Thu Jun 1 05:23:09 UTC 2023 I: starting to build mrbayes/bookworm/armhf on jenkins on '2023-06-01 05:22' Thu Jun 1 05:23:09 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_44/2057/console.log Thu Jun 1 05:23:09 UTC 2023 I: Downloading source for bookworm/mrbayes=3.2.7a-6 --2023-06-01 05:23:09-- 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% 174M=0s 2023-06-01 05:23:09 (174 MB/s) - ‘mrbayes_3.2.7a-6.dsc’ saved [2184/2184] Thu Jun 1 05:23:09 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----- Thu Jun 1 05:23:09 UTC 2023 I: Checking whether the package is not for us Thu Jun 1 05:23:09 UTC 2023 I: Starting 1st build on remote node cbxi4pro0-armhf-rb.debian.net. Thu Jun 1 05:23:09 UTC 2023 I: Preparing to do remote build '1' on cbxi4pro0-armhf-rb.debian.net. Thu Jun 1 06:36:05 UTC 2023 I: Deleting $TMPDIR on cbxi4pro0-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed May 31 17:23:23 -12 2023 I: pbuilder-time-stamp: 1685597003 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: 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/9251/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='307c780c21f247a2b7991bfed70f0975' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='9251' 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.917SVKqy/pbuilderrc_6Vwf --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.917SVKqy/b1 --logfile b1/build.log mrbayes_3.2.7a-6.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux cbxi4pro0 5.10.0-23-armmp #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 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 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 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 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 02:43 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 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 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/9251/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: armhf 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 ... 19324 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} libarchive-zip-perl{a} libbsd0{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} 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, 108 newly installed, 0 to remove and 0 not upgraded. Need to get 101 MB of archives. After unpacking 487 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf readline-common all 8.2-1.3 [69.0 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf libbsd0 armhf 0.11.7-2 [113 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf libedit2 armhf 3.1-20221030-2 [77.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf libcbor0.8 armhf 0.8.0-2+b1 [23.1 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf libfido2-1 armhf 1.12.0-2+b1 [69.3 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf openssh-client armhf 1:9.2p1-2 [893 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 28 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 30 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf libgfortran5 armhf 12.2.0-14 [246 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf libgfortran-12-dev armhf 12.2.0-14 [298 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf gfortran-12 armhf 12.2.0-14 [7633 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf libnl-3-200 armhf 3.7.0-0.2+b1 [55.8 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf libnl-route-3-200 armhf 3.7.0-0.2+b1 [156 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf libibverbs1 armhf 44.0-2 [53.6 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf ibverbs-providers armhf 44.0-2 [28.4 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf libz3-4 armhf 4.8.12-3.1 [6061 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf libllvm15 armhf 1:15.0.6-4+b1 [20.5 MB] Get: 47 http://deb.debian.org/debian bookworm/main armhf libclang-common-15-dev armhf 1:15.0.6-4+b1 [3481 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf libclang-cpp15 armhf 1:15.0.6-4+b1 [9846 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf libclc-15-dev all 1:15.0.6-4 [53.6 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf libclc-15 all 1:15.0.6-4 [10.1 MB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libdrm-common all 2.4.114-1 [7112 B] Get: 52 http://deb.debian.org/debian bookworm/main armhf libdrm2 armhf 2.4.114-1+b1 [33.0 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf libdrm-amdgpu1 armhf 2.4.114-1+b1 [19.3 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libdrm-nouveau2 armhf 2.4.114-1+b1 [16.7 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf libdrm-radeon1 armhf 2.4.114-1+b1 [19.3 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf libevent-2.1-7 armhf 2.1.12-stable-8 [161 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-8 [120 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-8 [97.5 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-8 [53.2 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-8 [58.3 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf libevent-dev armhf 2.1.12-stable-8 [290 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf librdmacm1 armhf 44.0-2 [60.6 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf libfabric1 armhf 1.17.0-3 [385 kB] Get: 65 http://deb.debian.org/debian bookworm/main armhf ocl-icd-libopencl1 armhf 2.3.1-1 [40.1 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf libllvmspirvlib15 armhf 15.0.0-2 [619 kB] Get: 67 http://deb.debian.org/debian bookworm/main armhf libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf libsensors5 armhf 1:3.6.0-7.1 [31.6 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf mesa-opencl-icd armhf 22.3.6-1+deb12u1 [10.5 MB] Get: 70 http://deb.debian.org/debian bookworm/main armhf libhmsbeagle1v5 armhf 3.1.2+dfsg-13 [86.8 kB] Get: 71 http://deb.debian.org/debian bookworm/main armhf libhmsbeagle-dev armhf 3.1.2+dfsg-13 [227 kB] Get: 72 http://deb.debian.org/debian bookworm/main armhf libhwloc15 armhf 2.9.0-1 [127 kB] Get: 73 http://deb.debian.org/debian bookworm/main armhf libnuma1 armhf 2.0.16-1 [17.8 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf libnuma-dev armhf 2.0.16-1 [33.0 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf libltdl7 armhf 2.4.7-5 [390 kB] Get: 76 http://deb.debian.org/debian bookworm/main armhf libltdl-dev armhf 2.4.7-5 [162 kB] Get: 77 http://deb.debian.org/debian bookworm/main armhf libhwloc-dev armhf 2.9.0-1 [214 kB] Get: 78 http://deb.debian.org/debian bookworm/main armhf libpciaccess0 armhf 0.17-2 [48.7 kB] Get: 79 http://deb.debian.org/debian bookworm/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 80 http://deb.debian.org/debian bookworm/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 81 http://deb.debian.org/debian bookworm/main armhf libxcb1 armhf 1.15-1 [140 kB] Get: 82 http://deb.debian.org/debian bookworm/main armhf libx11-data all 2:1.8.4-2 [292 kB] Get: 83 http://deb.debian.org/debian bookworm/main armhf libx11-6 armhf 2:1.8.4-2 [695 kB] Get: 84 http://deb.debian.org/debian bookworm/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB] Get: 85 http://deb.debian.org/debian bookworm/main armhf libxnvctrl0 armhf 525.85.05-1 [12.2 kB] Get: 86 http://deb.debian.org/debian bookworm/main armhf libhwloc-plugins armhf 2.9.0-1 [15.9 kB] Get: 87 http://deb.debian.org/debian bookworm/main armhf libnl-3-dev armhf 3.7.0-0.2+b1 [98.4 kB] Get: 88 http://deb.debian.org/debian bookworm/main armhf libnl-route-3-dev armhf 3.7.0-0.2+b1 [183 kB] Get: 89 http://deb.debian.org/debian bookworm/main armhf libibverbs-dev armhf 44.0-2 [195 kB] Get: 90 http://deb.debian.org/debian bookworm/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 91 http://deb.debian.org/debian bookworm/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 92 http://deb.debian.org/debian bookworm/main armhf libmunge2 armhf 0.5.15-2 [15.7 kB] Get: 93 http://deb.debian.org/debian bookworm/main armhf libncurses6 armhf 6.4-4 [81.1 kB] Get: 94 http://deb.debian.org/debian bookworm/main armhf libncurses-dev armhf 6.4-4 [311 kB] Get: 95 http://deb.debian.org/debian bookworm/main armhf libpmix2 armhf 4.2.2-1+b1 [553 kB] Get: 96 http://deb.debian.org/debian bookworm/main armhf libopenmpi3 armhf 4.1.4-3+b1 [1849 kB] Get: 97 http://deb.debian.org/debian bookworm/main armhf openmpi-common all 4.1.4-3 [167 kB] Get: 98 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Get: 99 http://deb.debian.org/debian bookworm/main armhf libpmix-dev armhf 4.2.2-1+b1 [864 kB] Get: 100 http://deb.debian.org/debian bookworm/main armhf openmpi-bin armhf 4.1.4-3+b1 [194 kB] Get: 101 http://deb.debian.org/debian bookworm/main armhf libopenmpi-dev armhf 4.1.4-3+b1 [920 kB] Get: 102 http://deb.debian.org/debian bookworm/main armhf libpkgconf3 armhf 1.8.1-1 [31.3 kB] Get: 103 http://deb.debian.org/debian bookworm/main armhf libreadline8 armhf 8.2-1.3 [144 kB] Get: 104 http://deb.debian.org/debian bookworm/main armhf libreadline-dev armhf 8.2-1.3 [136 kB] Get: 105 http://deb.debian.org/debian bookworm/main armhf mpi-default-dev armhf 1.14 [5548 B] Get: 106 http://deb.debian.org/debian bookworm/main armhf pkgconf-bin armhf 1.8.1-1 [28.5 kB] Get: 107 http://deb.debian.org/debian bookworm/main armhf pkgconf armhf 1.8.1-1 [25.9 kB] Get: 108 http://deb.debian.org/debian bookworm/main armhf pkg-config armhf 1.8.1-1 [13.7 kB] Fetched 101 MB in 20s (5187 kB/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 ... 19324 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_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../004-libmagic1_1%3a5.44-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.44-3_armhf.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.21-12_armhf.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../007-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.22.4-10_armhf.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.38.1-5+b1_armhf.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../010-libpipeline1_1.5.7-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.11.2-2_armhf.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package libbsd0:armhf. Preparing to unpack .../012-libbsd0_0.11.7-2_armhf.deb ... Unpacking libbsd0:armhf (0.11.7-2) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../013-libedit2_3.1-20221030-2_armhf.deb ... Unpacking libedit2:armhf (3.1-20221030-2) ... Selecting previously unselected package libcbor0.8:armhf. Preparing to unpack .../014-libcbor0.8_0.8.0-2+b1_armhf.deb ... Unpacking libcbor0.8:armhf (0.8.0-2+b1) ... Selecting previously unselected package libfido2-1:armhf. Preparing to unpack .../015-libfido2-1_1.12.0-2+b1_armhf.deb ... Unpacking libfido2-1:armhf (1.12.0-2+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../016-openssh-client_1%3a9.2p1-2_armhf.deb ... Unpacking openssh-client (1:9.2p1-2) ... Selecting previously unselected package m4. Preparing to unpack .../017-m4_1.4.19-3_armhf.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:armhf. Preparing to unpack .../029-libelf1_0.188-2.1_armhf.deb ... Unpacking libelf1:armhf (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../030-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../031-libicu72_72.1-3_armhf.deb ... Unpacking libicu72:armhf (72.1-3) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../032-libxml2_2.9.14+dfsg-1.2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../033-gettext_0.21-12_armhf.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:armhf. Preparing to unpack .../037-libgfortran5_12.2.0-14_armhf.deb ... Unpacking libgfortran5:armhf (12.2.0-14) ... Selecting previously unselected package libgfortran-12-dev:armhf. Preparing to unpack .../038-libgfortran-12-dev_12.2.0-14_armhf.deb ... Unpacking libgfortran-12-dev:armhf (12.2.0-14) ... Selecting previously unselected package gfortran-12. Preparing to unpack .../039-gfortran-12_12.2.0-14_armhf.deb ... Unpacking gfortran-12 (12.2.0-14) ... Selecting previously unselected package libnl-3-200:armhf. Preparing to unpack .../040-libnl-3-200_3.7.0-0.2+b1_armhf.deb ... Unpacking libnl-3-200:armhf (3.7.0-0.2+b1) ... Selecting previously unselected package libnl-route-3-200:armhf. Preparing to unpack .../041-libnl-route-3-200_3.7.0-0.2+b1_armhf.deb ... Unpacking libnl-route-3-200:armhf (3.7.0-0.2+b1) ... Selecting previously unselected package libibverbs1:armhf. Preparing to unpack .../042-libibverbs1_44.0-2_armhf.deb ... Unpacking libibverbs1:armhf (44.0-2) ... Selecting previously unselected package ibverbs-providers:armhf. Preparing to unpack .../043-ibverbs-providers_44.0-2_armhf.deb ... Unpacking ibverbs-providers:armhf (44.0-2) ... Selecting previously unselected package libz3-4:armhf. Preparing to unpack .../044-libz3-4_4.8.12-3.1_armhf.deb ... Unpacking libz3-4:armhf (4.8.12-3.1) ... Selecting previously unselected package libllvm15:armhf. Preparing to unpack .../045-libllvm15_1%3a15.0.6-4+b1_armhf.deb ... Unpacking libllvm15:armhf (1:15.0.6-4+b1) ... Selecting previously unselected package libclang-common-15-dev. Preparing to unpack .../046-libclang-common-15-dev_1%3a15.0.6-4+b1_armhf.deb ... Unpacking libclang-common-15-dev (1:15.0.6-4+b1) ... Selecting previously unselected package libclang-cpp15. Preparing to unpack .../047-libclang-cpp15_1%3a15.0.6-4+b1_armhf.deb ... Unpacking libclang-cpp15 (1:15.0.6-4+b1) ... Selecting previously unselected package libclc-15-dev. Preparing to unpack .../048-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 .../049-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 .../050-libdrm-common_2.4.114-1_all.deb ... Unpacking libdrm-common (2.4.114-1) ... Selecting previously unselected package libdrm2:armhf. Preparing to unpack .../051-libdrm2_2.4.114-1+b1_armhf.deb ... Unpacking libdrm2:armhf (2.4.114-1+b1) ... Selecting previously unselected package libdrm-amdgpu1:armhf. Preparing to unpack .../052-libdrm-amdgpu1_2.4.114-1+b1_armhf.deb ... Unpacking libdrm-amdgpu1:armhf (2.4.114-1+b1) ... Selecting previously unselected package libdrm-nouveau2:armhf. Preparing to unpack .../053-libdrm-nouveau2_2.4.114-1+b1_armhf.deb ... Unpacking libdrm-nouveau2:armhf (2.4.114-1+b1) ... Selecting previously unselected package libdrm-radeon1:armhf. Preparing to unpack .../054-libdrm-radeon1_2.4.114-1+b1_armhf.deb ... Unpacking libdrm-radeon1:armhf (2.4.114-1+b1) ... Selecting previously unselected package libevent-2.1-7:armhf. Preparing to unpack .../055-libevent-2.1-7_2.1.12-stable-8_armhf.deb ... Unpacking libevent-2.1-7:armhf (2.1.12-stable-8) ... Selecting previously unselected package libevent-core-2.1-7:armhf. Preparing to unpack .../056-libevent-core-2.1-7_2.1.12-stable-8_armhf.deb ... Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-8) ... Selecting previously unselected package libevent-extra-2.1-7:armhf. Preparing to unpack .../057-libevent-extra-2.1-7_2.1.12-stable-8_armhf.deb ... Unpacking libevent-extra-2.1-7:armhf (2.1.12-stable-8) ... Selecting previously unselected package libevent-pthreads-2.1-7:armhf. Preparing to unpack .../058-libevent-pthreads-2.1-7_2.1.12-stable-8_armhf.deb ... Unpacking libevent-pthreads-2.1-7:armhf (2.1.12-stable-8) ... Selecting previously unselected package libevent-openssl-2.1-7:armhf. Preparing to unpack .../059-libevent-openssl-2.1-7_2.1.12-stable-8_armhf.deb ... Unpacking libevent-openssl-2.1-7:armhf (2.1.12-stable-8) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../060-libevent-dev_2.1.12-stable-8_armhf.deb ... Unpacking libevent-dev (2.1.12-stable-8) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../061-libexpat1_2.5.0-1_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-1) ... Selecting previously unselected package librdmacm1:armhf. Preparing to unpack .../062-librdmacm1_44.0-2_armhf.deb ... Unpacking librdmacm1:armhf (44.0-2) ... Selecting previously unselected package libfabric1:armhf. Preparing to unpack .../063-libfabric1_1.17.0-3_armhf.deb ... Unpacking libfabric1:armhf (1.17.0-3) ... Selecting previously unselected package ocl-icd-libopencl1:armhf. Preparing to unpack .../064-ocl-icd-libopencl1_2.3.1-1_armhf.deb ... Unpacking ocl-icd-libopencl1:armhf (2.3.1-1) ... Selecting previously unselected package libllvmspirvlib15:armhf. Preparing to unpack .../065-libllvmspirvlib15_15.0.0-2_armhf.deb ... Unpacking libllvmspirvlib15:armhf (15.0.0-2) ... Selecting previously unselected package libsensors-config. Preparing to unpack .../066-libsensors-config_1%3a3.6.0-7.1_all.deb ... Unpacking libsensors-config (1:3.6.0-7.1) ... Selecting previously unselected package libsensors5:armhf. Preparing to unpack .../067-libsensors5_1%3a3.6.0-7.1_armhf.deb ... Unpacking libsensors5:armhf (1:3.6.0-7.1) ... Selecting previously unselected package mesa-opencl-icd:armhf. Preparing to unpack .../068-mesa-opencl-icd_22.3.6-1+deb12u1_armhf.deb ... Unpacking mesa-opencl-icd:armhf (22.3.6-1+deb12u1) ... Selecting previously unselected package libhmsbeagle1v5:armhf. Preparing to unpack .../069-libhmsbeagle1v5_3.1.2+dfsg-13_armhf.deb ... Unpacking libhmsbeagle1v5:armhf (3.1.2+dfsg-13) ... Selecting previously unselected package libhmsbeagle-dev. Preparing to unpack .../070-libhmsbeagle-dev_3.1.2+dfsg-13_armhf.deb ... Unpacking libhmsbeagle-dev (3.1.2+dfsg-13) ... Selecting previously unselected package libhwloc15:armhf. Preparing to unpack .../071-libhwloc15_2.9.0-1_armhf.deb ... Unpacking libhwloc15:armhf (2.9.0-1) ... Selecting previously unselected package libnuma1:armhf. Preparing to unpack .../072-libnuma1_2.0.16-1_armhf.deb ... Unpacking libnuma1:armhf (2.0.16-1) ... Selecting previously unselected package libnuma-dev:armhf. Preparing to unpack .../073-libnuma-dev_2.0.16-1_armhf.deb ... Unpacking libnuma-dev:armhf (2.0.16-1) ... Selecting previously unselected package libltdl7:armhf. Preparing to unpack .../074-libltdl7_2.4.7-5_armhf.deb ... Unpacking libltdl7:armhf (2.4.7-5) ... Selecting previously unselected package libltdl-dev:armhf. Preparing to unpack .../075-libltdl-dev_2.4.7-5_armhf.deb ... Unpacking libltdl-dev:armhf (2.4.7-5) ... Selecting previously unselected package libhwloc-dev:armhf. Preparing to unpack .../076-libhwloc-dev_2.9.0-1_armhf.deb ... Unpacking libhwloc-dev:armhf (2.9.0-1) ... Selecting previously unselected package libpciaccess0:armhf. Preparing to unpack .../077-libpciaccess0_0.17-2_armhf.deb ... 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Setting up libmunge2 (0.5.15-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up libncurses6:armhf (6.4-4) ... Setting up libhwloc15:armhf (2.9.0-1) ... Setting up libevent-core-2.1-7:armhf (2.1.12-stable-8) ... Setting up libevent-2.1-7:armhf (2.1.12-stable-8) ... Setting up autopoint (0.21-12) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libsensors5:armhf (1:3.6.0-7.1) ... Setting up libltdl7:armhf (2.4.7-5) ... Setting up libgfortran5:armhf (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Setting up libnuma1:armhf (2.0.16-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up ocl-icd-libopencl1:armhf (2.3.1-1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libnl-3-200:armhf (3.7.0-0.2+b1) ... Setting up openmpi-common (4.1.4-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:armhf (1.12.0-2+b1) ... Setting up libbsd0:armhf (0.11.7-2) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:armhf (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:armhf (2.9.14+dfsg-1.2) ... Setting up libevent-pthreads-2.1-7:armhf (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:armhf (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:armhf (2.1.12-stable-8) ... Setting up libncurses-dev:armhf (6.4-4) ... Setting up libxcb1:armhf (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libedit2:armhf (3.1-20221030-2) ... Setting up libreadline8:armhf (8.2-1.3) ... Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-8) ... Setting up libgfortran-12-dev:armhf (12.2.0-14) ... Setting up libreadline-dev:armhf (8.2-1.3) ... Setting up pkgconf:armhf (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:armhf (2.0.16-1) ... Setting up libnl-route-3-200:armhf (3.7.0-0.2+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:armhf (2.4.7-5) ... Setting up gfortran-12 (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:armhf (1.8.1-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:armhf (2.4.114-1+b1) ... Setting up dwz (0.15-1) ... Setting up libnl-3-dev:armhf (3.7.0-0.2+b1) ... Setting up groff-base (1.22.4-10) ... Setting up libllvm15:armhf (1:15.0.6-4+b1) ... Setting up libx11-6:armhf (2:1.8.4-2) ... Setting up libhwloc-dev:armhf (2.9.0-1) ... Setting up libdrm-amdgpu1:armhf (2.4.114-1+b1) ... Setting up libibverbs1:armhf (44.0-2) ... Setting up libdrm-nouveau2:armhf (2.4.114-1+b1) ... Setting up libllvmspirvlib15:armhf (15.0.0-2) ... Setting up libclang-common-15-dev (1:15.0.6-4+b1) ... Setting up ibverbs-providers:armhf (44.0-2) ... Setting up libdrm-radeon1:armhf (2.4.114-1+b1) ... Setting up openssh-client (1:9.2p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:armhf (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:armhf (525.85.05-1) ... Setting up libnl-route-3-dev:armhf (3.7.0-0.2+b1) ... Setting up libclang-cpp15 (1:15.0.6-4+b1) ... Setting up libclc-15 (1:15.0.6-4) ... Setting up mesa-opencl-icd:armhf (22.3.6-1+deb12u1) ... Setting up librdmacm1:armhf (44.0-2) ... Setting up libhmsbeagle1v5:armhf (3.1.2+dfsg-13) ... Setting up debhelper (13.11.4) ... Setting up libibverbs-dev:armhf (44.0-2) ... Setting up libhwloc-plugins:armhf (2.9.0-1) ... Setting up libfabric1:armhf (1.17.0-3) ... Setting up libhmsbeagle-dev (3.1.2+dfsg-13) ... Setting up libpmix2:armhf (4.2.2-1+b1) ... Setting up libopenmpi3:armhf (4.1.4-3+b1) ... Setting up libpmix-dev:armhf (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 libopenmpi-dev:armhf (4.1.4-3+b1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) 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 armhf 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=arm-linux-gnueabihf --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/arm-linux-gnueabihf --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... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf 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 -j3 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 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; | ^~~~~~~ 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 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/arm-linux-gnueabihf/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); | ^ 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 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/arm-linux-gnueabihf/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 ()); | ~~~~~~~~~~~~~~~~~ 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 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 ()); | ~~~~~~~~~~~~~~~~~ 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 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ 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/arm-linux-gnueabihf/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=arm-linux-gnueabihf --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/arm-linux-gnueabihf --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... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf 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 -j3 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 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; | ^~~~~~~ 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 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/arm-linux-gnueabihf/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); | ^ 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 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/arm-linux-gnueabihf/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 ()); | ~~~~~~~~~~~~~~~~~ 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 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 ()); | ~~~~~~~~~~~~~~~~~ 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 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ 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/arm-linux-gnueabihf/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 -j3 check "TESTSUITEFLAGS=-j3 --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 -j3 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_armhf.deb'. dpkg-deb: building package 'mrbayes-mpi' in '../mrbayes-mpi_3.2.7a-6_armhf.deb'. dpkg-deb: building package 'mrbayes-doc' in '../mrbayes-doc_3.2.7a-6_all.deb'. dpkg-deb: building package 'mrbayes-mpi-dbgsym' in '../mrbayes-mpi-dbgsym_3.2.7a-6_armhf.deb'. dpkg-deb: building package 'mrbayes-dbgsym' in '../mrbayes-dbgsym_3.2.7a-6_armhf.deb'. dpkg-genbuildinfo --build=binary -O../mrbayes_3.2.7a-6_armhf.buildinfo dpkg-genchanges --build=binary -O../mrbayes_3.2.7a-6_armhf.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/9251 and its subdirectories I: Current time: Wed May 31 18:35:51 -12 2023 I: pbuilder-time-stamp: 1685601351 Thu Jun 1 06:36:07 UTC 2023 I: 1st build successful. Starting 2nd build on remote node jtx1c-armhf-rb.debian.net. Thu Jun 1 06:36:07 UTC 2023 I: Preparing to do remote build '2' on jtx1c-armhf-rb.debian.net. Thu Jun 1 06:44:34 UTC 2023 I: Deleting $TMPDIR on jtx1c-armhf-rb.debian.net. Thu Jun 1 06:44:37 UTC 2023 I: mrbayes_3.2.7a-6_armhf.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: armhf 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: b53bf9a3730875fd7f7baa76b33c8f210a76669a 1018116 mrbayes-dbgsym_3.2.7a-6_armhf.deb a6e3a7e5cc8c4d115902dd73fb3cec31dee5d97a 1329052 mrbayes-doc_3.2.7a-6_all.deb ee2a615323141e14ae273499ff999e7454bc645b 972 mrbayes-mpi-dbgsym_3.2.7a-6_armhf.deb 212454043ecd25cdbbf92578bebd60364c62cded 554832 mrbayes-mpi_3.2.7a-6_armhf.deb f9fcb758b6fe888dd2ce3fad5a512fcd57c646b4 8333 mrbayes_3.2.7a-6_armhf.buildinfo 15c7ed8d1523db69adee2a52cd907227bd705db3 617604 mrbayes_3.2.7a-6_armhf.deb Checksums-Sha256: f0728951d1217439d2c94e0abef7406c2bee8e1b27d22ce0f1f9b72bb49691aa 1018116 mrbayes-dbgsym_3.2.7a-6_armhf.deb a2be3335a6936f4b2c31edb757dc0f585423f0e39909184e1e15adcaac45a999 1329052 mrbayes-doc_3.2.7a-6_all.deb 79c7ec0f500388eb5c4f2fbbc6e6c415ef96f515f8331175063bb9b5a4827832 972 mrbayes-mpi-dbgsym_3.2.7a-6_armhf.deb 1b40c82dbb1a712ab47a049350db163624dd91849e3b9a0ffc2672ad4ca3bbbc 554832 mrbayes-mpi_3.2.7a-6_armhf.deb 51fd460d22aea06ef71aa1f0fb62634104ca0507dccc3f8d23c7ebb4c5f579bf 8333 mrbayes_3.2.7a-6_armhf.buildinfo 09247975427a76f4b9eb28da1d22c0b33f72cb7d8cc22fa7b84ab5953da5954f 617604 mrbayes_3.2.7a-6_armhf.deb Files: 55d57d207743c8715e325dadf02d806d 1018116 debug optional mrbayes-dbgsym_3.2.7a-6_armhf.deb 51512ec44320db06050bf9cff90a2a17 1329052 doc optional mrbayes-doc_3.2.7a-6_all.deb 005daae7e00acf15fbc99520932d642a 972 debug optional mrbayes-mpi-dbgsym_3.2.7a-6_armhf.deb 33c585df3273700d214c1c5cd53c5ae0 554832 science optional mrbayes-mpi_3.2.7a-6_armhf.deb a67cbc76de12af02fbe3070b831caf89 8333 science optional mrbayes_3.2.7a-6_armhf.buildinfo 04ff14431cdc6d1c890771e689e4230b 617604 science optional mrbayes_3.2.7a-6_armhf.deb Thu Jun 1 06:44:38 UTC 2023 I: diffoscope 242 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.917SVKqy/mrbayes_3.2.7a-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.917SVKqy/mrbayes_3.2.7a-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.917SVKqy/mrbayes_3.2.7a-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.917SVKqy/b1/mrbayes_3.2.7a-6_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.917SVKqy/b2/mrbayes_3.2.7a-6_armhf.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: 0.414s) 0.414s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.067s) 0.067s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Thu Jun 1 06:44:39 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Thu Jun 1 06:44:39 UTC 2023 I: mrbayes from bookworm built successfully and reproducibly on armhf. Thu Jun 1 06:44:40 UTC 2023 I: Submitting .buildinfo files to external archives: Thu Jun 1 06:44:40 UTC 2023 I: Submitting 12K b1/mrbayes_3.2.7a-6_armhf.buildinfo.asc Thu Jun 1 06:44:42 UTC 2023 I: Submitting 12K b2/mrbayes_3.2.7a-6_armhf.buildinfo.asc Thu Jun 1 06:44:43 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jun 1 06:44:43 UTC 2023 I: Done submitting .buildinfo files. Thu Jun 1 06:44:43 UTC 2023 I: Removing signed mrbayes_3.2.7a-6_armhf.buildinfo.asc files: removed './b1/mrbayes_3.2.7a-6_armhf.buildinfo.asc' removed './b2/mrbayes_3.2.7a-6_armhf.buildinfo.asc'