Wed May 15 20:23:55 UTC 2024 I: starting to build mrbayes/unstable/i386 on jenkins on '2024-05-15 20:23' Wed May 15 20:23:55 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_2/24079/console.log Wed May 15 20:23:55 UTC 2024 I: Downloading source for unstable/mrbayes=3.2.7a-7 --2024-05-15 20:23:55-- 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% 246M=0s 2024-05-15 20:23:55 (246 MB/s) - ‘mrbayes_3.2.7a-7.dsc’ saved [2184/2184] Wed May 15 20:23:55 UTC 2024 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----- Wed May 15 20:23:55 UTC 2024 I: Checking whether the package is not for us Wed May 15 20:23:55 UTC 2024 I: Starting 1st build on remote node ionos6-i386.debian.net. Wed May 15 20:23:55 UTC 2024 I: Preparing to do remote build '1' on ionos6-i386.debian.net. Wed May 15 20:26:08 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jun 17 14:47:01 -12 2025 I: pbuilder-time-stamp: 1750214821 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [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 gpgv: Signature made Sun Jan 14 13:54:21 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mrbayes_3.2.7a-7.dsc: no acceptable signature found 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/49548/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='94ddcbd727264be7be3360076363c526' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='49548' 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.oN8EeHke/pbuilderrc_xgbQ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oN8EeHke/b1 --logfile b1/build.log mrbayes_3.2.7a-7.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos6-i386 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 17 14:05 /bin -> usr/bin I: user script /srv/workspace/pbuilder/49548/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19686 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-13{a} gfortran-13-i686-linux-gnu{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcbor0.10{a} libclang-common-17-dev{a} libclang-cpp17t64{a} libclc-17{a} libclc-17-dev{a} libcom-err2{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-nouveau2{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} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-13-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhmsbeagle-dev{a} libhmsbeagle1v5{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} libllvmspirvlib17{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{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} libopenmpi3t64{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libpsm-infinipath1{a} librdmacm1t64{a} libreadline-dev{a} libreadline8t64{a} libsub-override-perl{a} libtool{a} libuchardet0{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} mesa-opencl-icd{a} mpi-default-dev{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} readline-common{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 libclang-rt-17-dev libcoarrays-openmpi-dev libgpm2 libmail-sendmail-perl lynx wget xauth 0 packages upgraded, 111 newly installed, 0 to remove and 0 not upgraded. Need to get 131 MB of archives. After unpacking 640 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-4 [69.3 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3 [42.9 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-4 [1194 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.1-1 [98.5 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 man-db i386 2.12.1-1 [1421 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 libbsd0 i386 0.12.2-1 [134 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 libedit2 i386 3.1-20230828-1+b1 [97.8 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 libcbor0.10 i386 0.10.2-1.2 [30.8 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libfido2-1 i386 1.14.0-1+b2 [87.4 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.20.1-6+b1 [36.1 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.1~rc2-1 [22.8 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.20.1-6+b1 [83.2 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] Get: 21 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.20.1-6+b1 [360 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.20.1-6+b1 [145 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 openssh-client i386 1:9.7p1-4 [991 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 autopoint all 0.21-14 [496 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-7 [517 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 36 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.9.14+dfsg-1.3+b3 [727 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 debhelper all 13.15.3 [901 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.1.0-1 [733 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 libgfortran-13-dev i386 13.2.0-25 [783 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 gfortran-13-i686-linux-gnu i386 13.2.0-25 [11.2 MB] Get: 47 http://deb.debian.org/debian unstable/main i386 gfortran-13 i386 13.2.0-25 [12.8 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 libnl-3-200 i386 3.7.0-0.3 [61.8 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 libnl-route-3-200 i386 3.7.0-0.3 [193 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 libibverbs1 i386 50.0-2+b1 [66.7 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 ibverbs-providers i386 50.0-2+b1 [377 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 libclang-common-17-dev i386 1:17.0.6-12 [682 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 libz3-4 i386 4.8.12-3.1+b2 [7989 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 libllvm17t64 i386 1:17.0.6-12 [27.7 MB] Get: 55 http://deb.debian.org/debian unstable/main i386 libclang-cpp17t64 i386 1:17.0.6-12 [14.0 MB] Get: 56 http://deb.debian.org/debian unstable/main i386 libclc-17-dev all 1:17.0.6-12 [61.3 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 libclc-17 all 1:17.0.6-12 [9858 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 libdrm-common all 2.4.120-2 [7688 B] Get: 59 http://deb.debian.org/debian unstable/main i386 libdrm2 i386 2.4.120-2 [41.4 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 libdrm-amdgpu1 i386 2.4.120-2 [24.4 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 libdrm-nouveau2 i386 2.4.120-2 [20.8 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 libdrm-radeon1 i386 2.4.120-2 [23.0 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libevent-2.1-7t64 i386 2.1.12-stable-8.1+b3 [195 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 libevent-core-2.1-7t64 i386 2.1.12-stable-8.1+b3 [140 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 libevent-extra-2.1-7t64 i386 2.1.12-stable-8.1+b3 [113 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 libevent-pthreads-2.1-7t64 i386 2.1.12-stable-8.1+b3 [54.3 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libevent-openssl-2.1-7t64 i386 2.1.12-stable-8.1+b3 [61.9 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 libevent-dev i386 2.1.12-stable-8.1+b3 [325 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libpsm-infinipath1 i386 3.3+20.604758e7-6.3 [177 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 librdmacm1t64 i386 50.0-2+b1 [76.0 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libfabric1 i386 1.17.0-3+b1 [540 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 ocl-icd-libopencl1 i386 2.3.2-1+b1 [43.5 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 libllvmspirvlib17 i386 17.0.0-5 [893 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 mesa-opencl-icd i386 24.0.7-1 [22.2 MB] Get: 76 http://deb.debian.org/debian unstable/main i386 libhmsbeagle1v5 i386 3.1.2+dfsg-13+b1 [107 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 libhmsbeagle-dev i386 3.1.2+dfsg-13+b1 [242 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libhwloc15 i386 2.10.0-1+b1 [175 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 libnuma1 i386 2.0.18-1 [23.5 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 libnuma-dev i386 2.0.18-1 [38.3 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 libltdl7 i386 2.4.7-7+b1 [395 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 libltdl-dev i386 2.4.7-7+b1 [167 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 libhwloc-dev i386 2.10.0-1+b1 [268 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 libpciaccess0 i386 0.17-3+b1 [53.8 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.9-1+b1 [18.5 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.2-3+b1 [24.8 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.17.0-1 [148 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.7-1+b1 [822 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libxnvctrl0 i386 535.171.04-1 [13.7 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 libhwloc-plugins i386 2.10.0-1+b1 [18.4 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 libnl-3-dev i386 3.7.0-0.3 [105 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libnl-route-3-dev i386 3.7.0-0.3 [223 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 libibverbs-dev i386 50.0-2+b1 [693 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 libncurses6 i386 6.5-2 [111 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 libncurses-dev i386 6.5-2 [380 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 libopenmpi3t64 i386 4.1.6-13.3 [2626 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 openmpi-common all 4.1.6-13.3 [169 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1 [915 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 openmpi-bin i386 4.1.6-13.3 [198 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 libopenmpi-dev i386 4.1.6-13.3 [1020 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 libpkgconf3 i386 1.8.1-1+b2 [38.5 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-4 [171 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 libreadline-dev i386 8.2-4 [164 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 mpi-default-dev i386 1.15 [3152 B] Get: 109 http://deb.debian.org/debian unstable/main i386 pkgconf-bin i386 1.8.1-1+b2 [30.2 kB] Get: 110 http://deb.debian.org/debian unstable/main i386 pkgconf i386 1.8.1-1+b2 [26.2 kB] Get: 111 http://deb.debian.org/debian unstable/main i386 pkg-config i386 1.8.1-1+b2 [14.0 kB] Fetched 131 MB in 3s (44.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19686 files and directories currently installed.) Preparing to unpack .../000-autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package readline-common. Preparing to unpack .../001-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package sensible-utils. 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Unpacking libxml2:i386 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../039-gettext_0.21-14+b1_i386.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../040-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 .../041-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../042-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libgfortran5:i386. Preparing to unpack .../043-libgfortran5_14.1.0-1_i386.deb ... Unpacking libgfortran5:i386 (14.1.0-1) ... Selecting previously unselected package libgfortran-13-dev:i386. Preparing to unpack .../044-libgfortran-13-dev_13.2.0-25_i386.deb ... Unpacking libgfortran-13-dev:i386 (13.2.0-25) ... Selecting previously unselected package gfortran-13-i686-linux-gnu. Preparing to unpack .../045-gfortran-13-i686-linux-gnu_13.2.0-25_i386.deb ... Unpacking gfortran-13-i686-linux-gnu (13.2.0-25) ... Selecting previously unselected package gfortran-13. Preparing to unpack .../046-gfortran-13_13.2.0-25_i386.deb ... Unpacking gfortran-13 (13.2.0-25) ... Selecting previously unselected package libnl-3-200:i386. Preparing to unpack .../047-libnl-3-200_3.7.0-0.3_i386.deb ... Unpacking libnl-3-200:i386 (3.7.0-0.3) ... Selecting previously unselected package libnl-route-3-200:i386. Preparing to unpack .../048-libnl-route-3-200_3.7.0-0.3_i386.deb ... Unpacking libnl-route-3-200:i386 (3.7.0-0.3) ... Selecting previously unselected package libibverbs1:i386. Preparing to unpack .../049-libibverbs1_50.0-2+b1_i386.deb ... Unpacking libibverbs1:i386 (50.0-2+b1) ... Selecting previously unselected package ibverbs-providers:i386. Preparing to unpack .../050-ibverbs-providers_50.0-2+b1_i386.deb ... Unpacking ibverbs-providers:i386 (50.0-2+b1) ... Selecting previously unselected package libclang-common-17-dev:i386. Preparing to unpack .../051-libclang-common-17-dev_1%3a17.0.6-12_i386.deb ... Unpacking libclang-common-17-dev:i386 (1:17.0.6-12) ... Selecting previously unselected package libz3-4:i386. Preparing to unpack .../052-libz3-4_4.8.12-3.1+b2_i386.deb ... Unpacking libz3-4:i386 (4.8.12-3.1+b2) ... Selecting previously unselected package libllvm17t64:i386. Preparing to unpack .../053-libllvm17t64_1%3a17.0.6-12_i386.deb ... Unpacking libllvm17t64:i386 (1:17.0.6-12) ... Selecting previously unselected package libclang-cpp17t64. Preparing to unpack .../054-libclang-cpp17t64_1%3a17.0.6-12_i386.deb ... Unpacking libclang-cpp17t64 (1:17.0.6-12) ... Selecting previously unselected package libclc-17-dev. Preparing to unpack .../055-libclc-17-dev_1%3a17.0.6-12_all.deb ... Unpacking libclc-17-dev (1:17.0.6-12) ... Selecting previously unselected package libclc-17. Preparing to unpack .../056-libclc-17_1%3a17.0.6-12_all.deb ... Unpacking libclc-17 (1:17.0.6-12) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../057-libdrm-common_2.4.120-2_all.deb ... Unpacking libdrm-common (2.4.120-2) ... Selecting previously unselected package libdrm2:i386. Preparing to unpack .../058-libdrm2_2.4.120-2_i386.deb ... Unpacking libdrm2:i386 (2.4.120-2) ... Selecting previously unselected package libdrm-amdgpu1:i386. Preparing to unpack .../059-libdrm-amdgpu1_2.4.120-2_i386.deb ... Unpacking libdrm-amdgpu1:i386 (2.4.120-2) ... Selecting previously unselected package libdrm-nouveau2:i386. Preparing to unpack .../060-libdrm-nouveau2_2.4.120-2_i386.deb ... Unpacking libdrm-nouveau2:i386 (2.4.120-2) ... Selecting previously unselected package libdrm-radeon1:i386. Preparing to unpack .../061-libdrm-radeon1_2.4.120-2_i386.deb ... Unpacking libdrm-radeon1:i386 (2.4.120-2) ... Selecting previously unselected package libevent-2.1-7t64:i386. Preparing to unpack .../062-libevent-2.1-7t64_2.1.12-stable-8.1+b3_i386.deb ... Unpacking libevent-2.1-7t64:i386 (2.1.12-stable-8.1+b3) ... Selecting previously unselected package libevent-core-2.1-7t64:i386. Preparing to unpack .../063-libevent-core-2.1-7t64_2.1.12-stable-8.1+b3_i386.deb ... Unpacking libevent-core-2.1-7t64:i386 (2.1.12-stable-8.1+b3) ... Selecting previously unselected package libevent-extra-2.1-7t64:i386. Preparing to unpack .../064-libevent-extra-2.1-7t64_2.1.12-stable-8.1+b3_i386.deb ... Unpacking libevent-extra-2.1-7t64:i386 (2.1.12-stable-8.1+b3) ... Selecting previously unselected package libevent-pthreads-2.1-7t64:i386. Preparing to unpack .../065-libevent-pthreads-2.1-7t64_2.1.12-stable-8.1+b3_i386.deb ... Unpacking libevent-pthreads-2.1-7t64:i386 (2.1.12-stable-8.1+b3) ... Selecting previously unselected package libevent-openssl-2.1-7t64:i386. Preparing to unpack .../066-libevent-openssl-2.1-7t64_2.1.12-stable-8.1+b3_i386.deb ... Unpacking libevent-openssl-2.1-7t64:i386 (2.1.12-stable-8.1+b3) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../067-libevent-dev_2.1.12-stable-8.1+b3_i386.deb ... Unpacking libevent-dev (2.1.12-stable-8.1+b3) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../068-libexpat1_2.6.2-1_i386.deb ... Unpacking libexpat1:i386 (2.6.2-1) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../069-libpsm-infinipath1_3.3+20.604758e7-6.3_i386.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3) ... Selecting previously unselected package librdmacm1t64:i386. Preparing to unpack .../070-librdmacm1t64_50.0-2+b1_i386.deb ... Unpacking librdmacm1t64:i386 (50.0-2+b1) ... Selecting previously unselected package libfabric1:i386. Preparing to unpack .../071-libfabric1_1.17.0-3+b1_i386.deb ... Unpacking libfabric1:i386 (1.17.0-3+b1) ... Selecting previously unselected package ocl-icd-libopencl1:i386. Preparing to unpack .../072-ocl-icd-libopencl1_2.3.2-1+b1_i386.deb ... Unpacking ocl-icd-libopencl1:i386 (2.3.2-1+b1) ... Selecting previously unselected package libllvmspirvlib17:i386. Preparing to unpack .../073-libllvmspirvlib17_17.0.0-5_i386.deb ... Unpacking libllvmspirvlib17:i386 (17.0.0-5) ... Selecting previously unselected package mesa-opencl-icd:i386. Preparing to unpack .../074-mesa-opencl-icd_24.0.7-1_i386.deb ... Unpacking mesa-opencl-icd:i386 (24.0.7-1) ... Selecting previously unselected package libhmsbeagle1v5:i386. Preparing to unpack .../075-libhmsbeagle1v5_3.1.2+dfsg-13+b1_i386.deb ... Unpacking libhmsbeagle1v5:i386 (3.1.2+dfsg-13+b1) ... Selecting previously unselected package libhmsbeagle-dev. Preparing to unpack .../076-libhmsbeagle-dev_3.1.2+dfsg-13+b1_i386.deb ... Unpacking libhmsbeagle-dev (3.1.2+dfsg-13+b1) ... Selecting previously unselected package libhwloc15:i386. Preparing to unpack .../077-libhwloc15_2.10.0-1+b1_i386.deb ... Unpacking libhwloc15:i386 (2.10.0-1+b1) ... Selecting previously unselected package libnuma1:i386. Preparing to unpack .../078-libnuma1_2.0.18-1_i386.deb ... Unpacking libnuma1:i386 (2.0.18-1) ... Selecting previously unselected package libnuma-dev:i386. Preparing to unpack .../079-libnuma-dev_2.0.18-1_i386.deb ... Unpacking libnuma-dev:i386 (2.0.18-1) ... Selecting previously unselected package libltdl7:i386. Preparing to unpack .../080-libltdl7_2.4.7-7+b1_i386.deb ... Unpacking libltdl7:i386 (2.4.7-7+b1) ... Selecting previously unselected package libltdl-dev:i386. Preparing to unpack .../081-libltdl-dev_2.4.7-7+b1_i386.deb ... Unpacking libltdl-dev:i386 (2.4.7-7+b1) ... Selecting previously unselected package libhwloc-dev:i386. Preparing to unpack .../082-libhwloc-dev_2.10.0-1+b1_i386.deb ... Unpacking libhwloc-dev:i386 (2.10.0-1+b1) ... Selecting previously unselected package libpciaccess0:i386. Preparing to unpack .../083-libpciaccess0_0.17-3+b1_i386.deb ... Unpacking libpciaccess0:i386 (0.17-3+b1) ... Selecting previously unselected package libxau6:i386. Preparing to unpack .../084-libxau6_1%3a1.0.9-1+b1_i386.deb ... Unpacking libxau6:i386 (1:1.0.9-1+b1) ... Selecting previously unselected package libxdmcp6:i386. Preparing to unpack .../085-libxdmcp6_1%3a1.1.2-3+b1_i386.deb ... Unpacking libxdmcp6:i386 (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:i386. Preparing to unpack .../086-libxcb1_1.17.0-1_i386.deb ... Unpacking libxcb1:i386 (1.17.0-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../087-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:i386. Preparing to unpack .../088-libx11-6_2%3a1.8.7-1+b1_i386.deb ... Unpacking libx11-6:i386 (2:1.8.7-1+b1) ... 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Unpacking libibverbs-dev:i386 (50.0-2+b1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../095-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 .../096-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../097-libncurses6_6.5-2_i386.deb ... Unpacking libncurses6:i386 (6.5-2) ... Selecting previously unselected package libncurses-dev:i386. Preparing to unpack .../098-libncurses-dev_6.5-2_i386.deb ... Unpacking libncurses-dev:i386 (6.5-2) ... Selecting previously unselected package libopenmpi3t64:i386. Preparing to unpack .../099-libopenmpi3t64_4.1.6-13.3_i386.deb ... Unpacking libopenmpi3t64:i386 (4.1.6-13.3) ... Selecting previously unselected package openmpi-common. 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Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-4) ... Selecting previously unselected package libreadline-dev:i386. Preparing to unpack .../106-libreadline-dev_8.2-4_i386.deb ... Unpacking libreadline-dev:i386 (8.2-4) ... Selecting previously unselected package mpi-default-dev. Preparing to unpack .../107-mpi-default-dev_1.15_i386.deb ... Unpacking mpi-default-dev (1.15) ... Selecting previously unselected package pkgconf-bin. 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Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:i386 (2.1.12-stable-8.1+b3) ... Setting up autoconf-archive (20220903-3) ... Setting up libcom-err2:i386 (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:i386 (0.191-1+b1) ... Setting up libkrb5support0:i386 (1.20.1-6+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:i386 (4.8.12-3.1+b2) ... Setting up libpkgconf3:i386 (1.8.1-1+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libclc-17-dev (1:17.0.6-12) ... Setting up libncurses6:i386 (6.5-2) ... Setting up libhwloc15:i386 (2.10.0-1+b1) ... Setting up autopoint (0.21-14) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libk5crypto3:i386 (1.20.1-6+b1) ... Setting up libltdl7:i386 (2.4.7-7+b1) ... Setting up libgfortran5:i386 (14.1.0-1) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1) ... Setting up libnuma1:i386 (2.0.18-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up ocl-icd-libopencl1:i386 (2.3.2-1+b1) ... Setting up libclang-common-17-dev:i386 (1:17.0.6-12) ... Setting up libclc-17 (1:17.0.6-12) ... Setting up libuchardet0:i386 (0.0.8-1+b1) ... Setting up libnl-3-200:i386 (3.7.0-0.3) ... Setting up openmpi-common (4.1.6-13.3) ... Setting up libsub-override-perl (0.10-1) ... Setting up libkrb5-3:i386 (1.20.1-6+b1) ... Setting up libevent-core-2.1-7t64:i386 (2.1.12-stable-8.1+b3) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/i386-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:i386 (1.14.0-1+b2) ... Setting up libgfortran-13-dev:i386 (13.2.0-25) ... Setting up libbsd0:i386 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up readline-common (8.2-4) ... 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Setting up libllvm17t64:i386 (1:17.0.6-12) ... Setting up gfortran-13 (13.2.0-25) ... Setting up libgssapi-krb5-2:i386 (1.20.1-6+b1) ... Setting up pkg-config:i386 (1.8.1-1+b2) ... Setting up libevent-extra-2.1-7t64:i386 (2.1.12-stable-8.1+b3) ... Setting up libreadline8t64:i386 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:i386 (2.4.120-2) ... Setting up libnl-3-dev:i386 (3.7.0-0.3) ... Setting up groff-base (1.23.0-4) ... Setting up libx11-6:i386 (2:1.8.7-1+b1) ... Setting up libhwloc-dev:i386 (2.10.0-1+b1) ... Setting up libllvmspirvlib17:i386 (17.0.0-5) ... Setting up libdrm-amdgpu1:i386 (2.4.120-2) ... Setting up libibverbs1:i386 (50.0-2+b1) ... Setting up libdrm-nouveau2:i386 (2.4.120-2) ... Setting up ibverbs-providers:i386 (50.0-2+b1) ... Setting up libdrm-radeon1:i386 (2.4.120-2) ... Setting up openssh-client (1:9.7p1-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up libreadline-dev:i386 (8.2-4) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:i386 (535.171.04-1) ... Setting up libclang-cpp17t64 (1:17.0.6-12) ... Setting up libnl-route-3-dev:i386 (3.7.0-0.3) ... Setting up libevent-dev (2.1.12-stable-8.1+b3) ... Setting up librdmacm1t64:i386 (50.0-2+b1) ... Setting up mesa-opencl-icd:i386 (24.0.7-1) ... Setting up libfabric1:i386 (1.17.0-3+b1) ... Setting up libhmsbeagle1v5:i386 (3.1.2+dfsg-13+b1) ... Setting up debhelper (13.15.3) ... Setting up libibverbs-dev:i386 (50.0-2+b1) ... Setting up libhwloc-plugins:i386 (2.10.0-1+b1) ... Setting up libopenmpi3t64:i386 (4.1.6-13.3) ... 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 libhmsbeagle-dev (3.1.2+dfsg-13+b1) ... Setting up libopenmpi-dev:i386 (4.1.6-13.3) ... update-alternatives: using /usr/lib/i386-linux-gnu/openmpi/include to provide /usr/include/i386-linux-gnu/mpi (mpi-i386-linux-gnu) in auto mode Setting up mpi-default-dev (1.15) ... Processing triggers for libc-bin (2.38-11) ... 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 i386 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead 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=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-beagle=/usr --enable-mpi=yes --enable-debug=yes 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 whether to enable maintainer-specific portions of Makefiles... no checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-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... yes checking for C compiler vendor... gnu checking for a sed that does not truncate output... /usr/bin/sed checking for C compiler version... 13.2.0 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 -j22 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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c 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, from utils.c:38: In function 'strncpy', inlined from 'CopyResults' at utils.c:311:9: /usr/include/i386-linux-gnu/bits/string_fortified.h:95:10: warning: '__builtin_strncpy' accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-Wrestrict] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'strncpy', inlined from 'CopyProcessSsFile' at utils.c:350:9: /usr/include/i386-linux-gnu/bits/string_fortified.h:95:10: warning: '__builtin_strncpy' accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-Wrestrict] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'strncpy', inlined from 'CopyTreeResults' at utils.c:422:9: /usr/include/i386-linux-gnu/bits/string_fortified.h:95:10: warning: '__builtin_strncpy' accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-Wrestrict] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __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:964, from bayes.h:32, from sumpt.c:38: In function 'sprintf', inlined from 'DoCompRefTree' at sumpt.c:4612:13: /usr/include/i386-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/i386-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/i386-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/i386-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:964, from bayes.h:32, from mcmc.c:45: In function 'sprintf', inlined from 'ReopenMBPrintFiles' at mcmc.c:15467:17: /usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ 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); | ^ 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/i386-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 ()); | ~~~~~~~~~~~~~~~~~ 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:964, from bayes.h:32, from model.c:38: In function 'sprintf', inlined from 'SetModelParams' at model.c:19111:21: /usr/include/i386-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 -Wformat -Werror=format-security -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' test -z "mb" || 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=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-beagle=/usr --enable-mpi=no --enable-debug=yes 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 whether to enable maintainer-specific portions of Makefiles... no checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-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... yes checking for C compiler vendor... gnu checking for a sed that does not truncate output... /usr/bin/sed checking for C compiler version... 13.2.0 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 -j22 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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c 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, from utils.c:38: In function 'strncpy', inlined from 'CopyResults' at utils.c:311:9: /usr/include/i386-linux-gnu/bits/string_fortified.h:95:10: warning: '__builtin_strncpy' accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-Wrestrict] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'strncpy', inlined from 'CopyProcessSsFile' at utils.c:350:9: /usr/include/i386-linux-gnu/bits/string_fortified.h:95:10: warning: '__builtin_strncpy' accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-Wrestrict] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'strncpy', inlined from 'CopyTreeResults' at utils.c:422:9: /usr/include/i386-linux-gnu/bits/string_fortified.h:95:10: warning: '__builtin_strncpy' accessing 0 or more bytes at offsets [-1073741824, 1073741823] and 0 may overlap up to 1073741824 bytes at offset [0, 1073741823] [-Wrestrict] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __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:964, from bayes.h:32, from sumpt.c:38: In function 'sprintf', inlined from 'DoCompRefTree' at sumpt.c:4612:13: /usr/include/i386-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/i386-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/i386-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/i386-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:964, from bayes.h:32, from mcmc.c:45: In function 'sprintf', inlined from 'ReopenMBPrintFiles' at mcmc.c:15467:17: /usr/include/i386-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 ()); | ~~~~~~~~~~~~~~~~~ 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); | ^ 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/i386-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 ()); | ~~~~~~~~~~~~~~~~~ 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:964, from bayes.h:32, from model.c:38: In function 'sprintf', inlined from 'SetModelParams' at model.c:19111:21: /usr/include/i386-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 -Wformat -Werror=format-security -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 -j22 check "TESTSUITEFLAGS=-j22 --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 -Wformat -Werror=format-security -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 -j22 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libreadline8t64 from: /lib/i386-linux-gnu/libreadline.so.8 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libreadline8t64 to: /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged diversion by libreadline8t64 from: /lib/i386-linux-gnu/libreadline.so.8 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libreadline8t64 to: /lib/i386-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_i386.deb'. dpkg-deb: building package 'mrbayes-dbgsym' in '../mrbayes-dbgsym_3.2.7a-7_i386.deb'. dpkg-deb: building package 'mrbayes-mpi' in '../mrbayes-mpi_3.2.7a-7_i386.deb'. dpkg-deb: building package 'mrbayes-mpi-dbgsym' in '../mrbayes-mpi-dbgsym_3.2.7a-7_i386.deb'. dpkg-deb: building package 'mrbayes-doc' in '../mrbayes-doc_3.2.7a-7_all.deb'. dpkg-genbuildinfo --build=binary -O../mrbayes_3.2.7a-7_i386.buildinfo dpkg-genchanges --build=binary -O../mrbayes_3.2.7a-7_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/49548 and its subdirectories I: Current time: Tue Jun 17 14:49:07 -12 2025 I: pbuilder-time-stamp: 1750214947 Wed May 15 20:26:09 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net. Wed May 15 20:26:09 UTC 2024 I: Preparing to do remote build '2' on ionos2-i386.debian.net. Wed May 15 20:29:20 UTC 2024 I: Deleting $TMPDIR on ionos2-i386.debian.net. Wed May 15 20:29:21 UTC 2024 I: mrbayes_3.2.7a-7_i386.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: i386 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: 496537e35b6a34db7e05912b904071eb137b502f 901872 mrbayes-dbgsym_3.2.7a-7_i386.deb 40070e1dee394b744ab432d75df7504da4ef3c58 1329088 mrbayes-doc_3.2.7a-7_all.deb ea2f882a861020d6b720bd05fd41acea06be16f3 972 mrbayes-mpi-dbgsym_3.2.7a-7_i386.deb e6ddfe59e95ea8e25651a4b91beaa519ecfa5254 618932 mrbayes-mpi_3.2.7a-7_i386.deb 420d165c0200553ffcdc9b14225fe3891410ed3d 8603 mrbayes_3.2.7a-7_i386.buildinfo a76739bf3493ccb4a8af69d515760e0ef1e72e02 681848 mrbayes_3.2.7a-7_i386.deb Checksums-Sha256: 85e8108b226de1de12b22e9cb1e84af70b594d91c5c07308b1a4fdbaa2fad639 901872 mrbayes-dbgsym_3.2.7a-7_i386.deb d517b4918e8e90f7d3d104fc315af1fd0da30aa7b8d47f04c8be55db0df1ac4b 1329088 mrbayes-doc_3.2.7a-7_all.deb e8a747365e8e5cff9c9decef93d8911e468eff3b69356f2d67d66dc9720baf0f 972 mrbayes-mpi-dbgsym_3.2.7a-7_i386.deb f1ecdf3dcf53ef98270628ae1d615918279301def0c2f24933605efbba4b9579 618932 mrbayes-mpi_3.2.7a-7_i386.deb f830a0701bb6d820ba06ab9e7f022bc050c6789b05bb2c52945ae9111a54aa13 8603 mrbayes_3.2.7a-7_i386.buildinfo b14f50323fc3306f0ac29319b156ede223c0987463f8163bf2ada2fb1c4bb695 681848 mrbayes_3.2.7a-7_i386.deb Files: f410993d56b402febd1d8c2c5dce01e3 901872 debug optional mrbayes-dbgsym_3.2.7a-7_i386.deb 40ef7277af5465fba89ea91467cd0a4a 1329088 doc optional mrbayes-doc_3.2.7a-7_all.deb e43528d70e5f57319a268b980e032731 972 debug optional mrbayes-mpi-dbgsym_3.2.7a-7_i386.deb ab66516ec81d4d577ced874efa644ec7 618932 science optional mrbayes-mpi_3.2.7a-7_i386.deb 72fd88a61f72c537c1511336e5a9d7d8 8603 science optional mrbayes_3.2.7a-7_i386.buildinfo 4caa20b41112b18622d7e89e057d265e 681848 science optional mrbayes_3.2.7a-7_i386.deb Wed May 15 20:29:28 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_2-24079.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.oN8EeHke/mrbayes_3.2.7a-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.oN8EeHke/mrbayes_3.2.7a-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.oN8EeHke/mrbayes_3.2.7a-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.oN8EeHke/b1/mrbayes_3.2.7a-7_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.oN8EeHke/b2/mrbayes_3.2.7a-7_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.423s) 0.423s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.057s) 0.057s 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: 789ms CPU time consumed: 788ms Wed May 15 20:29:30 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Wed May 15 20:29:30 UTC 2024 I: mrbayes from unstable built successfully and reproducibly on i386. Wed May 15 20:29:32 UTC 2024 I: Submitting .buildinfo files to external archives: Wed May 15 20:29:32 UTC 2024 I: Submitting 12K b1/mrbayes_3.2.7a-7_i386.buildinfo.asc Wed May 15 20:29:34 UTC 2024 I: Submitting 12K b2/mrbayes_3.2.7a-7_i386.buildinfo.asc Wed May 15 20:29:34 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 15 20:29:34 UTC 2024 I: Done submitting .buildinfo files. Wed May 15 20:29:34 UTC 2024 I: Removing signed mrbayes_3.2.7a-7_i386.buildinfo.asc files: removed './b1/mrbayes_3.2.7a-7_i386.buildinfo.asc' removed './b2/mrbayes_3.2.7a-7_i386.buildinfo.asc'