Sun Feb 9 00:00:34 UTC 2025 I: starting to build mrbayes/trixie/arm64 on jenkins on '2025-02-09 00:00' Sun Feb 9 00:00:34 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_5/81223/console.log Sun Feb 9 00:00:34 UTC 2025 I: Downloading source for trixie/mrbayes=3.2.7a-7 --2025-02-09 00:00:34-- http://deb.debian.org/debian/pool/main/m/mrbayes/mrbayes_3.2.7a-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2184 (2.1K) [text/prs.lines.tag] Saving to: ‘mrbayes_3.2.7a-7.dsc’ 0K .. 100% 386M=0s 2025-02-09 00:00:34 (386 MB/s) - ‘mrbayes_3.2.7a-7.dsc’ saved [2184/2184] Sun Feb 9 00:00:34 UTC 2025 I: mrbayes_3.2.7a-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: mrbayes Binary: mrbayes, mrbayes-mpi, mrbayes-doc Architecture: any all Version: 3.2.7a-7 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Homepage: http://mrbayes.csit.fsu.edu/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/mrbayes Vcs-Git: https://salsa.debian.org/med-team/mrbayes.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libreadline-dev, mpi-default-dev, libhmsbeagle-dev, autoconf-archive, pkg-config Package-List: mrbayes deb science optional arch=any mrbayes-doc deb doc optional arch=all mrbayes-mpi deb science optional arch=any Checksums-Sha1: 3073ebd54fe7f4e8db88918f061b2856ee4bf0d9 9819346 mrbayes_3.2.7a.orig.tar.gz 99911ffc510775938111912889d2da7745b83cc9 7380 mrbayes_3.2.7a-7.debian.tar.xz Checksums-Sha256: 3eed2e3b1d9e46f265b6067a502a89732b6f430585d258b886e008e846ecc5c6 9819346 mrbayes_3.2.7a.orig.tar.gz 58f4e433e222389b50b62dbb92ed4667c7c5ed19c258b3802f1bbe1da988aa84 7380 mrbayes_3.2.7a-7.debian.tar.xz Files: 504236626ce9a2de1066a8520672f0cc 9819346 mrbayes_3.2.7a.orig.tar.gz 3a68c8efba2dcdf1502e2378ed7ff21b 7380 mrbayes_3.2.7a-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWj540RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtG/kQ/9G3rB+YHqnesvCJ0pA6E8mJ8v2Q0DSiTF sMwFzhWFLrTaBKW37P68WSlecn3XydmKyZCCk8RWGH18bIKKGPk/DScZoFhWntdN cwKTzhoMcmnDIHqs/vpZvX9gTJEe/uGfflT3h6Rpi165rymLIGlfioxzJ4GYwWta qx8HDlKJPCl4qJcjKV48iTnqG6n/X3xlXlHUwFeTRglinClD4bwmEFS6aEKbySXh DJ4+cTlM9wO1iAnF47sVMlpRAJ95zbPXrKmQvZBoNf8eCLMEAVkiP6R9TZk5sxRU c8Txaf+a6eAZLGN9vP1yoyIFXz78F8ihT5QckxZvWvA+MkmEQFOYE0/M87sYWiqX xt7NQbXsDqbAcMsXoo0KzQEe3x1Px6SByHIpFwo248ejby+OqUTzczRIvwFDp3qK iwHhyhE0VjWGfvQ5HN35q0SnkAPnDgFRQEBuiZ1eJs7qfbboGspUWOn2zIx1FEwa L56gEtq49QZ9fGvVomX3luRnSLsHu3gd0T3bl1Oz8IEa/835qK2uxSJ4kPTrVJV5 I9u0LHSMSKHtMtHUom70uAwjtDBmp0g8s+LUrMeQuwo41BWLq3lHGUmUSnPqhyai 2+7dBXc710u5UdAT35Gvhtu9iewVeeQ3Ir+kBvoV2L2wc0aR90H4Q0e/nIrDTaR7 g4OMlLz0ez0= =yzAx -----END PGP SIGNATURE----- Sun Feb 9 00:00:34 UTC 2025 I: Checking whether the package is not for us Sun Feb 9 00:00:34 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Sun Feb 9 00:00:34 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Sun Feb 9 00:02:47 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Mar 13 18:23:36 -12 2026 I: pbuilder-time-stamp: 1773469416 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 [mrbayes_3.2.7a-7.dsc] I: copying [./mrbayes_3.2.7a.orig.tar.gz] I: copying [./mrbayes_3.2.7a-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./mrbayes_3.2.7a-7.dsc: unsupported subcommand dpkg-source: info: extracting mrbayes in mrbayes-3.2.7a dpkg-source: info: unpacking mrbayes_3.2.7a.orig.tar.gz dpkg-source: info: unpacking mrbayes_3.2.7a-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_rpath.patch dpkg-source: info: applying autoreconf.patch dpkg-source: info: applying no_baseline_violation.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3476716/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='3eb06d58748646f0a7e3502cbb77ea97' 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='3476716' 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.58U33rYX/pbuilderrc_vCtu --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.58U33rYX/b1 --logfile b1/build.log mrbayes_3.2.7a-7.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3476716/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), libreadline-dev, mpi-default-dev, libhmsbeagle-dev, autoconf-archive, pkg-config dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19956 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libreadline-dev; however: Package libreadline-dev is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on libhmsbeagle-dev; however: Package libhmsbeagle-dev is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config 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} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{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} libclang-common-19-dev{a} libclang-cpp19{a} libclc-19{a} libclc-19-dev{a} libcom-err2{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libfabric1{a} libffi8{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhmsbeagle-dev{a} libhmsbeagle1v5{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} libllvm19{a} libllvmspirvlib19.1{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmunge2{a} libncurses-dev{a} libncurses6{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi40{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} librdmacm1t64{a} libreadline-dev{a} libreadline8t64{a} libtool{a} libuchardet0{a} libucx0{a} libunistring5{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libz3-4{a} m4{a} man-db{a} media-types{a} mesa-opencl-icd{a} mpi-default-dev{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-snowballstemmer{a} python3-sphinx{a} python3-urllib3{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libclang-rt-19-dev libcoarrays-openmpi-dev libgpm2 libjson-xs-perl libmail-sendmail-perl libpaper-utils lynx python3-pil wget xauth 0 packages upgraded, 158 newly installed, 0 to remove and 0 not upgraded. Need to get 184 MB of archives. After unpacking 920 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libpython3.13-minimal arm64 3.13.1-3+b1 [852 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3.13-minimal arm64 3.13.1-3+b1 [1987 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-6 [257 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libpython3.13-stdlib arm64 3.13.1-3+b1 [1913 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 python3.13 arm64 3.13.1-3+b1 [740 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B] Get: 15 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.13.1-2 [28.0 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.4.0-2 [1385 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20241223 [164 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-2 [91.5 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libcbor0.10 arm64 0.10.2-2 [27.4 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libfido2-1 arm64 1.15.0-1+b1 [74.3 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 36 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 openssh-client arm64 1:9.9p1-3 [928 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 50 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-12 [361 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libgfortran-14-dev arm64 14.2.0-12 [427 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-12 [9791 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 gfortran-14 arm64 14.2.0-12 [13.4 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libnl-3-200 arm64 3.7.0-0.3+b1 [57.0 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libnl-route-3-200 arm64 3.7.0-0.3+b1 [167 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libibverbs1 arm64 55.0-1 [58.6 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 ibverbs-providers arm64 55.0-1 [328 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libllvm17t64 arm64 1:17.0.6-20+b2 [21.3 MB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b2 [12.1 MB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libdrm-common all 2.4.123-1 [8084 B] Get: 73 http://deb.debian.org/debian trixie/main arm64 libdrm2 arm64 2.4.123-1 [38.0 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libdrm-amdgpu1 arm64 2.4.123-1 [21.6 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libnuma1 arm64 2.0.18-1+b1 [21.8 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libhsakmt1 arm64 6.1.2+ds-1 [56.9 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libhsa-runtime64-1 arm64 5.7.1-3 [278 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libamdhip64-5 arm64 5.7.1-5 [8823 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libclang-common-19-dev arm64 1:19.1.7-1+b1 [740 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libllvm19 arm64 1:19.1.7-1+b1 [23.3 MB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libclang-cpp19 arm64 1:19.1.7-1+b1 [12.0 MB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libclc-19-dev all 1:19.1.7-1 [65.7 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libclc-19 all 1:19.1.7-1 [12.1 MB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libdrm-radeon1 arm64 2.4.123-1 [21.3 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10+b1 [126 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-10+b1 [102 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10+b1 [54.4 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-10+b1 [60.4 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libevent-dev arm64 2.1.12-stable-10+b1 [304 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 librdmacm1t64 arm64 55.0-1 [67.0 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libfabric1 arm64 1.17.0-3.1 [480 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b2 [39.3 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libllvmspirvlib19.1 arm64 19.1.3-1 [795 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 mesa-opencl-icd arm64 24.3.4-3 [17.3 MB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libhmsbeagle1v5 arm64 4.0.1+dfsg-3 [112 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libhmsbeagle-dev arm64 4.0.1+dfsg-3 [17.6 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libhwloc15 arm64 2.11.2-1 [141 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libnuma-dev arm64 2.0.18-1+b1 [37.8 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libltdl7 arm64 2.5.4-3 [415 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libltdl-dev arm64 2.5.4-3 [168 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libhwloc-dev arm64 2.11.2-1 [237 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libpciaccess0 arm64 0.17-3+b3 [51.2 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libxnvctrl0 arm64 535.171.04-1+b2 [14.0 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libhwloc-plugins arm64 2.11.2-1 [17.9 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libibumad3 arm64 55.0-1 [27.2 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libibmad5 arm64 55.0-1 [41.3 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libnl-3-dev arm64 3.7.0-0.3+b1 [101 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libnl-route-3-dev arm64 3.7.0-0.3+b1 [198 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libibverbs-dev arm64 55.0-1 [637 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libmunge2 arm64 0.5.16-1 [19.2 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libncurses-dev arm64 6.5-2+b1 [338 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libpmix2t64 arm64 5.0.6-1 [577 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libucx0 arm64 1.17.0+ds-3 [959 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libopenmpi40 arm64 5.0.6-3 [2087 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 openmpi-common all 5.0.6-3 [97.0 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 sphinx-common all 8.1.3-4 [616 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 python3-babel all 2.17.0-1 [117 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 python3-roman all 5.0-1 [10.6 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 138 http://deb.debian.org/debian trixie/main arm64 python3-markupsafe arm64 2.1.5-1+b3 [14.0 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 python3-jinja2 all 3.1.5-2 [107 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 python3-certifi all 2024.12.14+ds-1 [9624 B] Get: 143 http://deb.debian.org/debian trixie/main arm64 python3-charset-normalizer arm64 3.4.0-1+b1 [129 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 python3-idna all 3.8-2 [41.6 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 python3-urllib3 all 2.3.0-1 [114 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 python3-sphinx all 8.1.3-4 [468 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libpmix-dev arm64 5.0.6-1 [3933 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 openmpi-bin arm64 5.0.6-3 [180 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libopenmpi-dev arm64 5.0.6-3 [1088 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 libreadline-dev arm64 8.2-6 [155 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 mpi-default-dev arm64 1.18 [3372 B] Get: 156 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-4 [14.0 kB] Fetched 184 MB in 1s (172 MB/s) Preconfiguring packages ... Selecting previously unselected package autoconf-archive. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19956 files and directories currently installed.) Preparing to unpack .../autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.1-3+b1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.1-3+b1) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.1-3+b1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.1-3+b1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.1-3+b1_arm64.deb ... Unpacking python3.13 (3.13.1-3+b1) ... 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Setting up libopenmpi-dev:arm64 (5.0.6-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode Setting up mpi-default-dev (1.18) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/mrbayes-3.2.7a/ && 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 > ../mrbayes_3.2.7a-7_source.changes dpkg-buildpackage: info: source package mrbayes dpkg-buildpackage: info: source version 3.2.7a-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a' dh_auto_configure -- --with-beagle=/usr --enable-mpi=yes --enable-debug=yes ./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 --with-beagle=/usr --enable-mpi=yes --enable-debug=yes checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking whether to enable maintainer-specific portions of Makefiles... no checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for pdflatex... no checking for bibtex... no configure: WARNING: pdflatex or bibtex is missing, documentation will not be rebuilt checking whether make supports the include directive... yes (GNU style) checking whether to compile using MPI... no 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... unsupported checking for gcc option to enable C99 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for sqrt 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 configure: Trying to locate Beagle (hmsbeagle-1) in '/usr' checking for libhmsbeagle/beagle.h... yes checking for beagleCreateInstance in -lhmsbeagle... yes configure: Found Beagle in '/usr' checking for beagleSetCPUThreadCount in -lhmsbeagle... yes configure: Using BEAGLE_CFLAGS="-I/usr/include/libhmsbeagle-1 -pthread" configure: Using BEAGLE_LIBS="-L/usr/lib -lhmsbeagle" checking for a readline compatible library... -lreadline checking for readline.h... no checking for readline/readline.h... yes checking whether readline supports history... yes checking for history.h... no checking for readline/history.h... yes checking for float.h... yes checking for limits.h... yes checking for memory.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for size_t... yes checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking for C compiler vendor... gnu checking for a sed that does not truncate output... /usr/bin/sed checking for C compiler version... 14.2.0 checking CFLAGS for most reasonable warnings... -Wall checking for floor... yes checking for memset... yes checking for pow... yes checking for sqrt... yes checking for strchr... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/manual/Makefile config.status: creating doc/tutorial/Makefile config.status: creating examples/Makefile config.status: creating src/Makefile config.status: creating src/config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a' # build mb-mpi (from initial config) LIBS="-Wl,--as-needed" dh_auto_build make -j12 make[2]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a' Making all in src make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/src' make all-am make[4]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-bayes.o `test -f 'bayes.c' || echo './'`bayes.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-best.o `test -f 'best.c' || echo './'`best.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-command.o `test -f 'command.c' || echo './'`command.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-likelihood.o `test -f 'likelihood.c' || echo './'`likelihood.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-mbbeagle.o `test -f 'mbbeagle.c' || echo './'`mbbeagle.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-model.o `test -f 'model.c' || echo './'`model.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-proposal.o `test -f 'proposal.c' || echo './'`proposal.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-sumpt.o `test -f 'sumpt.c' || echo './'`sumpt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c In file included from bayes.h:63, from mbbeagle.c:32: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from model.c:38: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from likelihood.c:38: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from utils.c:38: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from bayes.c:38: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from best.c:18: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from command.c:38: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from proposal.c:38: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from sumpt.c:38: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from mcmc.c:45: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ sumpt.c: In function 'DoSump': sumpt.c:335:5: warning: '__builtin_strncpy' output may be truncated copying 90 bytes from a string of length 119 [-Wstringop-truncation] 335 | strncpy (temp, sumpParams.sumpOutfile, 90); | ^ In file included from /usr/include/string.h:548, from /usr/include/memory.h:29, from bayes.h:31: In function 'strncpy', inlined from 'CopyResults' at utils.c:311:9: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:100:10: warning: '__builtin_strncpy' accessing between 11 and 2147483647 bytes at offsets [13, 2147483649] and 0 may overlap up to 2147483634 bytes at offset [13, 2147483646] [-Wrestrict] 100 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'strncpy', inlined from 'CopyProcessSsFile' at utils.c:350:9: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:100:10: warning: '__builtin_strncpy' accessing between 11 and 2147483647 bytes at offsets [13, 2147483649] and 0 may overlap up to 2147483634 bytes at offset [13, 2147483646] [-Wrestrict] 100 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'strncpy', inlined from 'CopyTreeResults' at utils.c:422:9: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:100:10: warning: '__builtin_strncpy' accessing between 11 and 2147483647 bytes at offsets [13, 2147483649] and 0 may overlap up to 2147483634 bytes at offset [13, 2147483646] [-Wrestrict] 100 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c: In function 'DoCompRefTree': sumpt.c:4612:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 7 and 126 [-Wformat-overflow=] 4612 | sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1); | ^~ sumpt.c:4612:33: note: directive argument in the range [1, 2147483647] 4612 | sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1); | ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from bayes.h:32: In function 'sprintf', inlined from 'DoCompRefTree' at sumpt.c:4612:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 136 bytes into a destination of size 130 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'ShowConTree' at sumpt.c:8173:21: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin_sprintf' argument 3 may overlap destination object 'printLine' [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sumpt.c: In function 'DoSumt': sumpt.c:4958:39: warning: '.run' directive writing 4 bytes into a region of size between 1 and 120 [-Wformat-overflow=] 4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1); | ^~~~ sumpt.c:4958:36: note: directive argument in the range [-2147483647, 2147483647] 4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1); | ^~~~~~~~~~~~ In function 'sprintf', inlined from 'DoSumt' at sumpt.c:4958:17: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 137 bytes into a destination of size 120 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sumpt.c: In function 'DoSumt': sumpt.c:4956:39: warning: '.t' directive writing 2 bytes into a region of size between 1 and 120 [-Wformat-overflow=] 4956 | sprintf (tempName, "%s.t", fileName); | ^~ In function 'sprintf', inlined from 'DoSumt' at sumpt.c:4956:17: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 122 bytes into a destination of size 120 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mcmc.c: In function 'ReopenMBPrintFiles': mcmc.c:15467:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 2 and 110 [-Wformat-overflow=] 15467 | sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1); | ^~ mcmc.c:15467:36: note: directive argument in the range [1, 2147483647] 15467 | sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from bayes.h:32: In function 'sprintf', inlined from 'ReopenMBPrintFiles' at mcmc.c:15467:17: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 14 and 131 bytes into a destination of size 120 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mcmc.c: In function 'RunChain': mcmc.c:17362:46: warning: '.ss' directive writing 3 bytes into a region of size between 1 and 220 [-Wformat-overflow=] 17362 | sprintf (bkupFileName,"%s.ss%d", ckpFileName,chainParams.numStepsSS-stepIndexSS); | ^~~ In function 'sprintf', inlined from 'RunChain' at mcmc.c:17362:21: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 234 bytes into a destination of size 220 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command.c: In function 'DoExecute': command.c:3560:5: warning: '__builtin_strncpy' output may be truncated copying 98 bytes from a string of length 99 [-Wstringop-truncation] 3560 | strncpy (exeFileName, inputFileName, 98); | ^ model.c: In function 'SetModelParams': model.c:19111:48: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 19111 | sprintf (tempMult, "g_m{%d}", i+1); | ^ In file included from /usr/include/stdio.h:970, from bayes.h:32: In function 'sprintf', inlined from 'SetModelParams' at model.c:19111:21: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o mb mb-bayes.o mb-best.o mb-command.o mb-likelihood.o mb-mbbeagle.o mb-mcmc.o mb-model.o mb-proposal.o mb-sumpt.o mb-utils.o -L/usr/lib -lhmsbeagle -lm -lreadline make[4]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/src' make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/src' Making all in doc make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc' Making all in manual make[4]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc/manual' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc/manual' Making all in tutorial make[4]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc/tutorial' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc/tutorial' make[4]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc' make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc' Making all in examples make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/examples' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/examples' make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a' make[2]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a' mv src/mb ./mb-mpi # Now - build mb ( cd src ; make clean ) make[2]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/src' rm -f mb rm -f *.o make[2]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/src' dh_auto_configure -- --with-beagle=/usr --enable-mpi=no --enable-debug=yes ./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 --with-beagle=/usr --enable-mpi=no --enable-debug=yes checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking whether to enable maintainer-specific portions of Makefiles... no checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for pdflatex... no checking for bibtex... no configure: WARNING: pdflatex or bibtex is missing, documentation will not be rebuilt checking whether make supports the include directive... yes (GNU style) checking whether to compile using MPI... no 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... unsupported checking for gcc option to enable C99 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for sqrt 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 configure: Trying to locate Beagle (hmsbeagle-1) in '/usr' checking for libhmsbeagle/beagle.h... yes checking for beagleCreateInstance in -lhmsbeagle... yes configure: Found Beagle in '/usr' checking for beagleSetCPUThreadCount in -lhmsbeagle... yes configure: Using BEAGLE_CFLAGS="-I/usr/include/libhmsbeagle-1 -pthread" configure: Using BEAGLE_LIBS="-L/usr/lib -lhmsbeagle" checking for a readline compatible library... -lreadline checking for readline.h... no checking for readline/readline.h... yes checking whether readline supports history... yes checking for history.h... no checking for readline/history.h... yes checking for float.h... yes checking for limits.h... yes checking for memory.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for size_t... yes checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking for C compiler vendor... gnu checking for a sed that does not truncate output... /usr/bin/sed checking for C compiler version... 14.2.0 checking CFLAGS for most reasonable warnings... -Wall checking for floor... yes checking for memset... yes checking for pow... yes checking for sqrt... yes checking for strchr... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/manual/Makefile config.status: creating doc/tutorial/Makefile config.status: creating examples/Makefile config.status: creating src/Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands LIBS="-Wl,--as-needed" dh_auto_build make -j12 make[2]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a' Making all in src make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/src' make all-am make[4]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-bayes.o `test -f 'bayes.c' || echo './'`bayes.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-best.o `test -f 'best.c' || echo './'`best.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-command.o `test -f 'command.c' || echo './'`command.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-likelihood.o `test -f 'likelihood.c' || echo './'`likelihood.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-mbbeagle.o `test -f 'mbbeagle.c' || echo './'`mbbeagle.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-model.o `test -f 'model.c' || echo './'`model.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-proposal.o `test -f 'proposal.c' || echo './'`proposal.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-sumpt.o `test -f 'sumpt.c' || echo './'`sumpt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c In file included from bayes.h:63, from best.c:18: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from utils.c:38: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from proposal.c:38: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from command.c:38: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from bayes.c:38: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from likelihood.c:38: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from mbbeagle.c:32: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from mcmc.c:45: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from model.c:38: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ In file included from bayes.h:63, from sumpt.c:38: /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:176:45: warning: enumerator value for 'BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO' is not an integer constant expression [-Wpedantic] 176 | BEAGLE_FLAG_PREORDER_TRANSPOSE_AUTO = 1 << 31 /**< Automatically transpose pre-order transition matrices */ | ^ sumpt.c: In function 'DoSump': sumpt.c:335:5: warning: '__builtin_strncpy' output may be truncated copying 90 bytes from a string of length 119 [-Wstringop-truncation] 335 | strncpy (temp, sumpParams.sumpOutfile, 90); | ^ In file included from /usr/include/string.h:548, from /usr/include/memory.h:29, from bayes.h:31: In function 'strncpy', inlined from 'CopyResults' at utils.c:311:9: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:100:10: warning: '__builtin_strncpy' accessing between 11 and 2147483647 bytes at offsets [13, 2147483649] and 0 may overlap up to 2147483634 bytes at offset [13, 2147483646] [-Wrestrict] 100 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'strncpy', inlined from 'CopyProcessSsFile' at utils.c:350:9: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:100:10: warning: '__builtin_strncpy' accessing between 11 and 2147483647 bytes at offsets [13, 2147483649] and 0 may overlap up to 2147483634 bytes at offset [13, 2147483646] [-Wrestrict] 100 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'strncpy', inlined from 'CopyTreeResults' at utils.c:422:9: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:100:10: warning: '__builtin_strncpy' accessing between 11 and 2147483647 bytes at offsets [13, 2147483649] and 0 may overlap up to 2147483634 bytes at offset [13, 2147483646] [-Wrestrict] 100 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ sumpt.c: In function 'DoCompRefTree': sumpt.c:4612:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 7 and 126 [-Wformat-overflow=] 4612 | sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1); | ^~ sumpt.c:4612:33: note: directive argument in the range [1, 2147483647] 4612 | sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1); | ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from bayes.h:32: In function 'sprintf', inlined from 'DoCompRefTree' at sumpt.c:4612:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 136 bytes into a destination of size 130 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'ShowConTree' at sumpt.c:8173:21: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: warning: '__builtin_sprintf' argument 3 may overlap destination object 'printLine' [-Wrestrict] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sumpt.c: In function 'DoSumt': sumpt.c:4958:39: warning: '.run' directive writing 4 bytes into a region of size between 1 and 120 [-Wformat-overflow=] 4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1); | ^~~~ sumpt.c:4958:36: note: directive argument in the range [-2147483647, 2147483647] 4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1); | ^~~~~~~~~~~~ In function 'sprintf', inlined from 'DoSumt' at sumpt.c:4958:17: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 8 and 137 bytes into a destination of size 120 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ sumpt.c: In function 'DoSumt': sumpt.c:4956:39: warning: '.t' directive writing 2 bytes into a region of size between 1 and 120 [-Wformat-overflow=] 4956 | sprintf (tempName, "%s.t", fileName); | ^~ In function 'sprintf', inlined from 'DoSumt' at sumpt.c:4956:17: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 3 and 122 bytes into a destination of size 120 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mcmc.c: In function 'ReopenMBPrintFiles': mcmc.c:15467:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 2 and 110 [-Wformat-overflow=] 15467 | sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1); | ^~ mcmc.c:15467:36: note: directive argument in the range [1, 2147483647] 15467 | sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from bayes.h:32: In function 'sprintf', inlined from 'ReopenMBPrintFiles' at mcmc.c:15467:17: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 14 and 131 bytes into a destination of size 120 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ mcmc.c: In function 'RunChain': mcmc.c:17362:46: warning: '.ss' directive writing 3 bytes into a region of size between 1 and 220 [-Wformat-overflow=] 17362 | sprintf (bkupFileName,"%s.ss%d", ckpFileName,chainParams.numStepsSS-stepIndexSS); | ^~~ In function 'sprintf', inlined from 'RunChain' at mcmc.c:17362:21: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 5 and 234 bytes into a destination of size 220 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command.c: In function 'DoExecute': command.c:3560:5: warning: '__builtin_strncpy' output may be truncated copying 98 bytes from a string of length 99 [-Wstringop-truncation] 3560 | strncpy (exeFileName, inputFileName, 98); | ^ model.c: In function 'SetModelParams': model.c:19111:48: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 19111 | sprintf (tempMult, "g_m{%d}", i+1); | ^ In file included from /usr/include/stdio.h:970, from bayes.h:32: In function 'sprintf', inlined from 'SetModelParams' at model.c:19111:21: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o mb mb-bayes.o mb-best.o mb-command.o mb-likelihood.o mb-mbbeagle.o mb-mcmc.o mb-model.o mb-proposal.o mb-sumpt.o mb-utils.o -L/usr/lib -lhmsbeagle -lm -lreadline make[4]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/src' make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/src' Making all in doc make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc' Making all in manual make[4]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc/manual' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc/manual' Making all in tutorial make[4]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc/tutorial' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc/tutorial' make[4]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc' make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc' Making all in examples make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/examples' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/examples' make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a' make[2]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a' mv src/mb . make[1]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a' Making check in src make[2]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/src' gcc -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mrbayes-3.2.7a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o mb mb-bayes.o mb-best.o mb-command.o mb-likelihood.o mb-mbbeagle.o mb-mcmc.o mb-model.o mb-proposal.o mb-sumpt.o mb-utils.o -L/usr/lib -lhmsbeagle -lm -lreadline make[2]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/src' Making check in doc make[2]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc' Making check in manual make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc/manual' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc/manual' Making check in tutorial make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc/tutorial' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc/tutorial' make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc' make[2]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc' Making check in examples make[2]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/examples' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/examples' make[2]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a' make[1]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j12 install DESTDIR=/build/reproducible-path/mrbayes-3.2.7a/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a' Making install in src make[2]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/src' make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/mrbayes-3.2.7a/debian/tmp/usr/bin' /usr/bin/install -c mb '/build/reproducible-path/mrbayes-3.2.7a/debian/tmp/usr/bin' make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/src' make[2]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/src' Making install in doc make[2]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc' Making install in manual make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc/manual' make[4]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc/manual' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/install -c -m 644 Manual_MrBayes_v3.2.pdf '/build/reproducible-path/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' make[4]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc/manual' make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc/manual' Making install in tutorial make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc/tutorial' make[4]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc/tutorial' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/mkdir -p '/build/reproducible-path/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/install -c -m 644 hym.nex '/build/reproducible-path/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/install -c -m 644 MBDating.pdf '/build/reproducible-path/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' make[4]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc/tutorial' make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc/tutorial' make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc' make[4]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/doc' 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/mrbayes-3.2.7a/doc' make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc' make[2]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/doc' Making install in examples make[2]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/examples' make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a/examples' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/mrbayes-3.2.7a/debian/tmp/usr/share/examples/mrbayes' /usr/bin/install -c -m 644 avian_ovomucoids.nex codon.nex cynmix.nex finch.nex hymfossil.nex primates.nex replicase.nex sceloporus.nex '/build/reproducible-path/mrbayes-3.2.7a/debian/tmp/usr/share/examples/mrbayes' make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/examples' make[2]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a/examples' make[2]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a' make[3]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/install -c -m 644 COPYING README NEWS '/build/reproducible-path/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' make[3]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a' make[2]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a' make[1]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a' dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a' dh_installexamples find debian -name "Makefile*" -delete make[1]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a' dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a' dh_fixperms debian/rules override_dh_missing make[1]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a' dh_missing --list-missing dh_missing: warning: usr/bin/mb exists in debian/tmp but is not installed to anywhere (related file: "mb") dh_missing: warning: usr/share/doc/mrbayes/COPYING exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/doc/mrbayes/MBDating.pdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/doc/mrbayes/Manual_MrBayes_v3.2.pdf exists in debian/tmp but is not installed to anywhere (related file: "doc/manual/Manual_MrBayes_v3.2.pdf") dh_missing: warning: usr/share/doc/mrbayes/NEWS exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/doc/mrbayes/README exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/doc/mrbayes/hym.nex exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/examples/mrbayes/avian_ovomucoids.nex exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/examples/mrbayes/codon.nex exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/examples/mrbayes/cynmix.nex exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/examples/mrbayes/finch.nex exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/examples/mrbayes/hymfossil.nex exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/examples/mrbayes/primates.nex exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/examples/mrbayes/replicase.nex exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/examples/mrbayes/sceloporus.nex exists in debian/tmp but is not installed to anywhere While detecting missing files, dh_missing noted some files with a similar name to those that were missing. This warning /might/ be resolved by replacing references to the missing files with the similarly named ones that dh_missing found - assuming the content is identical. As an example, you might want to replace: * mb with: * usr/bin/mb in a file in debian/ or as argument to one of the dh_* tools called from debian/rules. (Note it is possible the paths are not used verbatim but instead directories containing or globs matching them are used instead) Alternatively, add the missing file to debian/not-installed if it cannot and should not be used. The following debhelper tools have reported what they installed (with files per package) * dh_install: mrbayes (1), mrbayes-doc (1), mrbayes-mpi (2) * dh_installdocs: mrbayes (3), mrbayes-doc (0), mrbayes-mpi (0) * dh_installexamples: mrbayes (0), mrbayes-doc (0), mrbayes-mpi (0) * dh_installman: mrbayes (1), mrbayes-doc (0), mrbayes-mpi (1) If the missing files are installed by another tool, please file a bug against it. When filing the report, if the tool is not part of debhelper itself, please reference the "Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+). (in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.md.gz) Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built If the omission is intentional or no other helper can take care of this consider adding the paths to debian/not-installed. make[1]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a' dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libreadline8t64 from: /lib/aarch64-linux-gnu/libreadline.so.8 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libreadline8t64 to: /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 diversion by libreadline8t64 from: /lib/aarch64-linux-gnu/libreadline.so.8 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libreadline8t64 to: /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged debian/rules override_dh_installdeb make[1]: Entering directory '/build/reproducible-path/mrbayes-3.2.7a' # FIXME: That's a dirty hack by simply removing debug information in mrbayes-mpi-dbgsym # Due to the duplicated build above this is just a duplicate of mrbayes-dbgsym and creates a file conflict if [ -d debian/.debhelper/mrbayes-mpi/dbgsym-root/usr/lib/debug ] ; then \ find debian/.debhelper/mrbayes-mpi/dbgsym-root/usr/lib/debug -name "*.debug" -delete ; \ fi dh_installdeb make[1]: Leaving directory '/build/reproducible-path/mrbayes-3.2.7a' dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'mrbayes' in '../mrbayes_3.2.7a-7_arm64.deb'. dpkg-deb: building package 'mrbayes-dbgsym' in '../mrbayes-dbgsym_3.2.7a-7_arm64.deb'. dpkg-deb: building package 'mrbayes-mpi' in '../mrbayes-mpi_3.2.7a-7_arm64.deb'. dpkg-deb: building package 'mrbayes-doc' in '../mrbayes-doc_3.2.7a-7_all.deb'. dpkg-deb: building package 'mrbayes-mpi-dbgsym' in '../mrbayes-mpi-dbgsym_3.2.7a-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../mrbayes_3.2.7a-7_arm64.buildinfo dpkg-genchanges --build=binary -O../mrbayes_3.2.7a-7_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/3476716 and its subdirectories I: Current time: Fri Mar 13 18:25:45 -12 2026 I: pbuilder-time-stamp: 1773469545 Sun Feb 9 00:02:48 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Sun Feb 9 00:02:48 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Sun Feb 9 00:06:36 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Sun Feb 9 00:06:37 UTC 2025 I: mrbayes_3.2.7a-7_arm64.changes: Format: 1.8 Date: Sun, 14 Jan 2024 14:35:17 +0100 Source: mrbayes Binary: mrbayes mrbayes-dbgsym mrbayes-doc mrbayes-mpi mrbayes-mpi-dbgsym Architecture: arm64 all Version: 3.2.7a-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: mrbayes - Bayesian Inference of Phylogeny mrbayes-doc - Bayesian Inference of Phylogeny - manual mrbayes-mpi - Bayesian Inference of Phylogeny - mpi version Closes: 1045400 1049739 Changes: mrbayes (3.2.7a-7) unstable; urgency=medium . * Fix clean target Closes: #1045400, #1049739 * Standards-Version: 4.6.2 (routine-update) * Remove trailing whitespace in debian/changelog (routine-update) Checksums-Sha1: 27bad5f00ca90c16303f993ad9127e4ce951dd30 1069100 mrbayes-dbgsym_3.2.7a-7_arm64.deb 40070e1dee394b744ab432d75df7504da4ef3c58 1329088 mrbayes-doc_3.2.7a-7_all.deb 0c9eb6eecff817852faaa3db5e94c98a7499b944 972 mrbayes-mpi-dbgsym_3.2.7a-7_arm64.deb a04e9d359c26c5896839b3ef37e06a6c3e4d8849 550080 mrbayes-mpi_3.2.7a-7_arm64.deb 2ce5835926eb7fa941907bc0ad5eb03f188817d5 10041 mrbayes_3.2.7a-7_arm64.buildinfo 85e9bcda230a4e170f130f55da2097513605809d 613120 mrbayes_3.2.7a-7_arm64.deb Checksums-Sha256: 4c29d19dce18d2df90d48b0231ecfc3ff99265654896f079e6bcc29a1e92ff81 1069100 mrbayes-dbgsym_3.2.7a-7_arm64.deb d517b4918e8e90f7d3d104fc315af1fd0da30aa7b8d47f04c8be55db0df1ac4b 1329088 mrbayes-doc_3.2.7a-7_all.deb e5d2cd2532e7de0663c1c2ab421d72e2a65175b6c3ebcaad2482d103696b8294 972 mrbayes-mpi-dbgsym_3.2.7a-7_arm64.deb 65e18a3b7418622a7dc9817b22b4e79033706d1caa3d4a4bfaa68680fa2cee51 550080 mrbayes-mpi_3.2.7a-7_arm64.deb d2b54dbd3bf78b8ef152546d501bc562a396ca90f53dd69561bc6a2b667d2a71 10041 mrbayes_3.2.7a-7_arm64.buildinfo fb45609a45165fda041620058209ef05606a577bf7869bafac4a9bea07824120 613120 mrbayes_3.2.7a-7_arm64.deb Files: 9235f8e2b4fa92805c4e4385b2ce6b99 1069100 debug optional mrbayes-dbgsym_3.2.7a-7_arm64.deb 40ef7277af5465fba89ea91467cd0a4a 1329088 doc optional mrbayes-doc_3.2.7a-7_all.deb f72df4a0c0135b547d41416e8637ae7d 972 debug optional mrbayes-mpi-dbgsym_3.2.7a-7_arm64.deb f86ba79b89aa9c256180a8563ce022d1 550080 science optional mrbayes-mpi_3.2.7a-7_arm64.deb 5ffc7758e5bf7bfb67dd393af0dfe37e 10041 science optional mrbayes_3.2.7a-7_arm64.buildinfo 7bdcc8600997f3ba73da241c3645c335 613120 science optional mrbayes_3.2.7a-7_arm64.deb Sun Feb 9 00:06:38 UTC 2025 I: diffoscope 288 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_5-81223.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.58U33rYX/mrbayes_3.2.7a-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.58U33rYX/mrbayes_3.2.7a-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.58U33rYX/mrbayes_3.2.7a-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.58U33rYX/b1/mrbayes_3.2.7a-7_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.58U33rYX/b2/mrbayes_3.2.7a-7_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.004s) 0.004s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 239ms CPU time consumed: 240ms Sun Feb 9 00:06:39 UTC 2025 I: diffoscope 288 found no differences in the changes files, and a .buildinfo file also exists. Sun Feb 9 00:06:39 UTC 2025 I: mrbayes from trixie built successfully and reproducibly on arm64. Sun Feb 9 00:06:40 UTC 2025 I: Submitting .buildinfo files to external archives: Sun Feb 9 00:06:40 UTC 2025 I: Submitting 12K b1/mrbayes_3.2.7a-7_arm64.buildinfo.asc Sun Feb 9 00:06:41 UTC 2025 I: Submitting 12K b2/mrbayes_3.2.7a-7_arm64.buildinfo.asc Sun Feb 9 00:06:43 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Feb 9 00:06:43 UTC 2025 I: Done submitting .buildinfo files. Sun Feb 9 00:06:43 UTC 2025 I: Removing signed mrbayes_3.2.7a-7_arm64.buildinfo.asc files: removed './b1/mrbayes_3.2.7a-7_arm64.buildinfo.asc' removed './b2/mrbayes_3.2.7a-7_arm64.buildinfo.asc'