Tue Apr 18 10:21:27 UTC 2023 I: starting to build mrbayes/bookworm/i386 on jenkins on '2023-04-18 10:21' Tue Apr 18 10:21:27 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_4/12469/console.log Tue Apr 18 10:21:27 UTC 2023 I: Downloading source for bookworm/mrbayes=3.2.7a-6 --2023-04-18 10:21:27-- http://cdn-fastly.deb.debian.org/debian/pool/main/m/mrbayes/mrbayes_3.2.7a-6.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2184 (2.1K) [text/prs.lines.tag] Saving to: ‘mrbayes_3.2.7a-6.dsc’ 0K .. 100% 120M=0s 2023-04-18 10:21:27 (120 MB/s) - ‘mrbayes_3.2.7a-6.dsc’ saved [2184/2184] Tue Apr 18 10:21:27 UTC 2023 I: mrbayes_3.2.7a-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: mrbayes Binary: mrbayes, mrbayes-mpi, mrbayes-doc Architecture: any all Version: 3.2.7a-6 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Homepage: http://mrbayes.csit.fsu.edu/ Standards-Version: 4.6.1 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 8b9526bc52c293a5a630d8fd0f8baeddc93566ab 7304 mrbayes_3.2.7a-6.debian.tar.xz Checksums-Sha256: 3eed2e3b1d9e46f265b6067a502a89732b6f430585d258b886e008e846ecc5c6 9819346 mrbayes_3.2.7a.orig.tar.gz e27a201610c459f77ab22877ee7fd00def16562d41970e75eed28600a5497d9a 7304 mrbayes_3.2.7a-6.debian.tar.xz Files: 504236626ce9a2de1066a8520672f0cc 9819346 mrbayes_3.2.7a.orig.tar.gz 30acb34b134a17b7764ece286f625c35 7304 mrbayes_3.2.7a-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmN/XNkRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEIFQ//TRR2tKxTq5zpiGUVxz++cKD43BLU7nJb KgPF/G/hG7w8QTrWT1WUMrJk+mDblG1ZLmaiGOAwsfD/Ur2tvaEP42r5/P3rtx9u zL2coQnpWMWawoYpvW6upUIwOPW/IOcIEscvGPDsiDajqo5kzYKuPudRuaicw1ET UBCzzs/6JwJYkVJiCrLO0YVmqr7kK+EKOVlF7Ip01syEfMjawzujdJBI7sC/nNNr xp4+iF6Ye07yD+v619ABmxWayWrQ5BFyXFo7kgolWnbYIrqTyv2EnYBPrTK9KWYi 5nZTrilKx6yQZ7uamsaQl7AKwQ7f0hlEfdNqWXn3Vh7L46SKK8isI96YiqnwCko1 1Mi10slsPedi+jVM0O9uH1vtA2ABAKkE1kteQLAgWsGD6HfcllTybq59RztpRQZv tgVXHUwzyzZurr2kuHGTDNIddH/eqNUNDNZVHWAlUQ5LYI/M7SJdkEVNwrVRion4 PVvb+ggjoc+6Bw3csA0AzKR1VFOAfAufitbQkTKMciZI7/Iy3s5O8ddSwhzBiX4/ KlTj5jrIQ15EFC7A7s16q2nQAF7ffaaRbEamB6RxLv1x3eNkSd7pWoEXyHj67hzd TV4pnaQb6Tr851WWV4XFfqUbcGb7ezQchWHmXRRng+x9DH6C97Cz+JcFD27CB06R SUfsYkGIjUc= =9aTW -----END PGP SIGNATURE----- Tue Apr 18 10:21:27 UTC 2023 I: Checking whether the package is not for us Tue Apr 18 10:21:27 UTC 2023 I: Starting 1st build on remote node ionos16-i386.debian.net. Tue Apr 18 10:21:27 UTC 2023 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Tue Apr 18 10:23:48 UTC 2023 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon May 20 04:44:29 -12 2024 I: pbuilder-time-stamp: 1716223469 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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-6.dsc] I: copying [./mrbayes_3.2.7a.orig.tar.gz] I: copying [./mrbayes_3.2.7a-6.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Nov 24 00:00:25 2022 -12 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-6.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-6.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/4842/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=16' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='e61d919955e74e669ec4c46bf8dbf8af' 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='4842' 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.i20pI8E9/pbuilderrc_AyNA --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.i20pI8E9/b1 --logfile b1/build.log mrbayes_3.2.7a-6.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://85.184.249.68:3128' I: uname -a Linux ionos16-i386 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Feb 12 2023 bash -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash -rwxr-xr-x 1 root root 137160 Sep 20 2022 date -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd -rwxr-xr-x 1 root root 108940 Sep 20 2022 df -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir -rwxr-xr-x 1 root root 87760 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 84272 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln -rwxr-xr-x 1 root root 55600 Mar 22 2023 login -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls -rwxr-xr-x 1 root root 214568 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 22 2023 more -rwsr-xr-x 1 root root 58912 Mar 22 2023 mount -rwxr-xr-x 1 root root 13856 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty -rwsr-xr-x 1 root root 83492 Mar 22 2023 su -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar -rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch -rwxr-xr-x 1 root root 34664 Sep 20 2022 true -rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 22 2023 umount -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/4842/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 ... 19604 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-12{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} lib64atomic1{a} lib64gcc-s1{a} lib64stdc++6{a} libarchive-zip-perl{a} libbsd0{a} libc6-amd64{a} libcbor0.8{a} libclang-common-15-dev{a} libclang-cpp15{a} libclc-15{a} libclc-15-dev{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libelf1{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-12-dev{a} libgfortran5{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} libllvm15{a} libllvmspirvlib15{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{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} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2{a} libpsm-infinipath1{a} librdmacm1{a} libreadline-dev{a} libreadline8{a} libsensors-config{a} libsensors5{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 libarchive-cpio-perl libcoarrays-openmpi-dev libgpm2 libmail-sendmail-perl lynx wget xauth 0 packages upgraded, 113 newly installed, 0 to remove and 0 not upgraded. Need to get 133 MB of archives. After unpacking 663 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 libedit2 i386 3.1-20221030-2 [97.2 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 libcbor0.8 i386 0.8.0-2+b1 [29.8 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 libfido2-1 i386 1.12.0-2+b1 [87.0 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 openssh-client i386 1:9.2p1-2 [1004 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 28 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 30 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.1+b3 [720 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 libgfortran5 i386 12.2.0-14 [698 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 libgfortran-12-dev i386 12.2.0-14 [761 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 gfortran-12 i386 12.2.0-14 [10.5 MB] Get: 41 http://deb.debian.org/debian bookworm/main i386 libnl-3-200 i386 3.7.0-0.2+b1 [66.2 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 libnl-route-3-200 i386 3.7.0-0.2+b1 [196 kB] Get: 43 http://deb.debian.org/debian bookworm/main i386 libibverbs1 i386 44.0-2 [65.8 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 ibverbs-providers i386 44.0-2 [368 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 libc6-amd64 i386 2.36-9 [2584 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 lib64atomic1 i386 12.2.0-14 [9292 B] Get: 47 http://deb.debian.org/debian bookworm/main i386 lib64gcc-s1 i386 12.2.0-14 [49.7 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 lib64stdc++6 i386 12.2.0-14 [594 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 libz3-4 i386 4.8.12-3.1 [7853 kB] Get: 50 http://deb.debian.org/debian bookworm/main i386 libllvm15 i386 1:15.0.6-4+b1 [26.5 MB] Get: 51 http://deb.debian.org/debian bookworm/main i386 libclang-common-15-dev i386 1:15.0.6-4+b1 [5935 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 libclang-cpp15 i386 1:15.0.6-4+b1 [13.3 MB] Get: 53 http://deb.debian.org/debian bookworm/main i386 libclc-15-dev all 1:15.0.6-4 [53.6 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 libclc-15 all 1:15.0.6-4 [10.1 MB] Get: 55 http://deb.debian.org/debian bookworm/main i386 libdrm-common all 2.4.114-1 [7112 B] Get: 56 http://deb.debian.org/debian bookworm/main i386 libdrm2 i386 2.4.114-1+b1 [40.8 kB] Get: 57 http://deb.debian.org/debian bookworm/main i386 libdrm-amdgpu1 i386 2.4.114-1+b1 [24.1 kB] Get: 58 http://deb.debian.org/debian bookworm/main i386 libdrm-nouveau2 i386 2.4.114-1+b1 [20.7 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 libdrm-radeon1 i386 2.4.114-1+b1 [22.8 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 libevent-2.1-7 i386 2.1.12-stable-8 [194 kB] Get: 61 http://deb.debian.org/debian bookworm/main i386 libevent-core-2.1-7 i386 2.1.12-stable-8 [139 kB] Get: 62 http://deb.debian.org/debian bookworm/main i386 libevent-extra-2.1-7 i386 2.1.12-stable-8 [112 kB] Get: 63 http://deb.debian.org/debian bookworm/main i386 libevent-pthreads-2.1-7 i386 2.1.12-stable-8 [53.7 kB] Get: 64 http://deb.debian.org/debian bookworm/main i386 libevent-openssl-2.1-7 i386 2.1.12-stable-8 [61.5 kB] Get: 65 http://deb.debian.org/debian bookworm/main i386 libevent-dev i386 2.1.12-stable-8 [325 kB] Get: 66 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB] Get: 67 http://deb.debian.org/debian bookworm/main i386 libpsm-infinipath1 i386 3.3+20.604758e7-6.2 [177 kB] Get: 68 http://deb.debian.org/debian bookworm/main i386 librdmacm1 i386 44.0-2 [74.6 kB] Get: 69 http://deb.debian.org/debian bookworm/main i386 libfabric1 i386 1.17.0-3 [538 kB] Get: 70 http://deb.debian.org/debian bookworm/main i386 ocl-icd-libopencl1 i386 2.3.1-1 [45.4 kB] Get: 71 http://deb.debian.org/debian bookworm/main i386 libllvmspirvlib15 i386 15.0.0-1 [906 kB] Get: 72 http://deb.debian.org/debian bookworm/main i386 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 73 http://deb.debian.org/debian bookworm/main i386 libsensors5 i386 1:3.6.0-7.1 [35.1 kB] Get: 74 http://deb.debian.org/debian bookworm/main i386 mesa-opencl-icd i386 22.3.6-1+deb12u1 [18.2 MB] Get: 75 http://deb.debian.org/debian bookworm/main i386 libhmsbeagle1v5 i386 3.1.2+dfsg-13 [105 kB] Get: 76 http://deb.debian.org/debian bookworm/main i386 libhmsbeagle-dev i386 3.1.2+dfsg-13 [232 kB] Get: 77 http://deb.debian.org/debian bookworm/main i386 libhwloc15 i386 2.9.0-1 [168 kB] Get: 78 http://deb.debian.org/debian bookworm/main i386 libnuma1 i386 2.0.16-1 [22.7 kB] Get: 79 http://deb.debian.org/debian bookworm/main i386 libnuma-dev i386 2.0.16-1 [37.3 kB] Get: 80 http://deb.debian.org/debian bookworm/main i386 libltdl7 i386 2.4.7-5 [394 kB] Get: 81 http://deb.debian.org/debian bookworm/main i386 libltdl-dev i386 2.4.7-5 [167 kB] Get: 82 http://deb.debian.org/debian bookworm/main i386 libhwloc-dev i386 2.9.0-1 [259 kB] Get: 83 http://deb.debian.org/debian bookworm/main i386 libpciaccess0 i386 0.17-2 [53.4 kB] Get: 84 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 85 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 86 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 87 http://deb.debian.org/debian bookworm/main i386 libx11-data all 2:1.8.4-2 [292 kB] Get: 88 http://deb.debian.org/debian bookworm/main i386 libx11-6 i386 2:1.8.4-2 [782 kB] Get: 89 http://deb.debian.org/debian bookworm/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 90 http://deb.debian.org/debian bookworm/main i386 libxnvctrl0 i386 525.85.05-1 [13.3 kB] Get: 91 http://deb.debian.org/debian bookworm/main i386 libhwloc-plugins i386 2.9.0-1 [17.8 kB] Get: 92 http://deb.debian.org/debian bookworm/main i386 libnl-3-dev i386 3.7.0-0.2+b1 [109 kB] Get: 93 http://deb.debian.org/debian bookworm/main i386 libnl-route-3-dev i386 3.7.0-0.2+b1 [226 kB] Get: 94 http://deb.debian.org/debian bookworm/main i386 libibverbs-dev i386 44.0-2 [683 kB] Get: 95 http://deb.debian.org/debian bookworm/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 96 http://deb.debian.org/debian bookworm/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 97 http://deb.debian.org/debian bookworm/main i386 libmunge2 i386 0.5.15-2 [20.3 kB] Get: 98 http://deb.debian.org/debian bookworm/main i386 libncurses6 i386 6.4-2 [111 kB] Get: 99 http://deb.debian.org/debian bookworm/main i386 libncurses-dev i386 6.4-2 [379 kB] Get: 100 http://deb.debian.org/debian bookworm/main i386 libpmix2 i386 4.2.2-1+b1 [652 kB] Get: 101 http://deb.debian.org/debian bookworm/main i386 libopenmpi3 i386 4.1.4-3+b1 [2183 kB] Get: 102 http://deb.debian.org/debian bookworm/main i386 openmpi-common all 4.1.4-3 [167 kB] Get: 103 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB] Get: 104 http://deb.debian.org/debian bookworm/main i386 libpmix-dev i386 4.2.2-1+b1 [975 kB] Get: 105 http://deb.debian.org/debian bookworm/main i386 openmpi-bin i386 4.1.4-3+b1 [196 kB] Get: 106 http://deb.debian.org/debian bookworm/main i386 libopenmpi-dev i386 4.1.4-3+b1 [920 kB] Get: 107 http://deb.debian.org/debian bookworm/main i386 libpkgconf3 i386 1.8.1-1 [38.3 kB] Get: 108 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB] Get: 109 http://deb.debian.org/debian bookworm/main i386 libreadline-dev i386 8.2-1.3 [164 kB] Get: 110 http://deb.debian.org/debian bookworm/main i386 mpi-default-dev i386 1.14 [5552 B] Get: 111 http://deb.debian.org/debian bookworm/main i386 pkgconf-bin i386 1.8.1-1 [29.8 kB] Get: 112 http://deb.debian.org/debian bookworm/main i386 pkgconf i386 1.8.1-1 [25.9 kB] Get: 113 http://deb.debian.org/debian bookworm/main i386 pkg-config i386 1.8.1-1 [13.7 kB] Fetched 133 MB in 2s (61.8 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 ... 19604 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_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.44-3_i386.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../004-libmagic1_1%3a5.44-3_i386.deb ... Unpacking libmagic1:i386 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.44-3_i386.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.21-12_i386.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../007-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.22.4-10_i386.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.38.1-5+b1_i386.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../010-libpipeline1_1.5.7-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.11.2-2_i386.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../012-libbsd0_0.11.7-2_i386.deb ... Unpacking libbsd0:i386 (0.11.7-2) ... Selecting previously unselected package libedit2:i386. Preparing to unpack .../013-libedit2_3.1-20221030-2_i386.deb ... Unpacking libedit2:i386 (3.1-20221030-2) ... Selecting previously unselected package libcbor0.8:i386. Preparing to unpack .../014-libcbor0.8_0.8.0-2+b1_i386.deb ... Unpacking libcbor0.8:i386 (0.8.0-2+b1) ... Selecting previously unselected package libfido2-1:i386. Preparing to unpack .../015-libfido2-1_1.12.0-2+b1_i386.deb ... Unpacking libfido2-1:i386 (1.12.0-2+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../016-openssh-client_1%3a9.2p1-2_i386.deb ... Unpacking openssh-client (1:9.2p1-2) ... Selecting previously unselected package m4. Preparing to unpack .../017-m4_1.4.19-3_i386.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../018-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../019-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../020-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../021-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../022-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../023-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../024-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../025-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../026-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../027-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../028-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../029-libelf1_0.188-2.1_i386.deb ... Unpacking libelf1:i386 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../030-dwz_0.15-1_i386.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../031-libicu72_72.1-3_i386.deb ... Unpacking libicu72:i386 (72.1-3) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../032-libxml2_2.9.14+dfsg-1.1+b3_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../033-gettext_0.21-12_i386.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../034-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 .../035-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../036-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libgfortran5:i386. Preparing to unpack .../037-libgfortran5_12.2.0-14_i386.deb ... Unpacking libgfortran5:i386 (12.2.0-14) ... Selecting previously unselected package libgfortran-12-dev:i386. Preparing to unpack .../038-libgfortran-12-dev_12.2.0-14_i386.deb ... Unpacking libgfortran-12-dev:i386 (12.2.0-14) ... Selecting previously unselected package gfortran-12. Preparing to unpack .../039-gfortran-12_12.2.0-14_i386.deb ... Unpacking gfortran-12 (12.2.0-14) ... Selecting previously unselected package libnl-3-200:i386. Preparing to unpack .../040-libnl-3-200_3.7.0-0.2+b1_i386.deb ... Unpacking libnl-3-200:i386 (3.7.0-0.2+b1) ... Selecting previously unselected package libnl-route-3-200:i386. Preparing to unpack .../041-libnl-route-3-200_3.7.0-0.2+b1_i386.deb ... Unpacking libnl-route-3-200:i386 (3.7.0-0.2+b1) ... Selecting previously unselected package libibverbs1:i386. Preparing to unpack .../042-libibverbs1_44.0-2_i386.deb ... Unpacking libibverbs1:i386 (44.0-2) ... Selecting previously unselected package ibverbs-providers:i386. Preparing to unpack .../043-ibverbs-providers_44.0-2_i386.deb ... Unpacking ibverbs-providers:i386 (44.0-2) ... Selecting previously unselected package libc6-amd64. Preparing to unpack .../044-libc6-amd64_2.36-9_i386.deb ... Unpacking libc6-amd64 (2.36-9) ... Selecting previously unselected package lib64atomic1. Preparing to unpack .../045-lib64atomic1_12.2.0-14_i386.deb ... Unpacking lib64atomic1 (12.2.0-14) ... Selecting previously unselected package lib64gcc-s1. Preparing to unpack .../046-lib64gcc-s1_12.2.0-14_i386.deb ... Unpacking lib64gcc-s1 (12.2.0-14) ... Selecting previously unselected package lib64stdc++6. Preparing to unpack .../047-lib64stdc++6_12.2.0-14_i386.deb ... Unpacking lib64stdc++6 (12.2.0-14) ... Selecting previously unselected package libz3-4:i386. Preparing to unpack .../048-libz3-4_4.8.12-3.1_i386.deb ... Unpacking libz3-4:i386 (4.8.12-3.1) ... Selecting previously unselected package libllvm15:i386. Preparing to unpack .../049-libllvm15_1%3a15.0.6-4+b1_i386.deb ... Unpacking libllvm15:i386 (1:15.0.6-4+b1) ... Selecting previously unselected package libclang-common-15-dev. Preparing to unpack .../050-libclang-common-15-dev_1%3a15.0.6-4+b1_i386.deb ... Unpacking libclang-common-15-dev (1:15.0.6-4+b1) ... Selecting previously unselected package libclang-cpp15. Preparing to unpack .../051-libclang-cpp15_1%3a15.0.6-4+b1_i386.deb ... Unpacking libclang-cpp15 (1:15.0.6-4+b1) ... Selecting previously unselected package libclc-15-dev. Preparing to unpack .../052-libclc-15-dev_1%3a15.0.6-4_all.deb ... Unpacking libclc-15-dev (1:15.0.6-4) ... Selecting previously unselected package libclc-15. Preparing to unpack .../053-libclc-15_1%3a15.0.6-4_all.deb ... Unpacking libclc-15 (1:15.0.6-4) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../054-libdrm-common_2.4.114-1_all.deb ... Unpacking libdrm-common (2.4.114-1) ... Selecting previously unselected package libdrm2:i386. Preparing to unpack .../055-libdrm2_2.4.114-1+b1_i386.deb ... Unpacking libdrm2:i386 (2.4.114-1+b1) ... Selecting previously unselected package libdrm-amdgpu1:i386. Preparing to unpack .../056-libdrm-amdgpu1_2.4.114-1+b1_i386.deb ... Unpacking libdrm-amdgpu1:i386 (2.4.114-1+b1) ... Selecting previously unselected package libdrm-nouveau2:i386. Preparing to unpack .../057-libdrm-nouveau2_2.4.114-1+b1_i386.deb ... Unpacking libdrm-nouveau2:i386 (2.4.114-1+b1) ... Selecting previously unselected package libdrm-radeon1:i386. Preparing to unpack .../058-libdrm-radeon1_2.4.114-1+b1_i386.deb ... Unpacking libdrm-radeon1:i386 (2.4.114-1+b1) ... Selecting previously unselected package libevent-2.1-7:i386. Preparing to unpack .../059-libevent-2.1-7_2.1.12-stable-8_i386.deb ... Unpacking libevent-2.1-7:i386 (2.1.12-stable-8) ... Selecting previously unselected package libevent-core-2.1-7:i386. Preparing to unpack .../060-libevent-core-2.1-7_2.1.12-stable-8_i386.deb ... Unpacking libevent-core-2.1-7:i386 (2.1.12-stable-8) ... Selecting previously unselected package libevent-extra-2.1-7:i386. Preparing to unpack .../061-libevent-extra-2.1-7_2.1.12-stable-8_i386.deb ... Unpacking libevent-extra-2.1-7:i386 (2.1.12-stable-8) ... Selecting previously unselected package libevent-pthreads-2.1-7:i386. Preparing to unpack .../062-libevent-pthreads-2.1-7_2.1.12-stable-8_i386.deb ... Unpacking libevent-pthreads-2.1-7:i386 (2.1.12-stable-8) ... Selecting previously unselected package libevent-openssl-2.1-7:i386. Preparing to unpack .../063-libevent-openssl-2.1-7_2.1.12-stable-8_i386.deb ... Unpacking libevent-openssl-2.1-7:i386 (2.1.12-stable-8) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../064-libevent-dev_2.1.12-stable-8_i386.deb ... Unpacking libevent-dev (2.1.12-stable-8) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../065-libexpat1_2.5.0-1_i386.deb ... Unpacking libexpat1:i386 (2.5.0-1) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../066-libpsm-infinipath1_3.3+20.604758e7-6.2_i386.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.2) ... Selecting previously unselected package librdmacm1:i386. Preparing to unpack .../067-librdmacm1_44.0-2_i386.deb ... Unpacking librdmacm1:i386 (44.0-2) ... Selecting previously unselected package libfabric1:i386. Preparing to unpack .../068-libfabric1_1.17.0-3_i386.deb ... Unpacking libfabric1:i386 (1.17.0-3) ... Selecting previously unselected package ocl-icd-libopencl1:i386. Preparing to unpack .../069-ocl-icd-libopencl1_2.3.1-1_i386.deb ... Unpacking ocl-icd-libopencl1:i386 (2.3.1-1) ... Selecting previously unselected package libllvmspirvlib15:i386. Preparing to unpack .../070-libllvmspirvlib15_15.0.0-1_i386.deb ... Unpacking libllvmspirvlib15:i386 (15.0.0-1) ... Selecting previously unselected package libsensors-config. Preparing to unpack .../071-libsensors-config_1%3a3.6.0-7.1_all.deb ... Unpacking libsensors-config (1:3.6.0-7.1) ... Selecting previously unselected package libsensors5:i386. Preparing to unpack .../072-libsensors5_1%3a3.6.0-7.1_i386.deb ... Unpacking libsensors5:i386 (1:3.6.0-7.1) ... Selecting previously unselected package mesa-opencl-icd:i386. 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Unpacking libreadline-dev:i386 (8.2-1.3) ... Selecting previously unselected package mpi-default-dev. Preparing to unpack .../109-mpi-default-dev_1.14_i386.deb ... Unpacking mpi-default-dev (1.14) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../110-pkgconf-bin_1.8.1-1_i386.deb ... Unpacking pkgconf-bin (1.8.1-1) ... Selecting previously unselected package pkgconf:i386. Preparing to unpack .../111-pkgconf_1.8.1-1_i386.deb ... Unpacking pkgconf:i386 (1.8.1-1) ... Selecting previously unselected package pkg-config:i386. Preparing to unpack .../112-pkg-config_1.8.1-1_i386.deb ... Unpacking pkg-config:i386 (1.8.1-1) ... Setting up libexpat1:i386 (2.5.0-1) ... Setting up libpipeline1:i386 (1.5.7-1) ... Setting up libpciaccess0:i386 (0.17-2) ... Setting up libclc-15-dev (1:15.0.6-4) ... Setting up libxau6:i386 (1:1.0.9-1) ... Setting up libicu72:i386 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libcbor0.8:i386 (0.8.0-2+b1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libsensors-config (1:3.6.0-7.1) ... Setting up libmagic1:i386 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up autoconf-archive (20220903-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:i386 (4.8.12-3.1) ... Setting up libpkgconf3:i386 (1.8.1-1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up libncurses6:i386 (6.4-2) ... Setting up libhwloc15:i386 (2.9.0-1) ... Setting up libevent-core-2.1-7:i386 (2.1.12-stable-8) ... Setting up libevent-2.1-7:i386 (2.1.12-stable-8) ... Setting up autopoint (0.21-12) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libsensors5:i386 (1:3.6.0-7.1) ... Setting up libltdl7:i386 (2.4.7-5) ... Setting up libgfortran5:i386 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:i386 (1:1.2.13.dfsg-1) ... Setting up libnuma1:i386 (2.0.16-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up ocl-icd-libopencl1:i386 (2.3.1-1) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libnl-3-200:i386 (3.7.0-0.2+b1) ... Setting up openmpi-common (4.1.4-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.2) ... 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 libc6-amd64 (2.36-9) ... Setting up libfido2-1:i386 (1.12.0-2+b1) ... Setting up libbsd0:i386 (0.11.7-2) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:i386 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:i386 (2.9.14+dfsg-1.1+b3) ... Setting up libevent-pthreads-2.1-7:i386 (2.1.12-stable-8) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:i386 (2.1.12-stable-8) ... Setting up libncurses-dev:i386 (6.4-2) ... Setting up libxcb1:i386 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libedit2:i386 (3.1-20221030-2) ... Setting up libreadline8:i386 (8.2-1.3) ... Setting up lib64atomic1 (12.2.0-14) ... Setting up libevent-openssl-2.1-7:i386 (2.1.12-stable-8) ... Setting up libgfortran-12-dev:i386 (12.2.0-14) ... Setting up libreadline-dev:i386 (8.2-1.3) ... Setting up pkgconf:i386 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:i386 (2.0.16-1) ... Setting up libnl-route-3-200:i386 (3.7.0-0.2+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:i386 (2.4.7-5) ... Setting up gfortran-12 (12.2.0-14) ... Setting up lib64gcc-s1 (12.2.0-14) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libevent-dev (2.1.12-stable-8) ... Setting up pkg-config:i386 (1.8.1-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:i386 (2.4.114-1+b1) ... Setting up dwz (0.15-1) ... Setting up libnl-3-dev:i386 (3.7.0-0.2+b1) ... Setting up groff-base (1.22.4-10) ... Setting up libllvm15:i386 (1:15.0.6-4+b1) ... Setting up libx11-6:i386 (2:1.8.4-2) ... Setting up libhwloc-dev:i386 (2.9.0-1) ... Setting up libdrm-amdgpu1:i386 (2.4.114-1+b1) ... Setting up libibverbs1:i386 (44.0-2) ... Setting up libdrm-nouveau2:i386 (2.4.114-1+b1) ... Setting up libllvmspirvlib15:i386 (15.0.0-1) ... Setting up ibverbs-providers:i386 (44.0-2) ... Setting up libdrm-radeon1:i386 (2.4.114-1+b1) ... Setting up openssh-client (1:9.2p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:i386 (525.85.05-1) ... Setting up lib64stdc++6 (12.2.0-14) ... Setting up libnl-route-3-dev:i386 (3.7.0-0.2+b1) ... Setting up libclang-cpp15 (1:15.0.6-4+b1) ... Setting up librdmacm1:i386 (44.0-2) ... Setting up libclang-common-15-dev (1:15.0.6-4+b1) ... Setting up debhelper (13.11.4) ... Setting up libibverbs-dev:i386 (44.0-2) ... Setting up libhwloc-plugins:i386 (2.9.0-1) ... Setting up libclc-15 (1:15.0.6-4) ... Setting up mesa-opencl-icd:i386 (22.3.6-1+deb12u1) ... Setting up libfabric1:i386 (1.17.0-3) ... Setting up libpmix2:i386 (4.2.2-1+b1) ... Setting up libopenmpi3:i386 (4.1.4-3+b1) ... Setting up libhmsbeagle1v5:i386 (3.1.2+dfsg-13) ... Setting up libpmix-dev:i386 (4.2.2-1+b1) ... Setting up openmpi-bin (4.1.4-3+b1) ... 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) ... Setting up libopenmpi-dev:i386 (4.1.4-3+b1) ... 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 (1.14) ... Processing triggers for libc-bin (2.36-9) ... 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/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-6_source.changes dpkg-buildpackage: info: source package mrbayes dpkg-buildpackage: info: source version 3.2.7a-6 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 dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/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... /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... /bin/sed checking for C compiler version... 12.2.0 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/mrbayes-3.2.7a' debian/rules override_dh_auto_build make[1]: Entering directory '/build/mrbayes-3.2.7a' # build mb-mpi (from initial config) LIBS="-Wl,--as-needed" dh_auto_build make -j16 make[2]: Entering directory '/build/mrbayes-3.2.7a' Making all in src make[3]: Entering directory '/build/mrbayes-3.2.7a/src' make all-am make[4]: Entering directory '/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c mbbeagle.c: In function 'TreeLikelihood_BeagleMultiPartition': mbbeagle.c:2618:33: warning: 'nStates' may be used uninitialized [-Wmaybe-uninitialized] 2618 | int i, j, d, c = 0, nStates, beagleReturn, site, dIndex, divisionOffset; | ^~~~~~~ In file included from /usr/include/string.h:535, 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 '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); | ^ 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:906, 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:906, 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:906, 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 -ffile-prefix-map=/build/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/mrbayes-3.2.7a/src' make[3]: Leaving directory '/build/mrbayes-3.2.7a/src' Making all in doc make[3]: Entering directory '/build/mrbayes-3.2.7a/doc' Making all in manual make[4]: Entering directory '/build/mrbayes-3.2.7a/doc/manual' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/mrbayes-3.2.7a/doc/manual' Making all in tutorial make[4]: Entering directory '/build/mrbayes-3.2.7a/doc/tutorial' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/mrbayes-3.2.7a/doc/tutorial' make[4]: Entering directory '/build/mrbayes-3.2.7a/doc' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/mrbayes-3.2.7a/doc' make[3]: Leaving directory '/build/mrbayes-3.2.7a/doc' Making all in examples make[3]: Entering directory '/build/mrbayes-3.2.7a/examples' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/mrbayes-3.2.7a/examples' make[3]: Entering directory '/build/mrbayes-3.2.7a' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/mrbayes-3.2.7a' make[2]: Leaving directory '/build/mrbayes-3.2.7a' mv src/mb ./mb-mpi # Now - build mb ( cd src ; make clean ) make[2]: Entering directory '/build/mrbayes-3.2.7a/src' test -z "mb" || rm -f mb rm -f *.o make[2]: Leaving directory '/build/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... /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... /bin/sed checking for C compiler version... 12.2.0 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 -j16 make[2]: Entering directory '/build/mrbayes-3.2.7a' Making all in src make[3]: Entering directory '/build/mrbayes-3.2.7a/src' make all-am make[4]: Entering directory '/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/mrbayes-3.2.7a=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c mbbeagle.c: In function 'TreeLikelihood_BeagleMultiPartition': mbbeagle.c:2618:33: warning: 'nStates' may be used uninitialized [-Wmaybe-uninitialized] 2618 | int i, j, d, c = 0, nStates, beagleReturn, site, dIndex, divisionOffset; | ^~~~~~~ In file included from /usr/include/string.h:535, 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 '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); | ^ 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:906, 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:906, 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 ()); | ~~~~~~~~~~~~~~~~~ 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 ()); | ~~~~~~~~~~~~~~~~~ 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:906, 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 -ffile-prefix-map=/build/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/mrbayes-3.2.7a/src' make[3]: Leaving directory '/build/mrbayes-3.2.7a/src' Making all in doc make[3]: Entering directory '/build/mrbayes-3.2.7a/doc' Making all in manual make[4]: Entering directory '/build/mrbayes-3.2.7a/doc/manual' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/mrbayes-3.2.7a/doc/manual' Making all in tutorial make[4]: Entering directory '/build/mrbayes-3.2.7a/doc/tutorial' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/mrbayes-3.2.7a/doc/tutorial' make[4]: Entering directory '/build/mrbayes-3.2.7a/doc' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/mrbayes-3.2.7a/doc' make[3]: Leaving directory '/build/mrbayes-3.2.7a/doc' Making all in examples make[3]: Entering directory '/build/mrbayes-3.2.7a/examples' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/mrbayes-3.2.7a/examples' make[3]: Entering directory '/build/mrbayes-3.2.7a' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/mrbayes-3.2.7a' make[2]: Leaving directory '/build/mrbayes-3.2.7a' mv src/mb . make[1]: Leaving directory '/build/mrbayes-3.2.7a' dh_auto_test make -j16 check "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1 make[1]: Entering directory '/build/mrbayes-3.2.7a' Making check in src make[2]: Entering directory '/build/mrbayes-3.2.7a/src' gcc -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/build/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/mrbayes-3.2.7a/src' Making check in doc make[2]: Entering directory '/build/mrbayes-3.2.7a/doc' Making check in manual make[3]: Entering directory '/build/mrbayes-3.2.7a/doc/manual' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/mrbayes-3.2.7a/doc/manual' Making check in tutorial make[3]: Entering directory '/build/mrbayes-3.2.7a/doc/tutorial' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/mrbayes-3.2.7a/doc/tutorial' make[3]: Entering directory '/build/mrbayes-3.2.7a/doc' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/mrbayes-3.2.7a/doc' make[2]: Leaving directory '/build/mrbayes-3.2.7a/doc' Making check in examples make[2]: Entering directory '/build/mrbayes-3.2.7a/examples' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/mrbayes-3.2.7a/examples' make[2]: Entering directory '/build/mrbayes-3.2.7a' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/mrbayes-3.2.7a' make[1]: Leaving directory '/build/mrbayes-3.2.7a' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j16 install DESTDIR=/build/mrbayes-3.2.7a/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/mrbayes-3.2.7a' Making install in src make[2]: Entering directory '/build/mrbayes-3.2.7a/src' make[3]: Entering directory '/build/mrbayes-3.2.7a/src' make[3]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/mrbayes-3.2.7a/debian/tmp/usr/bin' /usr/bin/install -c mb '/build/mrbayes-3.2.7a/debian/tmp/usr/bin' make[3]: Leaving directory '/build/mrbayes-3.2.7a/src' make[2]: Leaving directory '/build/mrbayes-3.2.7a/src' Making install in doc make[2]: Entering directory '/build/mrbayes-3.2.7a/doc' Making install in manual make[3]: Entering directory '/build/mrbayes-3.2.7a/doc/manual' make[4]: Entering directory '/build/mrbayes-3.2.7a/doc/manual' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/install -c -m 644 Manual_MrBayes_v3.2.pdf '/build/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' make[4]: Leaving directory '/build/mrbayes-3.2.7a/doc/manual' make[3]: Leaving directory '/build/mrbayes-3.2.7a/doc/manual' Making install in tutorial make[3]: Entering directory '/build/mrbayes-3.2.7a/doc/tutorial' make[4]: Entering directory '/build/mrbayes-3.2.7a/doc/tutorial' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /bin/mkdir -p '/build/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/install -c -m 644 hym.nex '/build/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/install -c -m 644 MBDating.pdf '/build/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' make[4]: Leaving directory '/build/mrbayes-3.2.7a/doc/tutorial' make[3]: Leaving directory '/build/mrbayes-3.2.7a/doc/tutorial' make[3]: Entering directory '/build/mrbayes-3.2.7a/doc' make[4]: Entering directory '/build/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/mrbayes-3.2.7a/doc' make[3]: Leaving directory '/build/mrbayes-3.2.7a/doc' make[2]: Leaving directory '/build/mrbayes-3.2.7a/doc' Making install in examples make[2]: Entering directory '/build/mrbayes-3.2.7a/examples' make[3]: Entering directory '/build/mrbayes-3.2.7a/examples' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/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/mrbayes-3.2.7a/debian/tmp/usr/share/examples/mrbayes' make[3]: Leaving directory '/build/mrbayes-3.2.7a/examples' make[2]: Leaving directory '/build/mrbayes-3.2.7a/examples' make[2]: Entering directory '/build/mrbayes-3.2.7a' make[3]: Entering directory '/build/mrbayes-3.2.7a' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' /usr/bin/install -c -m 644 COPYING README NEWS '/build/mrbayes-3.2.7a/debian/tmp/usr/share/doc/mrbayes' make[3]: Leaving directory '/build/mrbayes-3.2.7a' make[2]: Leaving directory '/build/mrbayes-3.2.7a' make[1]: Leaving directory '/build/mrbayes-3.2.7a' dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/mrbayes-3.2.7a' dh_installexamples find debian -name "Makefile*" -delete make[1]: Leaving directory '/build/mrbayes-3.2.7a' dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/mrbayes-3.2.7a' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/mrbayes-3.2.7a' dh_fixperms debian/rules override_dh_missing make[1]: Entering directory '/build/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.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/mrbayes-3.2.7a' dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a debian/rules override_dh_installdeb make[1]: Entering directory '/build/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/mrbayes-3.2.7a' dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'mrbayes' in '../mrbayes_3.2.7a-6_i386.deb'. dpkg-deb: building package 'mrbayes-dbgsym' in '../mrbayes-dbgsym_3.2.7a-6_i386.deb'. dpkg-deb: building package 'mrbayes-mpi' in '../mrbayes-mpi_3.2.7a-6_i386.deb'. dpkg-deb: building package 'mrbayes-mpi-dbgsym' in '../mrbayes-mpi-dbgsym_3.2.7a-6_i386.deb'. dpkg-deb: building package 'mrbayes-doc' in '../mrbayes-doc_3.2.7a-6_all.deb'. dpkg-genbuildinfo --build=binary -O../mrbayes_3.2.7a-6_i386.buildinfo dpkg-genchanges --build=binary -O../mrbayes_3.2.7a-6_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/4842 and its subdirectories I: Current time: Mon May 20 04:46:47 -12 2024 I: pbuilder-time-stamp: 1716223607 Tue Apr 18 10:23:48 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net. Tue Apr 18 10:23:48 UTC 2023 I: Preparing to do remote build '2' on ionos2-i386.debian.net. Tue Apr 18 10:28:12 UTC 2023 I: Deleting $TMPDIR on ionos2-i386.debian.net. Tue Apr 18 10:28:12 UTC 2023 I: mrbayes_3.2.7a-6_i386.changes: Format: 1.8 Date: Thu, 24 Nov 2022 12:52:27 +0100 Source: mrbayes Binary: mrbayes mrbayes-dbgsym mrbayes-doc mrbayes-mpi mrbayes-mpi-dbgsym Architecture: i386 all Version: 3.2.7a-6 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 Changes: mrbayes (3.2.7a-6) unstable; urgency=medium . * Fix watch file * Standards-Version: 4.6.1 (routine-update) Checksums-Sha1: b08e6eb4f9a16443952777e1d079024c80322429 905804 mrbayes-dbgsym_3.2.7a-6_i386.deb a6e3a7e5cc8c4d115902dd73fb3cec31dee5d97a 1329052 mrbayes-doc_3.2.7a-6_all.deb 3359a886b2ef8cff5276090cc57a4af03f866599 976 mrbayes-mpi-dbgsym_3.2.7a-6_i386.deb 3900dbdb6e12f9914417bba02bdc02825f8ade08 618860 mrbayes-mpi_3.2.7a-6_i386.deb 061adcd087e71152f6db8fc03caa4fb44f6a429f 8599 mrbayes_3.2.7a-6_i386.buildinfo d74e6c5e64594aa49c43a81372664c00483c7c0a 681872 mrbayes_3.2.7a-6_i386.deb Checksums-Sha256: 809c36b728b224c2b71f3c2a2cc9a308b2017efd7f99e4571c2c01c582b87235 905804 mrbayes-dbgsym_3.2.7a-6_i386.deb a2be3335a6936f4b2c31edb757dc0f585423f0e39909184e1e15adcaac45a999 1329052 mrbayes-doc_3.2.7a-6_all.deb 8a9ea91ecac972a81c8ba8e6ae97e2fb32274ae8a2bb161604594196ff45e45b 976 mrbayes-mpi-dbgsym_3.2.7a-6_i386.deb 5df4d2ab28fbea7a55dda9505023df4e233a03fa09f287f8aa5fdcc55ca9b201 618860 mrbayes-mpi_3.2.7a-6_i386.deb 8cbf5732c31fbb339be1d6b22ec7c4b476a9b3942dec7f38ef2bd604fcb0ccfa 8599 mrbayes_3.2.7a-6_i386.buildinfo 95dc1380a00a94a7d06ff265d2dd38d8e13d9867083ed911fc3f64dc848ddf76 681872 mrbayes_3.2.7a-6_i386.deb Files: 13a2663998e22efe7a7e5911d854098b 905804 debug optional mrbayes-dbgsym_3.2.7a-6_i386.deb 51512ec44320db06050bf9cff90a2a17 1329052 doc optional mrbayes-doc_3.2.7a-6_all.deb 640a289e7075ae186b02f197f26bb2ea 976 debug optional mrbayes-mpi-dbgsym_3.2.7a-6_i386.deb 4b114f0ddebb429caf45cf22d2be650b 618860 science optional mrbayes-mpi_3.2.7a-6_i386.deb b7ff8e89ee959bf50d494c1cea3b3b47 8599 science optional mrbayes_3.2.7a-6_i386.buildinfo 4b2aa3443d0da0479716d888aa86de29 681872 science optional mrbayes_3.2.7a-6_i386.deb Tue Apr 18 10:28:13 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.i20pI8E9/mrbayes_3.2.7a-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.i20pI8E9/mrbayes_3.2.7a-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.i20pI8E9/mrbayes_3.2.7a-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.i20pI8E9/b1/mrbayes_3.2.7a-6_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.i20pI8E9/b2/mrbayes_3.2.7a-6_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: 0.510s) 0.510s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.073s) 0.073s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Tue Apr 18 10:28:15 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 18 10:28:15 UTC 2023 I: mrbayes from bookworm built successfully and reproducibly on i386. Tue Apr 18 10:28:17 UTC 2023 I: Submitting .buildinfo files to external archives: Tue Apr 18 10:28:17 UTC 2023 I: Submitting 12K b1/mrbayes_3.2.7a-6_i386.buildinfo.asc Tue Apr 18 10:28:18 UTC 2023 I: Submitting 12K b2/mrbayes_3.2.7a-6_i386.buildinfo.asc Tue Apr 18 10:28:19 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 18 10:28:19 UTC 2023 I: Done submitting .buildinfo files. Tue Apr 18 10:28:19 UTC 2023 I: Removing signed mrbayes_3.2.7a-6_i386.buildinfo.asc files: removed './b1/mrbayes_3.2.7a-6_i386.buildinfo.asc' removed './b2/mrbayes_3.2.7a-6_i386.buildinfo.asc'