb9e349ca5a021b026eb97308e0e9158daac5b52fab81d04be84dcf8 2039612 phyml-dbgsym_3.3.20220408-4_arm64.deb 53bbf049d9d9c2667a6cb613a88199a3124936cd9487cb2711fa99240991abb6 9203 phyml_3.3.20220408-4_arm64.buildinfo 03a496b76defd70bda6cf91d3fa6915392d39dfd4fdff4fe8dfe5a6503ece9cb 1086244 phyml_3.3.20220408-4_arm64.deb Files: 90bc0e0963d08b0c5413956d93466ae1 2039612 debug optional phyml-dbgsym_3.3.20220408-4_arm64.deb e55d696f3fac5c8b63fe653d9a1834ba 9203 science optional phyml_3.3.20220408-4_arm64.buildinfo 511e6618ca0e409ce1dd3bec2252f91e 1086244 science optional phyml_3.3.20220408-4_arm64.deb Thu Dec 5 10:20:47 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_24-64658.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.t0Sb80fs/phyml_3.3.20220408-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.t0Sb80fs/phyml_3.3.20220408-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.t0Sb80fs/phyml_3.3.20220408-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.t0Sb80fs/b1/phyml_3.3.20220408-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.t0Sb80fs/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 abc.DotChangesFile ## main (total time: 0.369s) 0.369s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.042s) 0.042s 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: 686ms CPU time consumed: 686ms Thu Dec 5 10:20:48 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Thu Dec 5 10:20:48 UTC 2024 I: phyml from trixie built successfully and reproducibly on arm64. Thu Dec 5 10:20:49 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Dec 5 10:20:49 UTC 2024 I: Submitting 12K b1/phyml_3.3.20220408-4_arm64.buildinfo.asc Thu Dec 5 10:20:49 UTC 2024 I: Submitting 12K b2/phyml_3.3.20220408-4_arm64.buildinfo.asc Thu Dec 5 10:20:50 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Dec 5 10:20:50 UTC 2024 I: Done submitting .buildinfo files. Thu Dec 5 10:20:50 UTC 2024 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'