Sat May 18 02:55:28 UTC 2024 I: starting to build phyml/trixie/arm64 on jenkins on '2024-05-18 02:55' Sat May 18 02:55:28 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_4/19013/console.log Sat May 18 02:55:28 UTC 2024 I: Downloading source for trixie/phyml=3:3.3.20220408-3 --2024-05-18 02:55:28-- http://deb.debian.org/debian/pool/main/p/phyml/phyml_3.3.20220408-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2258 (2.2K) [text/prs.lines.tag] Saving to: ‘phyml_3.3.20220408-3.dsc’ 0K .. 100% 307M=0s 2024-05-18 02:55:28 (307 MB/s) - ‘phyml_3.3.20220408-3.dsc’ saved [2258/2258] Sat May 18 02:55:28 UTC 2024 I: phyml_3.3.20220408-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phyml Binary: phyml Architecture: any Version: 3:3.3.20220408-3 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Kevin Murray , Étienne Mollier Homepage: http://www.atgc-montpellier.fr/phyml Standards-Version: 4.6.1 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), pkg-config, libopenmpi-dev, chrpath Package-List: phyml deb science optional arch=any Checksums-Sha1: 1dd5067ba9094eb54ff9f9c2c39c1c35ee750944 1803950 phyml_3.3.20220408.orig.tar.gz 900ecd3fb8c487cd822c9a41910ea200245869d5 26856 phyml_3.3.20220408-3.debian.tar.xz Checksums-Sha256: 9cef375c0186e8a8d4db72ac02148707624c97174ffac244167a138ceb9f65bd 1803950 phyml_3.3.20220408.orig.tar.gz ea1529f70db828cd7ea9b3a8fa0c68508b008268581782ce8e0f2960b95a4fe5 26856 phyml_3.3.20220408-3.debian.tar.xz Files: b35e641af77d7f058cf1ddc73be5e0b7 1803950 phyml_3.3.20220408.orig.tar.gz c428b64514d9b5b84482081427fd1293 26856 phyml_3.3.20220408-3.debian.tar.xz Dgit: 909b3d88c87473a003362f16e7d0108038e3206c debian archive/debian/3%3.3.20220408-3 https://git.dgit.debian.org/phyml -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmNZegcUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrBaxAAl0Ur2Q8fdsVnvBlO5pzGBATQrNW0 paC6/OyPfqgQyy7S8X2Jc2GpmSasyOHkbl0f3H8Q4tBLCGKOF7+yEH91+K7AVBmB NVKCrm94Xg8VGFAPybI6nw8s56Oa4vF8Yr6oYCp8lzH9n9Wqa5HYebpVJUa0GkD1 Jr0KP28iX4jhGIe4xgimXm24Eng398Ab1POxEQ7A6n7qnNqKJ2VQnYh8RWK943rr PstWDJb1d4coIx36btygth/Gz9uGFnBlNC3r+Nl+LPdo25IPk7FuULpr9pZ1KWFb nKcrbX/zlOut9D6N92QTVh7vbbpWzx7D5DdvCXfOHcBYrLnh1y8WI5UtmP8TcHtF YbE62pPw06ZQUCNE7BxSNRPrRvEMHwzTDVa8SopnyAAevA/ItbV1+M0qgaaDKdHG EO2pdaP+NW2zvI/N+fi8PPdMeWYyGjAi9mvTNjBMLTrIfeut/ybqlT5aox0K3aPS 9hffFEqYsHPYpjjBXo1HbuHdqWvCcGiWKynLgG3SLeen2mFeByATGt2c8C/PmLML Kz80YmE96nebHhKaBkWKzBx+hMh4XOrtIyqcKqO1MXXURKIb8NU9XPk0OICMnEdA gM74MJmmxXWS/Kj0kPQz2MtFijNgi1fQ9N1pK95JlMkTGMW0vQylis6hxbBgUj71 CT/mDEvNVnotyfU= =nQAF -----END PGP SIGNATURE----- Sat May 18 02:55:28 UTC 2024 I: Checking whether the package is not for us Sat May 18 02:55:28 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Sat May 18 02:55:28 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Sat May 18 02:56:47 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri May 17 14:55:30 -12 2024 I: pbuilder-time-stamp: 1716000930 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_3.3.20220408-3.dsc] I: copying [./phyml_3.3.20220408.orig.tar.gz] I: copying [./phyml_3.3.20220408-3.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Oct 26 18:18:47 2022 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_3.3.20220408-3.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_3.3.20220408-3.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 cross.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/2935378/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='89b8287f4d76425e87c2a11b60947c26' 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='2935378' 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.g2c9mFsu/pbuilderrc_yoDE --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.g2c9mFsu/b1 --logfile b1/build.log phyml_3.3.20220408-3.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 codethink02-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 15 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2935378/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), pkg-config, libopenmpi-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 ... 19744 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 pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev; however: Package libopenmpi-dev is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} chrpath{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-13{a} gfortran-13-aarch64-linux-gnu{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libbsd0{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} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-13-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{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} libopenmpi3t64{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} librdmacm1t64{a} libsub-override-perl{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} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{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 libmail-sendmail-perl lynx wget xauth 0 packages upgraded, 101 newly installed, 0 to remove and 0 not upgraded. Need to get 95.5 MB of archives. After unpacking 422 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20230828-1+b1 [89.1 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libcbor0.10 arm64 0.10.2-1.1 [27.0 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libfido2-1 arm64 1.14.0-1+b2 [73.4 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 19 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 openssh-client arm64 1:9.7p1-4 [902 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 chrpath arm64 0.16-2+b1 [16.0 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 35 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14-20240330-1 [361 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libgfortran-13-dev arm64 13.2.0-24 [401 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-24 [9297 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 gfortran-13 arm64 13.2.0-24 [12.2 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libnl-3-200 arm64 3.7.0-0.3 [56.5 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libnl-route-3-200 arm64 3.7.0-0.3 [165 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libibverbs1 arm64 50.0-2+b1 [58.2 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 ibverbs-providers arm64 50.0-2+b1 [315 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libz3-4 arm64 4.8.12-3.1+b2 [6508 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libllvm17t64 arm64 1:17.0.6-12 [21.3 MB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b1 [12.1 MB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libdrm-common all 2.4.120-2 [7688 B] Get: 55 http://deb.debian.org/debian trixie/main arm64 libdrm2 arm64 2.4.120-2 [37.5 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [21.0 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libnuma1 arm64 2.0.18-1 [21.4 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libhsakmt1 arm64 5.7.0-1 [57.6 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libhsa-runtime64-1 arm64 5.7.1-2 [276 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libamdhip64-5 arm64 5.7.1-3 [8698 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [169 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [125 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [102 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [54.3 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [60.3 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libevent-dev arm64 2.1.12-stable-8.1+b3 [303 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 librdmacm1t64 arm64 50.0-2+b1 [66.6 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libfabric1 arm64 1.17.0-3+b1 [479 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libhwloc15 arm64 2.10.0-1+b1 [140 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libnuma-dev arm64 2.0.18-1 [37.4 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libltdl7 arm64 2.4.7-7+b1 [393 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libltdl-dev arm64 2.4.7-7+b1 [165 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libhwloc-dev arm64 2.10.0-1+b1 [234 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libpciaccess0 arm64 0.17-3+b1 [51.1 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libxnvctrl0 arm64 535.171.04-1 [13.8 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b1 [39.3 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libhwloc-plugins arm64 2.10.0-1+b1 [18.0 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libnl-3-dev arm64 3.7.0-0.3 [101 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libnl-route-3-dev arm64 3.7.0-0.3 [197 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libibverbs-dev arm64 50.0-2+b1 [626 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libmunge2 arm64 0.5.15-4 [19.2 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libpmix2t64 arm64 5.0.2-3 [580 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libucx0 arm64 1.16.0+ds-5 [938 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libopenmpi3t64 arm64 4.1.6-13.3 [2170 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 openmpi-common all 4.1.6-13.3 [169 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libpmix-dev arm64 5.0.2-3 [3921 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 openmpi-bin arm64 4.1.6-13.3 [225 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libopenmpi-dev arm64 4.1.6-13.3 [972 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-1+b2 [35.3 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-1+b2 [29.3 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-1+b2 [14.0 kB] Fetched 95.5 MB in 1s (172 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19744 files and directories currently installed.) Preparing to unpack .../000-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../001-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../002-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../003-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../004-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../005-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../006-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../007-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../008-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../009-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../010-libbsd0_0.12.2-1_arm64.deb ... Unpacking libbsd0:arm64 (0.12.2-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../011-libedit2_3.1-20230828-1+b1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20230828-1+b1) ... Selecting previously unselected package libcbor0.10:arm64. Preparing to unpack .../012-libcbor0.10_0.10.2-1.1_arm64.deb ... Unpacking libcbor0.10:arm64 (0.10.2-1.1) ... Selecting previously unselected package libfido2-1:arm64. Preparing to unpack .../013-libfido2-1_1.14.0-1+b2_arm64.deb ... Unpacking libfido2-1:arm64 (1.14.0-1+b2) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../014-libkrb5support0_1.20.1-6+b1_arm64.deb ... Unpacking libkrb5support0:arm64 (1.20.1-6+b1) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../015-libcom-err2_1.47.1~rc2-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1~rc2-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../016-libk5crypto3_1.20.1-6+b1_arm64.deb ... Unpacking libk5crypto3:arm64 (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../017-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../018-libkrb5-3_1.20.1-6+b1_arm64.deb ... Unpacking libkrb5-3:arm64 (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../019-libgssapi-krb5-2_1.20.1-6+b1_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.20.1-6+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../020-openssh-client_1%3a9.7p1-4_arm64.deb ... Unpacking openssh-client (1:9.7p1-4) ... Selecting previously unselected package m4. Preparing to unpack .../021-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../022-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../023-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../024-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 .../025-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package chrpath. Preparing to unpack .../026-chrpath_0.16-2+b1_arm64.deb ... Unpacking chrpath (0.16-2+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../027-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../028-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../029-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../030-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../031-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../032-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... 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Selecting previously unselected package intltool-debian. Preparing to unpack .../039-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 .../040-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../041-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../042-libgfortran5_14-20240330-1_arm64.deb ... Unpacking libgfortran5:arm64 (14-20240330-1) ... Selecting previously unselected package libgfortran-13-dev:arm64. Preparing to unpack .../043-libgfortran-13-dev_13.2.0-24_arm64.deb ... Unpacking libgfortran-13-dev:arm64 (13.2.0-24) ... Selecting previously unselected package gfortran-13-aarch64-linux-gnu. Preparing to unpack .../044-gfortran-13-aarch64-linux-gnu_13.2.0-24_arm64.deb ... Unpacking gfortran-13-aarch64-linux-gnu (13.2.0-24) ... Selecting previously unselected package gfortran-13. Preparing to unpack .../045-gfortran-13_13.2.0-24_arm64.deb ... Unpacking gfortran-13 (13.2.0-24) ... Selecting previously unselected package libnl-3-200:arm64. Preparing to unpack .../046-libnl-3-200_3.7.0-0.3_arm64.deb ... Unpacking libnl-3-200:arm64 (3.7.0-0.3) ... Selecting previously unselected package libnl-route-3-200:arm64. Preparing to unpack .../047-libnl-route-3-200_3.7.0-0.3_arm64.deb ... Unpacking libnl-route-3-200:arm64 (3.7.0-0.3) ... Selecting previously unselected package libibverbs1:arm64. Preparing to unpack .../048-libibverbs1_50.0-2+b1_arm64.deb ... Unpacking libibverbs1:arm64 (50.0-2+b1) ... Selecting previously unselected package ibverbs-providers:arm64. Preparing to unpack .../049-ibverbs-providers_50.0-2+b1_arm64.deb ... Unpacking ibverbs-providers:arm64 (50.0-2+b1) ... Selecting previously unselected package libz3-4:arm64. Preparing to unpack .../050-libz3-4_4.8.12-3.1+b2_arm64.deb ... Unpacking libz3-4:arm64 (4.8.12-3.1+b2) ... Selecting previously unselected package libllvm17t64:arm64. Preparing to unpack .../051-libllvm17t64_1%3a17.0.6-12_arm64.deb ... Unpacking libllvm17t64:arm64 (1:17.0.6-12) ... Selecting previously unselected package libamd-comgr2:arm64. Preparing to unpack .../052-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b1_arm64.deb ... Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../053-libdrm-common_2.4.120-2_all.deb ... Unpacking libdrm-common (2.4.120-2) ... Selecting previously unselected package libdrm2:arm64. Preparing to unpack .../054-libdrm2_2.4.120-2_arm64.deb ... Unpacking libdrm2:arm64 (2.4.120-2) ... Selecting previously unselected package libdrm-amdgpu1:arm64. Preparing to unpack .../055-libdrm-amdgpu1_2.4.120-2_arm64.deb ... Unpacking libdrm-amdgpu1:arm64 (2.4.120-2) ... Selecting previously unselected package libnuma1:arm64. Preparing to unpack .../056-libnuma1_2.0.18-1_arm64.deb ... Unpacking libnuma1:arm64 (2.0.18-1) ... Selecting previously unselected package libhsakmt1:arm64. Preparing to unpack .../057-libhsakmt1_5.7.0-1_arm64.deb ... Unpacking libhsakmt1:arm64 (5.7.0-1) ... Selecting previously unselected package libhsa-runtime64-1. Preparing to unpack .../058-libhsa-runtime64-1_5.7.1-2_arm64.deb ... Unpacking libhsa-runtime64-1 (5.7.1-2) ... Selecting previously unselected package libamdhip64-5. Preparing to unpack .../059-libamdhip64-5_5.7.1-3_arm64.deb ... Unpacking libamdhip64-5 (5.7.1-3) ... Selecting previously unselected package libevent-2.1-7t64:arm64. Preparing to unpack .../060-libevent-2.1-7t64_2.1.12-stable-8.1+b3_arm64.deb ... Unpacking libevent-2.1-7t64:arm64 (2.1.12-stable-8.1+b3) ... Selecting previously unselected package libevent-core-2.1-7t64:arm64. Preparing to unpack .../061-libevent-core-2.1-7t64_2.1.12-stable-8.1+b3_arm64.deb ... Unpacking libevent-core-2.1-7t64:arm64 (2.1.12-stable-8.1+b3) ... Selecting previously unselected package libevent-extra-2.1-7t64:arm64. Preparing to unpack .../062-libevent-extra-2.1-7t64_2.1.12-stable-8.1+b3_arm64.deb ... Unpacking libevent-extra-2.1-7t64:arm64 (2.1.12-stable-8.1+b3) ... Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. Preparing to unpack .../063-libevent-pthreads-2.1-7t64_2.1.12-stable-8.1+b3_arm64.deb ... Unpacking libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-8.1+b3) ... Selecting previously unselected package libevent-openssl-2.1-7t64:arm64. Preparing to unpack .../064-libevent-openssl-2.1-7t64_2.1.12-stable-8.1+b3_arm64.deb ... Unpacking libevent-openssl-2.1-7t64:arm64 (2.1.12-stable-8.1+b3) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../065-libevent-dev_2.1.12-stable-8.1+b3_arm64.deb ... Unpacking libevent-dev (2.1.12-stable-8.1+b3) ... Selecting previously unselected package librdmacm1t64:arm64. Preparing to unpack .../066-librdmacm1t64_50.0-2+b1_arm64.deb ... Unpacking librdmacm1t64:arm64 (50.0-2+b1) ... Selecting previously unselected package libfabric1:arm64. Preparing to unpack .../067-libfabric1_1.17.0-3+b1_arm64.deb ... Unpacking libfabric1:arm64 (1.17.0-3+b1) ... Selecting previously unselected package libhwloc15:arm64. Preparing to unpack .../068-libhwloc15_2.10.0-1+b1_arm64.deb ... Unpacking libhwloc15:arm64 (2.10.0-1+b1) ... Selecting previously unselected package libnuma-dev:arm64. Preparing to unpack .../069-libnuma-dev_2.0.18-1_arm64.deb ... Unpacking libnuma-dev:arm64 (2.0.18-1) ... Selecting previously unselected package libltdl7:arm64. Preparing to unpack .../070-libltdl7_2.4.7-7+b1_arm64.deb ... Unpacking libltdl7:arm64 (2.4.7-7+b1) ... Selecting previously unselected package libltdl-dev:arm64. Preparing to unpack .../071-libltdl-dev_2.4.7-7+b1_arm64.deb ... Unpacking libltdl-dev:arm64 (2.4.7-7+b1) ... Selecting previously unselected package libhwloc-dev:arm64. Preparing to unpack .../072-libhwloc-dev_2.10.0-1+b1_arm64.deb ... Unpacking libhwloc-dev:arm64 (2.10.0-1+b1) ... Selecting previously unselected package libpciaccess0:arm64. Preparing to unpack .../073-libpciaccess0_0.17-3+b1_arm64.deb ... Unpacking libpciaccess0:arm64 (0.17-3+b1) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../074-libxau6_1%3a1.0.9-1+b1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.9-1+b1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../075-libxdmcp6_1%3a1.1.2-3+b1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../076-libxcb1_1.15-1_arm64.deb ... Unpacking libxcb1:arm64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../077-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../078-libx11-6_2%3a1.8.7-1+b1_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.7-1+b1) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../079-libxext6_2%3a1.3.4-1+b1_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxnvctrl0:arm64. Preparing to unpack .../080-libxnvctrl0_535.171.04-1_arm64.deb ... Unpacking libxnvctrl0:arm64 (535.171.04-1) ... Selecting previously unselected package ocl-icd-libopencl1:arm64. Preparing to unpack .../081-ocl-icd-libopencl1_2.3.2-1+b1_arm64.deb ... Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1+b1) ... Selecting previously unselected package libhwloc-plugins:arm64. Preparing to unpack .../082-libhwloc-plugins_2.10.0-1+b1_arm64.deb ... Unpacking libhwloc-plugins:arm64 (2.10.0-1+b1) ... Selecting previously unselected package libnl-3-dev:arm64. Preparing to unpack .../083-libnl-3-dev_3.7.0-0.3_arm64.deb ... Unpacking libnl-3-dev:arm64 (3.7.0-0.3) ... Selecting previously unselected package libnl-route-3-dev:arm64. Preparing to unpack .../084-libnl-route-3-dev_3.7.0-0.3_arm64.deb ... Unpacking libnl-route-3-dev:arm64 (3.7.0-0.3) ... Selecting previously unselected package libibverbs-dev:arm64. Preparing to unpack .../085-libibverbs-dev_50.0-2+b1_arm64.deb ... Unpacking libibverbs-dev:arm64 (50.0-2+b1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../086-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../087-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... Selecting previously unselected package libmunge2:arm64. Preparing to unpack .../088-libmunge2_0.5.15-4_arm64.deb ... 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Setting up openmpi-bin (4.1.6-13.3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:arm64 (4.1.6-13.3) ... 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 Processing triggers for libc-bin (2.38-10) ... 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_3.3.20220408-3_source.changes dpkg-buildpackage: info: source package phyml dpkg-buildpackage: info: source version 3:3.3.20220408-3 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.m4:704: 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.m4:1766: 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 for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... 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 .: Building [phyml]. Version 3.3.3:3.3.20220408-3 :. 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 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 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 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/nexus.Po rm -f ./.deps/optimiz.Po rm -f ./.deps/pars.Po rm -f ./.deps/phyml_mpi-alrt.Po rm -f ./.deps/phyml_mpi-ancestral.Po rm -f ./.deps/phyml_mpi-avx.Po rm -f ./.deps/phyml_mpi-bionj.Po rm -f ./.deps/phyml_mpi-cl.Po rm -f ./.deps/phyml_mpi-draw.Po rm -f ./.deps/phyml_mpi-eigen.Po rm -f ./.deps/phyml_mpi-free.Po rm -f ./.deps/phyml_mpi-help.Po rm -f ./.deps/phyml_mpi-init.Po rm -f ./.deps/phyml_mpi-interface.Po rm -f ./.deps/phyml_mpi-io.Po rm -f ./.deps/phyml_mpi-lk.Po rm -f ./.deps/phyml_mpi-main.Po rm -f ./.deps/phyml_mpi-make.Po rm -f ./.deps/phyml_mpi-mixt.Po rm -f ./.deps/phyml_mpi-models.Po rm -f ./.deps/phyml_mpi-mpi_boot.Po rm -f ./.deps/phyml_mpi-nexus.Po rm -f ./.deps/phyml_mpi-optimiz.Po rm -f ./.deps/phyml_mpi-pars.Po rm -f ./.deps/phyml_mpi-simu.Po rm -f ./.deps/phyml_mpi-spr.Po rm -f ./.deps/phyml_mpi-sse.Po rm -f ./.deps/phyml_mpi-stats.Po rm -f ./.deps/phyml_mpi-tbe.Po rm -f ./.deps/phyml_mpi-utilities.Po rm -f ./.deps/phyml_mpi-xml.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 for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for mpi-c... 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 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-main.o `test -f 'main.c' || echo './'`main.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-utilities.o `test -f 'utilities.c' || echo './'`utilities.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-optimiz.o `test -f 'optimiz.c' || echo './'`optimiz.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-lk.o `test -f 'lk.c' || echo './'`lk.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-bionj.o `test -f 'bionj.c' || echo './'`bionj.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-models.o `test -f 'models.c' || echo './'`models.c .: Building [phyml-mpi]. Version 3.3.3:3.3.20220408-3 :. gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-free.o `test -f 'free.c' || echo './'`free.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-help.o `test -f 'help.c' || echo './'`help.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-simu.o `test -f 'simu.c' || echo './'`simu.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-eigen.o `test -f 'eigen.c' || echo './'`eigen.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-pars.o `test -f 'pars.c' || echo './'`pars.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-alrt.o `test -f 'alrt.c' || echo './'`alrt.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-interface.o `test -f 'interface.c' || echo './'`interface.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-cl.o `test -f 'cl.c' || echo './'`cl.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-spr.o `test -f 'spr.c' || echo './'`spr.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-draw.o `test -f 'draw.c' || echo './'`draw.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-stats.o `test -f 'stats.c' || echo './'`stats.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-io.o `test -f 'io.c' || echo './'`io.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-make.o `test -f 'make.c' || echo './'`make.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-nexus.o `test -f 'nexus.c' || echo './'`nexus.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-init.o `test -f 'init.c' || echo './'`init.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-xml.o `test -f 'xml.c' || echo './'`xml.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-mixt.o `test -f 'mixt.c' || echo './'`mixt.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-tbe.o `test -f 'tbe.c' || echo './'`tbe.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 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-sse.o `test -f 'sse.c' || echo './'`sse.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-avx.o `test -f 'avx.c' || echo './'`avx.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-ancestral.o `test -f 'ancestral.c' || echo './'`ancestral.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-mpi_boot.o `test -f 'mpi_boot.c' || echo './'`mpi_boot.c gcc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/aarch64-linux-gnu/openmpi/lib -lmpi -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' gcc -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -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 phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/aarch64-linux-gnu/openmpi/lib -lmpi -lm .: Building [phyml-mpi]. Version 3.3.3:3.3.20220408-3 :. 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 3.3.3:3.3.20220408-3 :. Done. make[4]: Entering directory '/build/reproducible-path/phyml-3.3.20220408/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/bin' /usr/bin/install -c phyml-mpi '/build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/bin' make[4]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408/src' make[3]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408/src' make[3]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' make[4]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' make[3]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' make[2]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' # install phyml binary we have kept safe above mkdir -p /build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/lib/phyml/bin mv /build/reproducible-path/phyml-3.3.20220408/debian/bin/* /build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/lib/phyml/bin chrpath --delete debian/phyml/usr/lib/phyml/bin/phyml* make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' dh_install debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' dh_installdocs mv /build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf /build/reproducible-path/phyml-3.3.20220408/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' dh_fixperms find debian/*/usr/share/doc -name "*.nxs" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.xml" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.mat" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.txt" -exec chmod -x \{\} \; chmod -x debian/*/usr/share/doc/phyml/examples/nucleic chmod -x debian/*/usr/share/doc/phyml/examples/proteic make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' dh_missing debian/rules override_dh_dwz make[1]: Entering directory '/build/reproducible-path/phyml-3.3.20220408' echo "Do not run dh_dwz" Do not run dh_dwz make[1]: Leaving directory '/build/reproducible-path/phyml-3.3.20220408' dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phyml' in '../phyml_3.3.20220408-3_arm64.deb'. dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.3.20220408-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../phyml_3.3.20220408-3_arm64.buildinfo dpkg-genchanges --build=binary -O../phyml_3.3.20220408-3_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/2935378 and its subdirectories I: Current time: Fri May 17 14:56:46 -12 2024 I: pbuilder-time-stamp: 1716001006 Sat May 18 02:56:48 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink01-arm64.debian.net. Sat May 18 02:56:48 UTC 2024 I: Preparing to do remote build '2' on codethink01-arm64.debian.net. Sat May 18 02:58:17 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. Sat May 18 02:58:17 UTC 2024 I: phyml_3.3.20220408-3_arm64.changes: Format: 1.8 Date: Wed, 26 Oct 2022 19:56:40 +0200 Source: phyml Binary: phyml phyml-dbgsym Architecture: arm64 Version: 3:3.3.20220408-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: phyml - Phylogenetic estimation using Maximum Likelihood Changes: phyml (3:3.3.20220408-3) unstable; urgency=medium . * d/watch: move to git tag scanning; fixes uscan following github changes. Checksums-Sha1: cad3c4c58dd8dc85cc69630818f971852cce2430 2054096 phyml-dbgsym_3.3.20220408-3_arm64.deb 506c9fc206127ab5f6fec9c32b1127a1c3dd631e 7510 phyml_3.3.20220408-3_arm64.buildinfo b5f26c4eaeebdbc470516c8ef1bb12a6019107fe 1081524 phyml_3.3.20220408-3_arm64.deb Checksums-Sha256: d7f4170907435bd9f5a10a7af16509ce71d4451ee9668e8fa7d483eec27f69b2 2054096 phyml-dbgsym_3.3.20220408-3_arm64.deb 4ea4eceedfd61fea5a47daac8a7ee12f6c50b6287ca486afa46b896404bf9d7f 7510 phyml_3.3.20220408-3_arm64.buildinfo c0088bef05c99f0bb4a7e4e3ef8c3e384cacf6b999e8c1007acb968441aeb6f9 1081524 phyml_3.3.20220408-3_arm64.deb Files: f20091e200ad0d8795ee05ab4f881d71 2054096 debug optional phyml-dbgsym_3.3.20220408-3_arm64.deb c9b48dfe083d5ef71bd4d195b5f51032 7510 science optional phyml_3.3.20220408-3_arm64.buildinfo 4654efe68b83d302ea6bf5e7ff4e2499 1081524 science optional phyml_3.3.20220408-3_arm64.deb Sat May 18 02:58:19 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_4-19013.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.g2c9mFsu/phyml_3.3.20220408-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.g2c9mFsu/phyml_3.3.20220408-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.g2c9mFsu/phyml_3.3.20220408-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.g2c9mFsu/b1/phyml_3.3.20220408-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.g2c9mFsu/b2/phyml_3.3.20220408-3_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: 0.534s) 0.534s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.056s) 0.056s 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: 968ms CPU time consumed: 969ms Sat May 18 02:58:20 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Sat May 18 02:58:20 UTC 2024 I: phyml from trixie built successfully and reproducibly on arm64. Sat May 18 02:58:21 UTC 2024 I: Submitting .buildinfo files to external archives: Sat May 18 02:58:21 UTC 2024 I: Submitting 12K b1/phyml_3.3.20220408-3_arm64.buildinfo.asc Sat May 18 02:58:22 UTC 2024 I: Submitting 12K b2/phyml_3.3.20220408-3_arm64.buildinfo.asc Sat May 18 02:58:23 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat May 18 02:58:23 UTC 2024 I: Done submitting .buildinfo files. Sat May 18 02:58:23 UTC 2024 I: Removing signed phyml_3.3.20220408-3_arm64.buildinfo.asc files: removed './b1/phyml_3.3.20220408-3_arm64.buildinfo.asc' removed './b2/phyml_3.3.20220408-3_arm64.buildinfo.asc'