Mon Jul 5 18:51:08 UTC 2021 I: starting to build murasaki/bullseye/i386 on jenkins on '2021-07-05 18:50' Mon Jul 5 18:51:08 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_16/16904/console.log Mon Jul 5 18:51:08 UTC 2021 I: Downloading source for bullseye/murasaki=1.68.6-12 --2021-07-05 18:51:09-- http://cdn-fastly.deb.debian.org/debian/pool/main/m/murasaki/murasaki_1.68.6-12.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2758 (2.7K) Saving to: ‘murasaki_1.68.6-12.dsc’ 0K .. 100% 28.0M=0s 2021-07-05 18:51:09 (28.0 MB/s) - ‘murasaki_1.68.6-12.dsc’ saved [2758/2758] Mon Jul 5 18:51:09 UTC 2021 I: murasaki_1.68.6-12.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: murasaki Binary: murasaki, murasaki-mpi, murasaki-common Architecture: any all Version: 1.68.6-12 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/murasaki Vcs-Git: https://salsa.debian.org/med-team/murasaki.git Testsuite: autopkgtest Testsuite-Triggers: libboost-filesystem-dev, libboost-iostreams-dev, libboost-regex-dev, libcrypto++-dev, libopenmpi-dev, libpstreams-dev, libterm-readkey-perl, libtext-wrapper-perl Build-Depends: debhelper-compat (= 13), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev Package-List: murasaki deb science optional arch=any murasaki-common deb science optional arch=all murasaki-mpi deb science optional arch=any Checksums-Sha1: 039363a4ee16888adc629ebbf658ccf2805370bd 3944341 murasaki_1.68.6.orig-debian-tests-data.tar.gz 398a53fe76476ec3c756754d13541dd25d98a58a 307745 murasaki_1.68.6.orig.tar.gz 5d88ef9b8c12b614768656afbc4108e2eac3a2d8 10768 murasaki_1.68.6-12.debian.tar.xz Checksums-Sha256: bb3fee13bdf2ee9184667c9a3535dcd54525d9d98782e67c8c8713393cbb7862 3944341 murasaki_1.68.6.orig-debian-tests-data.tar.gz ebb3f3df2c0b3dc9f43977685f6c5e37ea483fb4189f7d965acc634bd10aaefe 307745 murasaki_1.68.6.orig.tar.gz 6c71edd6fd55bdcf5a4b46b8285f6909db0f2da0d404cc845347336580e10f47 10768 murasaki_1.68.6-12.debian.tar.xz Files: f7c0e6bdc9dea8bc893e806db571d228 3944341 murasaki_1.68.6.orig-debian-tests-data.tar.gz 25477c77aa21246d4a639527836e6c77 307745 murasaki_1.68.6.orig.tar.gz f2f9b1479dcf7844457903d6612b8b59 10768 murasaki_1.68.6-12.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmBU9MwUHG5wYXRyYTk3 NEBnbWFpbC5jb20ACgkQALrnSzQzafE6CQ//YNMMi9LV58+u7vT4jsptFRUl6SIK tfpXK+Rpg4YS/LYVroHjRvzZzF1nvFsuYFDTgJM1mHUdYf2sl0BvmJmkvNGfSs1z p7UvnM4IVu7bejy0463E0IeopvC+uqgdhZqJct/MiLz5kqvqFpRYIF3HTEbdhiF8 AOQXWh9WfXW0rCMzKtkpHHQBbACyZajyLWtTzQ6IgpmuPTXRCJFM6f1UQfEYw/ib NUy8R8aZiV17sQOeFOAfzlCG/PndHzAhCpWcH8wLHYjVlVbyNO+PCSdLL0A0+IEJ q4P/r5ZF9eWim0tSIRtepQzAb9+S8S3qv4QBiYA3TsRXGdN2RmnsdE/M6nEkg/7J xyCpJf3IcwizGN51DeOnqspidRF9XGjwapUzyE45WhAIXFbM9ZiRgVUZ7QzCAWCm EtNio8cTg+8T9EshdbgZkHxjhKHp50Ntp1wGoFdkgx/si8ZlpAVjDrj2tyIcfHOY fTijAakDiCaJLpawQTlwrvlKNuMhDLSj6LtAYCXgMzQUDcoRqkdCfDSJ3vzj5W2a GHUy/5QGl30L6Npv9schLQAgzRgYiXYHaaAobmGBk8H5m2YlLV5ktFaIU79++hG4 siiSb0gJi1pqrKibi2Lkwlv2ZVZeQbKwZYDIz2WWMJj6vYx1tSGQJCDSmu9I/F45 kkgsKwIy2XH3CmU= =TZH+ -----END PGP SIGNATURE----- Mon Jul 5 18:51:09 UTC 2021 I: Checking whether the package is not for us Mon Jul 5 18:51:09 UTC 2021 I: Starting 1st build on remote node ionos16-i386.debian.net. Mon Jul 5 18:51:09 UTC 2021 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Mon Jul 5 18:52:45 UTC 2021 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Aug 7 13:14:10 -12 2022 I: pbuilder-time-stamp: 1659921250 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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 [murasaki_1.68.6-12.dsc] I: copying [./murasaki_1.68.6.orig-debian-tests-data.tar.gz] I: copying [./murasaki_1.68.6.orig.tar.gz] I: copying [./murasaki_1.68.6-12.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.Wq9qF2iH/trustedkeys.kbx': General error gpgv: Signature made Fri Mar 19 07:00:28 2021 -12 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./murasaki_1.68.6-12.dsc dpkg-source: info: extracting murasaki in murasaki-1.68.6 dpkg-source: info: unpacking murasaki_1.68.6.orig.tar.gz dpkg-source: info: unpacking murasaki_1.68.6.orig-debian-tests-data.tar.gz dpkg-source: info: unpacking murasaki_1.68.6-12.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_proper_libboost_names.patch dpkg-source: info: applying include_libpstream.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying man_syntax.patch dpkg-source: info: applying freebsd.patch dpkg-source: info: applying gcc-6.patch dpkg-source: info: applying fix_mpi.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/46125/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,-fixfilepath parallel=18' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='5227cdd8f2cc496ea2a6ecec1d648995' 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='46125' 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/tmp.F0enMlAcbx/pbuilderrc_O9Aa --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.F0enMlAcbx/b1 --logfile b1/build.log murasaki_1.68.6-12.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 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Jun 21 2021 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Feb 7 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 7 2021 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Feb 7 2021 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 7 2021 more -rwsr-xr-x 1 root root 50720 Feb 7 2021 mount -rwxr-xr-x 1 root root 13856 Feb 7 2021 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 2021 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 6 03:46 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Feb 7 2021 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 7 2021 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 7 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/46125/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), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19675 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 libboost-regex-dev; however: Package libboost-regex-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-filesystem-dev; however: Package libboost-filesystem-dev is not installed. pbuilder-satisfydepends-dummy depends on libterm-readkey-perl; however: Package libterm-readkey-perl is not installed. pbuilder-satisfydepends-dummy depends on libtext-wrapper-perl; however: Package libtext-wrapper-perl is not installed. pbuilder-satisfydepends-dummy depends on libcrypto++-dev; however: Package libcrypto++-dev is not installed. pbuilder-satisfydepends-dummy depends on libpstreams-dev; however: Package libpstreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev; however: Package libopenmpi-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-10{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-filesystem-dev{a} libboost-filesystem1.74-dev{a} libboost-filesystem1.74.0{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-regex-dev{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost1.74-dev{a} libbsd0{a} libcbor0{a} libcrypto++-dev{a} libcrypto++8{a} libdebhelper-perl{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} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-10-dev{a} libgfortran5{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu-dev{a} libicu67{a} libjs-jquery{a} libjs-jquery-ui{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmd0{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} libpmix-dev{a} libpmix2{a} libpsm-infinipath1{a} libpstreams-dev{a} librdmacm1{a} libsigsegv2{a} libsub-override-perl{a} libterm-readkey-perl{a} libtext-wrapper-perl{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} m4{a} man-db{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} po-debconf{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 libmail-sendmail-perl lynx wget xauth 0 packages upgraded, 99 newly installed, 0 to remove and 0 not upgraded. Need to get 67.6 MB of archives. After unpacking 384 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1 [111 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 libedit2 i386 3.1-20191231-2+b1 [101 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 libcbor0 i386 0.5.0+dfsg-2 [26.2 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 libfido2-1 i386 1.6.0-2 [59.9 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 openssh-client i386 1:8.4p1-5 [991 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-6 [8776 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libgfortran-10-dev i386 10.2.1-6 [705 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 gfortran-10 i386 10.2.1-6 [9642 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libnl-3-200 i386 3.4.0-1+b1 [66.4 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 libnl-route-3-200 i386 3.4.0-1+b1 [168 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libibverbs1 i386 33.2-1 [64.6 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 ibverbs-providers i386 33.2-1 [275 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 icu-devtools i386 67.1-6 [209 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 libboost1.74-dev i386 1.74.0-9 [9534 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libboost-filesystem1.74.0 i386 1.74.0-9 [288 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 libboost-system1.74.0 i386 1.74.0-9 [241 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libboost-system1.74-dev i386 1.74.0-9 [243 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 libboost-filesystem1.74-dev i386 1.74.0-9 [311 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 libboost-filesystem-dev i386 1.74.0.3 [4368 B] Get: 52 http://deb.debian.org/debian bullseye/main i386 libboost-regex1.74.0 i386 1.74.0-9 [542 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 libicu-dev i386 67.1-6 [9799 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 libboost-regex1.74-dev i386 1.74.0-9 [618 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 libboost-iostreams1.74-dev i386 1.74.0-9 [275 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 libboost-iostreams-dev i386 1.74.0.3 [4320 B] Get: 57 http://deb.debian.org/debian bullseye/main i386 libboost-regex-dev i386 1.74.0.3 [4596 B] Get: 58 http://deb.debian.org/debian bullseye/main i386 libcrypto++8 i386 8.4.0-1 [1225 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libcrypto++-dev i386 8.4.0-1 [1955 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 libevent-2.1-7 i386 2.1.12-stable-1 [203 kB] Get: 61 http://deb.debian.org/debian bullseye/main i386 libevent-core-2.1-7 i386 2.1.12-stable-1 [148 kB] Get: 62 http://deb.debian.org/debian bullseye/main i386 libevent-extra-2.1-7 i386 2.1.12-stable-1 [116 kB] Get: 63 http://deb.debian.org/debian bullseye/main i386 libevent-pthreads-2.1-7 i386 2.1.12-stable-1 [57.3 kB] Get: 64 http://deb.debian.org/debian bullseye/main i386 libevent-openssl-2.1-7 i386 2.1.12-stable-1 [64.9 kB] Get: 65 http://deb.debian.org/debian bullseye/main i386 libevent-dev i386 2.1.12-stable-1 [332 kB] Get: 66 http://deb.debian.org/debian bullseye/main i386 libpsm-infinipath1 i386 3.3+20.604758e7-6.1 [178 kB] Get: 67 http://deb.debian.org/debian bullseye/main i386 librdmacm1 i386 33.2-1 [75.2 kB] Get: 68 http://deb.debian.org/debian bullseye/main i386 libfabric1 i386 1.11.0-2 [518 kB] Get: 69 http://deb.debian.org/debian bullseye/main i386 libhwloc15 i386 2.4.1+dfsg-1 [164 kB] Get: 70 http://deb.debian.org/debian bullseye/main i386 libnuma1 i386 2.0.12-1+b1 [27.9 kB] Get: 71 http://deb.debian.org/debian bullseye/main i386 libnuma-dev i386 2.0.12-1+b1 [41.2 kB] Get: 72 http://deb.debian.org/debian bullseye/main i386 libltdl7 i386 2.4.6-15 [392 kB] Get: 73 http://deb.debian.org/debian bullseye/main i386 libltdl-dev i386 2.4.6-15 [164 kB] Get: 74 http://deb.debian.org/debian bullseye/main i386 libhwloc-dev i386 2.4.1+dfsg-1 [250 kB] Get: 75 http://deb.debian.org/debian bullseye/main i386 libpciaccess0 i386 0.16-1 [55.7 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 77 http://deb.debian.org/debian bullseye/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 78 http://deb.debian.org/debian bullseye/main i386 libxcb1 i386 1.14-3 [144 kB] Get: 79 http://deb.debian.org/debian bullseye/main i386 libx11-data all 2:1.7.1-1 [310 kB] Get: 80 http://deb.debian.org/debian bullseye/main i386 libx11-6 i386 2:1.7.1-1 [796 kB] Get: 81 http://deb.debian.org/debian bullseye/main i386 libxext6 i386 2:1.3.3-1.1 [55.2 kB] Get: 82 http://deb.debian.org/debian bullseye/main i386 libxnvctrl0 i386 460.73.01-1 [26.8 kB] Get: 83 http://deb.debian.org/debian bullseye/main i386 ocl-icd-libopencl1 i386 2.2.14-2 [45.0 kB] Get: 84 http://deb.debian.org/debian bullseye/main i386 libhwloc-plugins i386 2.4.1+dfsg-1 [22.0 kB] Get: 85 http://deb.debian.org/debian bullseye/main i386 libnl-3-dev i386 3.4.0-1+b1 [107 kB] Get: 86 http://deb.debian.org/debian bullseye/main i386 libnl-route-3-dev i386 3.4.0-1+b1 [192 kB] Get: 87 http://deb.debian.org/debian bullseye/main i386 libibverbs-dev i386 33.2-1 [521 kB] Get: 88 http://deb.debian.org/debian bullseye/main i386 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 89 http://deb.debian.org/debian bullseye/main i386 libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB] Get: 90 http://deb.debian.org/debian bullseye/main i386 libpmix2 i386 4.0.0-4 [582 kB] Get: 91 http://deb.debian.org/debian bullseye/main i386 libopenmpi3 i386 4.1.0-10 [2144 kB] Get: 92 http://deb.debian.org/debian bullseye/main i386 openmpi-common all 4.1.0-10 [179 kB] Get: 93 http://deb.debian.org/debian bullseye/main i386 libpmix-dev i386 4.0.0-4 [717 kB] Get: 94 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Get: 95 http://deb.debian.org/debian bullseye/main i386 openmpi-bin i386 4.1.0-10 [209 kB] Get: 96 http://deb.debian.org/debian bullseye/main i386 libopenmpi-dev i386 4.1.0-10 [1142 kB] Get: 97 http://deb.debian.org/debian bullseye/main i386 libpstreams-dev all 1.0.3-1 [134 kB] Get: 98 http://deb.debian.org/debian bullseye/main i386 libterm-readkey-perl i386 2.38-1+b2 [28.3 kB] Get: 99 http://deb.debian.org/debian bullseye/main i386 libtext-wrapper-perl all 1.05-2 [11.0 kB] Fetched 67.6 MB in 1s (94.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19675 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../01-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../03-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_i386.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../07-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_i386.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libmd0:i386. Preparing to unpack .../10-libmd0_1.0.3-3_i386.deb ... Unpacking libmd0:i386 (1.0.3-3) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../11-libbsd0_0.11.3-1_i386.deb ... Unpacking libbsd0:i386 (0.11.3-1) ... Selecting previously unselected package libedit2:i386. Preparing to unpack .../12-libedit2_3.1-20191231-2+b1_i386.deb ... Unpacking libedit2:i386 (3.1-20191231-2+b1) ... Selecting previously unselected package libcbor0:i386. Preparing to unpack .../13-libcbor0_0.5.0+dfsg-2_i386.deb ... Unpacking libcbor0:i386 (0.5.0+dfsg-2) ... Selecting previously unselected package libfido2-1:i386. Preparing to unpack .../14-libfido2-1_1.6.0-2_i386.deb ... Unpacking libfido2-1:i386 (1.6.0-2) ... Selecting previously unselected package openssh-client. Preparing to unpack .../15-openssh-client_1%3a8.4p1-5_i386.deb ... Unpacking openssh-client (1:8.4p1-5) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../16-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../17-m4_1.4.18-5_i386.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../18-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../19-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../20-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../21-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../22-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../23-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../24-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../25-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 .../26-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../27-libfile-stripnondeterminism-perl_1.11.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../28-dh-strip-nondeterminism_1.11.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.11.0-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../29-libelf1_0.183-1_i386.deb ... Unpacking libelf1:i386 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../30-dwz_0.13+20210201-1_i386.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:i386. Preparing to unpack .../31-libicu67_67.1-6_i386.deb ... Unpacking libicu67:i386 (67.1-6) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../32-libxml2_2.9.10+dfsg-6.7_i386.deb ... Unpacking libxml2:i386 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../33-gettext_0.21-4_i386.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../34-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../35-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../36-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libgfortran5:i386. Preparing to unpack .../37-libgfortran5_10.2.1-6_i386.deb ... Unpacking libgfortran5:i386 (10.2.1-6) ... Selecting previously unselected package libgfortran-10-dev:i386. Preparing to unpack .../38-libgfortran-10-dev_10.2.1-6_i386.deb ... Unpacking libgfortran-10-dev:i386 (10.2.1-6) ... Selecting previously unselected package gfortran-10. Preparing to unpack .../39-gfortran-10_10.2.1-6_i386.deb ... Unpacking gfortran-10 (10.2.1-6) ... Selecting previously unselected package libnl-3-200:i386. Preparing to unpack .../40-libnl-3-200_3.4.0-1+b1_i386.deb ... Unpacking libnl-3-200:i386 (3.4.0-1+b1) ... Selecting previously unselected package libnl-route-3-200:i386. Preparing to unpack .../41-libnl-route-3-200_3.4.0-1+b1_i386.deb ... Unpacking libnl-route-3-200:i386 (3.4.0-1+b1) ... Selecting previously unselected package libibverbs1:i386. Preparing to unpack .../42-libibverbs1_33.2-1_i386.deb ... Unpacking libibverbs1:i386 (33.2-1) ... Selecting previously unselected package ibverbs-providers:i386. Preparing to unpack .../43-ibverbs-providers_33.2-1_i386.deb ... Unpacking ibverbs-providers:i386 (33.2-1) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../44-icu-devtools_67.1-6_i386.deb ... Unpacking icu-devtools (67.1-6) ... Selecting previously unselected package libboost1.74-dev:i386. Preparing to unpack .../45-libboost1.74-dev_1.74.0-9_i386.deb ... Unpacking libboost1.74-dev:i386 (1.74.0-9) ... Selecting previously unselected package libboost-filesystem1.74.0:i386. Preparing to unpack .../46-libboost-filesystem1.74.0_1.74.0-9_i386.deb ... Unpacking libboost-filesystem1.74.0:i386 (1.74.0-9) ... Selecting previously unselected package libboost-system1.74.0:i386. Preparing to unpack .../47-libboost-system1.74.0_1.74.0-9_i386.deb ... Unpacking libboost-system1.74.0:i386 (1.74.0-9) ... Selecting previously unselected package libboost-system1.74-dev:i386. Preparing to unpack .../48-libboost-system1.74-dev_1.74.0-9_i386.deb ... Unpacking libboost-system1.74-dev:i386 (1.74.0-9) ... Selecting previously unselected package libboost-filesystem1.74-dev:i386. Preparing to unpack .../49-libboost-filesystem1.74-dev_1.74.0-9_i386.deb ... Unpacking libboost-filesystem1.74-dev:i386 (1.74.0-9) ... Selecting previously unselected package libboost-filesystem-dev:i386. Preparing to unpack .../50-libboost-filesystem-dev_1.74.0.3_i386.deb ... Unpacking libboost-filesystem-dev:i386 (1.74.0.3) ... Selecting previously unselected package libboost-regex1.74.0:i386. Preparing to unpack .../51-libboost-regex1.74.0_1.74.0-9_i386.deb ... Unpacking libboost-regex1.74.0:i386 (1.74.0-9) ... Selecting previously unselected package libicu-dev:i386. Preparing to unpack .../52-libicu-dev_67.1-6_i386.deb ... Unpacking libicu-dev:i386 (67.1-6) ... Selecting previously unselected package libboost-regex1.74-dev:i386. Preparing to unpack .../53-libboost-regex1.74-dev_1.74.0-9_i386.deb ... Unpacking libboost-regex1.74-dev:i386 (1.74.0-9) ... Selecting previously unselected package libboost-iostreams1.74-dev:i386. Preparing to unpack .../54-libboost-iostreams1.74-dev_1.74.0-9_i386.deb ... Unpacking libboost-iostreams1.74-dev:i386 (1.74.0-9) ... Selecting previously unselected package libboost-iostreams-dev:i386. Preparing to unpack .../55-libboost-iostreams-dev_1.74.0.3_i386.deb ... Unpacking libboost-iostreams-dev:i386 (1.74.0.3) ... Selecting previously unselected package libboost-regex-dev:i386. Preparing to unpack .../56-libboost-regex-dev_1.74.0.3_i386.deb ... Unpacking libboost-regex-dev:i386 (1.74.0.3) ... Selecting previously unselected package libcrypto++8:i386. Preparing to unpack .../57-libcrypto++8_8.4.0-1_i386.deb ... Unpacking libcrypto++8:i386 (8.4.0-1) ... Selecting previously unselected package libcrypto++-dev:i386. Preparing to unpack .../58-libcrypto++-dev_8.4.0-1_i386.deb ... Unpacking libcrypto++-dev:i386 (8.4.0-1) ... Selecting previously unselected package libevent-2.1-7:i386. Preparing to unpack .../59-libevent-2.1-7_2.1.12-stable-1_i386.deb ... Unpacking libevent-2.1-7:i386 (2.1.12-stable-1) ... Selecting previously unselected package libevent-core-2.1-7:i386. Preparing to unpack .../60-libevent-core-2.1-7_2.1.12-stable-1_i386.deb ... Unpacking libevent-core-2.1-7:i386 (2.1.12-stable-1) ... Selecting previously unselected package libevent-extra-2.1-7:i386. 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Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/murasaki-1.68.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package murasaki dpkg-buildpackage: info: source version 1.68.6-12 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_auto_clean make -j18 clean make[1]: Entering directory '/build/murasaki-1.68.6' rm -rf *.o *~ .*~ core make -C src clean make[2]: Entering directory '/build/murasaki-1.68.6/src' rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa make[2]: Leaving directory '/build/murasaki-1.68.6/src' make[1]: Leaving directory '/build/murasaki-1.68.6' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/murasaki-1.68.6' dh_auto_build -- USE_MPI=YES make -j18 "INSTALL=install --strip-program=true" USE_MPI=YES make[2]: Entering directory '/build/murasaki-1.68.6' make -C src all make[3]: Entering directory '/build/murasaki-1.68.6/src' mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c murasaki.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c timing.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c dinkymath.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c sequence.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c msethash.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c options.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecohash.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecolist.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c murasaki_mpi.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c arrayhash.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c seqread.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c scoring.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c openhash.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c genopts.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c binseq.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-image.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-compare.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-random.cc cgr.cc: In member function 'void Cgr::merge(Cgr&)': cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable] 140 | int redist=(unsigned long)(rez*rez)<=seedcount; | ^~~~~~ cgr.cc: In member function 'bool Cgr::savePNG(std::string)': cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable] 288 | int res; | ^~~ cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)': cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable] 435 | int wordwidth=1; | ^~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-sample.cc binseq.cc: In member function 'bool SequenceBinary::save(std::string)': binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 70 | }catch(ofstream::failure e){ | ^ binseq.cc: In member function 'void SequenceBinary::fillCopyVectors()': binseq.cc:158:67: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 158 | memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region)); | ^ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/istream:38, from /usr/include/c++/10/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/10/bits/stl_pair.h:211:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 211 | struct pair | ^~~~ binseq.cc:160:75: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 160 | memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region)); | ^ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/istream:38, from /usr/include/c++/10/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/10/bits/stl_pair.h:211:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 211 | struct pair | ^~~~ binseq.cc:162:75: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 162 | memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region)); | ^ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/istream:38, from /usr/include/c++/10/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/10/bits/stl_pair.h:211:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 211 | struct pair | ^~~~ dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)': dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] 40 | int last=0; | ^~~~ dinkymath.cc: In function 'std::string littleEndianPat(unsigned int, int)': dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] 53 | int last=0; | ^~~~ sequence.cc: In destructor 'Sequence::~Sequence()': sequence.cc:377:2: warning: 'throw' will always call 'terminate' [-Wterminate] 377 | throw MurasakiException("Couldn't mark System V IPC shared memory region for deletion for sequence "+name+strerror(errno)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence.cc:377:2: note: in C++11 destructors default to 'noexcept' sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)': sequence.cc:1113:136: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector >::val_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1113 | memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]); | ^ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/stl_tree.h:63, from /usr/include/c++/10/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/10/bits/stl_pair.h:211:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here 211 | struct pair | ^~~~ sequence.cc:1114:97: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector >::val_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1114 | memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]); | ^ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/stl_tree.h:63, from /usr/include/c++/10/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/10/bits/stl_pair.h:211:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here 211 | struct pair | ^~~~ sequence.cc: In destructor 'BitSequence::~BitSequence()': sequence.cc:1394:2: warning: 'throw' will always call 'terminate' [-Wterminate] 1394 | throw MurasakiException("Couldn't detach System V shared memory region for "+(seq ? seq->filename:string("(anon)"))+strerror(errno)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence.cc:1394:2: note: in C++11 destructors default to 'noexcept' murasaki_mpi.cc: In function 'void mpi_hasher_client_mode(BitSequence*)': murasaki_mpi.cc:561:9: warning: variable 'send_done' set but not used [-Wunused-but-set-variable] 561 | int send_done; | ^~~~~~~~~ murasaki_mpi.cc: In function 'word mpi_extract_checkSentQueue(std::vector >&, std::vector > >&, std::multimap&)': murasaki_mpi.cc:1025:7: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] 1025 | packetsLeft++; | ^~~~~~~~~~~ sequence.cc: In member function 'std::pair IntervalSet::entropy() const': sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable] 3332 | SeqPos shortest=0,shortlen=length(spaces[0]); | ^~~~~~~~ In file included from sequence.h:44, from murasaki.h:24, from sequence.cc:28: shmvector.hh: In instantiation of 'void ShmVector::shmRealloc(size_t) [with T = std::pair; size_t = unsigned int]': shmvector.hh:282:5: required from 'void ShmVector::resize(size_t) [with T = std::pair; size_t = unsigned int]' sequence.cc:1110:39: required from here shmvector.hh:225:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 225 | memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/stl_tree.h:63, from /usr/include/c++/10/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/10/bits/stl_pair.h:211:12: note: 'struct std::pair' declared here 211 | struct pair | ^~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c testeco.cc murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list&, int, int)': murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable] 1008 | bool revZero=false; | ^~~~~~~ cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::string)': cgr.cc:557:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:557:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized] mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-compare.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c alignments.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-or.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c geneparse.cc cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)': cgr.cc:485:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:485:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized] mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-and.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-best.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-coverage.cc cgr-sample.cc: In function 'int main(int, char**)': cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable] 54 | bool repeatmask=false,save=false; | ^~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c getsegments.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c mbfa.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now testeco.cc: In function 'long int bigrand()': testeco.cc:29:41: warning: left shift count >= width of type [-Wshift-count-overflow] 29 | return (long)(((unsigned long)(rand())<<32) + ((unsigned long)(rand()))); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~ getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::string)': getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=] 153 | }catch(bad_lexical_cast e){ | ^ align-coverage.cc: In function 'int main(int, char**)': align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable] 148 | bool seqStats=true; | ^~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/murasaki-1.68.6/src' make[2]: Leaving directory '/build/murasaki-1.68.6' for bin in geneparse mbfa murasaki cgr-* testeco align-* ; do \ mv ${bin} ${bin}-mpi ; \ done make clean make[2]: Entering directory '/build/murasaki-1.68.6' rm -rf *.o *~ .*~ core make -C src clean make[3]: Entering directory '/build/murasaki-1.68.6/src' rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa make[3]: Leaving directory '/build/murasaki-1.68.6/src' make[2]: Leaving directory '/build/murasaki-1.68.6' dh_auto_build -- USE_MPI=NO make -j18 "INSTALL=install --strip-program=true" USE_MPI=NO make[2]: Entering directory '/build/murasaki-1.68.6' make -C src all make[3]: Entering directory '/build/murasaki-1.68.6/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c murasaki.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c timing.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c dinkymath.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c sequence.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c msethash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c options.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c ecohash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c ecolist.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c murasaki_mpi.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c arrayhash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c seqread.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c scoring.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c openhash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c genopts.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c binseq.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-image.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-compare.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-random.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-sample.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c testeco.cc cgr.cc: In member function 'void Cgr::merge(Cgr&)': cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable] 140 | int redist=(unsigned long)(rez*rez)<=seedcount; | ^~~~~~ cgr.cc: In member function 'bool Cgr::savePNG(std::string)': cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable] 288 | int res; | ^~~ cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)': cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable] 435 | int wordwidth=1; | ^~~~~~~~~ binseq.cc: In member function 'bool SequenceBinary::save(std::string)': binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 70 | }catch(ofstream::failure e){ | ^ binseq.cc: In member function 'void SequenceBinary::fillCopyVectors()': binseq.cc:158:67: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 158 | memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region)); | ^ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/istream:38, from /usr/include/c++/10/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/10/bits/stl_pair.h:211:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 211 | struct pair | ^~~~ binseq.cc:160:75: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 160 | memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region)); | ^ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/istream:38, from /usr/include/c++/10/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/10/bits/stl_pair.h:211:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 211 | struct pair | ^~~~ binseq.cc:162:75: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 162 | memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region)); | ^ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/istream:38, from /usr/include/c++/10/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/10/bits/stl_pair.h:211:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 211 | struct pair | ^~~~ sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)': sequence.cc:1113:136: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector >::val_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1113 | memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]); | ^ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/stl_tree.h:63, from /usr/include/c++/10/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/10/bits/stl_pair.h:211:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here 211 | struct pair | ^~~~ sequence.cc:1114:97: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector >::val_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1114 | memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]); | ^ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/stl_tree.h:63, from /usr/include/c++/10/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/10/bits/stl_pair.h:211:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here 211 | struct pair | ^~~~ dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)': dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] 40 | int last=0; | ^~~~ dinkymath.cc: In function 'std::string littleEndianPat(unsigned int, int)': dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] 53 | int last=0; | ^~~~ sequence.cc: In member function 'std::pair IntervalSet::entropy() const': sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable] 3332 | SeqPos shortest=0,shortlen=length(spaces[0]); | ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-compare.cc In file included from sequence.h:44, from murasaki.h:24, from sequence.cc:28: shmvector.hh: In instantiation of 'void ShmVector::shmRealloc(size_t) [with T = std::pair; size_t = unsigned int]': shmvector.hh:282:5: required from 'void ShmVector::resize(size_t) [with T = std::pair; size_t = unsigned int]' sequence.cc:1110:39: required from here shmvector.hh:225:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 225 | memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/stl_tree.h:63, from /usr/include/c++/10/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/10/bits/stl_pair.h:211:12: note: 'struct std::pair' declared here 211 | struct pair | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c alignments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-or.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c geneparse.cc murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list&, int, int)': murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable] 1008 | bool revZero=false; | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-and.cc cgr-sample.cc: In function 'int main(int, char**)': cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable] 54 | bool repeatmask=false,save=false; | ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-best.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-coverage.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c getsegments.cc cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::string)': cgr.cc:557:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:557:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized] testeco.cc: In function 'long int bigrand()': testeco.cc:29:41: warning: left shift count >= width of type [-Wshift-count-overflow] 29 | return (long)(((unsigned long)(rand())<<32) + ((unsigned long)(rand()))); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c mbfa.cc cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)': cgr.cc:485:31: warning: 'height' may be used uninitialized in this function [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:485:31: warning: 'width' may be used uninitialized in this function [-Wmaybe-uninitialized] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now align-coverage.cc: In function 'int main(int, char**)': align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable] 148 | bool seqStats=true; | ^~~~~~~~ getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::string)': getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=] 153 | }catch(bad_lexical_cast e){ | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/murasaki-1.68.6/src' make[2]: Leaving directory '/build/murasaki-1.68.6' make[1]: Leaving directory '/build/murasaki-1.68.6' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install-arch make[1]: Entering directory '/build/murasaki-1.68.6' dh_install -a # using wildcards in install files is practical but it duplicates some files find debian/murasaki/usr -name "*-mpi" -delete make[1]: Leaving directory '/build/murasaki-1.68.6' dh_install -Nmurasaki -Nmurasaki-mpi dh_installdocs dh_installchangelogs debian/rules override_dh_installman-arch make[1]: Entering directory '/build/murasaki-1.68.6' dh_installman -a mkdir -p debian/murasaki-mpi/usr/share/man/man1 for man in debian/murasaki/usr/share/man/man1/*.1 ; do \ cp -a ${man} debian/murasaki-mpi/usr/share/man/man1/`basename ${man} .1`-mpi.1 ; \ done make[1]: Leaving directory '/build/murasaki-1.68.6' debian/rules override_dh_installman-indep make[1]: Entering directory '/build/murasaki-1.68.6' dh_installman -i # create manpages for PL files mkdir -p debian/murasaki-common/usr/share/man/man1 for pscript in debian/murasaki-common/usr/lib/debian-med/bin/* ; do \ pod2man ${pscript} > debian/murasaki-common/usr/share/man/man1/`basename ${pscript}`.1 ; \ done pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/anchors2maf.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/anchors2osfinder.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/antisense.pl debian/murasaki-common/usr/lib/debian-med/bin/chromostitch.pl around line 134: '=item' outside of any '=over' debian/murasaki-common/usr/lib/debian-med/bin/chromostitch.pl around line 141: You forgot a '=back' before '=head1' POD document had syntax errors at /usr/bin/pod2man line 69. pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/dna2binary.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/dnashuffle.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/geneparse.pl debian/murasaki-common/usr/lib/debian-med/bin/getcds.pl around line 646: '=item' outside of any '=over' debian/murasaki-common/usr/lib/debian-med/bin/getcds.pl around line 646: =over without closing =back POD document had syntax errors at /usr/bin/pod2man line 69. pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/humantime.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/osfinder2anchors.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/randpat.pl find debian/murasaki-common/usr/share/man/man1 -empty -delete make[1]: Leaving directory '/build/murasaki-1.68.6' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms-indep make[1]: Entering directory '/build/murasaki-1.68.6' dh_fixperms -i chmod a+x debian/murasaki-common/usr/share/perl5/murasaki/config.pl make[1]: Leaving directory '/build/murasaki-1.68.6' dh_fixperms -Nmurasaki-common dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package murasaki-common: substitution variable ${misc:perl} used, but is not defined dpkg-gencontrol: warning: package murasaki-common: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-12_i386.deb'. dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-12_i386.deb'. dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-12_i386.deb'. dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-12_i386.deb'. dpkg-deb: building package 'murasaki-common' in '../murasaki-common_1.68.6-12_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../murasaki_1.68.6-12_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) 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/46125 and its subdirectories I: Current time: Sun Aug 7 13:15:44 -12 2022 I: pbuilder-time-stamp: 1659921344 Mon Jul 5 18:52:45 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net. Mon Jul 5 18:52:45 UTC 2021 I: Preparing to do remote build '2' on ionos12-i386.debian.net. Mon Jul 5 19:01:25 UTC 2021 I: Deleting $TMPDIR on ionos12-i386.debian.net. Mon Jul 5 19:01:25 UTC 2021 I: murasaki_1.68.6-12_i386.changes: Format: 1.8 Date: Sat, 20 Mar 2021 00:16:09 +0530 Source: murasaki Binary: murasaki murasaki-common murasaki-dbgsym murasaki-mpi murasaki-mpi-dbgsym Architecture: all i386 Version: 1.68.6-12 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: murasaki - homology detection tool across multiple large genomes murasaki-common - homology detection tool across multiple large genomes (common fil murasaki-mpi - homology detection tool across multiple large genomes (MPI-versio Changes: murasaki (1.68.6-12) unstable; urgency=medium . * Team Upload. * Remove recommends on murasaki-examples which is non-existent Checksums-Sha1: 30820980d3c026118b970308ad8c634e83c15b2d 145496 murasaki-common_1.68.6-12_all.deb 3b3974214611763d2ea912a9e017075fb60ad54d 10496632 murasaki-dbgsym_1.68.6-12_i386.deb 3f0f79d58e871c12c0d48d5a8c0e047a70a4c759 11669756 murasaki-mpi-dbgsym_1.68.6-12_i386.deb fad30188ade38ff317c5ba40d597783077c03d83 656028 murasaki-mpi_1.68.6-12_i386.deb 143fc384371ec8f26116f8c4bbf1246ef493349b 8034 murasaki_1.68.6-12_i386.buildinfo 4fcbf6f6f6b059fc37c26ebbcf409302d9e48ae8 539188 murasaki_1.68.6-12_i386.deb Checksums-Sha256: 1e7d41a2b1653c577d5d3d0353da9dc44d2b2c7fadeea9324967f1f2b3684e53 145496 murasaki-common_1.68.6-12_all.deb 76ff30409af041b70a62070e577da7f8f303f44ae8bb1c0335309716fa9ef714 10496632 murasaki-dbgsym_1.68.6-12_i386.deb df94621eaa6e515c6322c77731eeb2233bd02db2b8aa0df1f9e4b06ed01f4bd9 11669756 murasaki-mpi-dbgsym_1.68.6-12_i386.deb 28c812945c56ca871e1bba3191a886da5345fa7253abb55d03c349184469a503 656028 murasaki-mpi_1.68.6-12_i386.deb aaa3b49c907b46484baf98f313de9189c9e8af8761a0285a3959dac38c5d0640 8034 murasaki_1.68.6-12_i386.buildinfo b42a374b2a6f6c202b0343a26a87757e797edf785bd9fa129cf1c54621783661 539188 murasaki_1.68.6-12_i386.deb Files: dfd990d768754ac72a7a8b110b53a97b 145496 science optional murasaki-common_1.68.6-12_all.deb a0fcd7c7c3ce3ed19948ab5c6f75b1a6 10496632 debug optional murasaki-dbgsym_1.68.6-12_i386.deb 6a0ee2ff5234347937f926edd9688f90 11669756 debug optional murasaki-mpi-dbgsym_1.68.6-12_i386.deb b1a0def4761b02a2cdab621bfa64a5ba 656028 science optional murasaki-mpi_1.68.6-12_i386.deb 205a8bb164109cafaec00409ab3b4f90 8034 science optional murasaki_1.68.6-12_i386.buildinfo 6bd4d7a821fb6e725344ba72fa9d5476 539188 science optional murasaki_1.68.6-12_i386.deb Mon Jul 5 19:01:26 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.F0enMlAcbx/murasaki_1.68.6-12.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.F0enMlAcbx/murasaki_1.68.6-12.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.F0enMlAcbx/murasaki_1.68.6-12.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.F0enMlAcbx/b1/murasaki_1.68.6-12_i386.changes /srv/reproducible-results/rbuild-debian/tmp.F0enMlAcbx/b2/murasaki_1.68.6-12_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: 0.568s) 0.568s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.264s) 0.264s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Jul 5 19:01:28 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Mon Jul 5 19:01:28 UTC 2021 I: murasaki from bullseye built successfully and reproducibly on i386. Mon Jul 5 19:01:29 UTC 2021 I: Submitting .buildinfo files to external archives: Mon Jul 5 19:01:29 UTC 2021 I: Submitting 12K b1/murasaki_1.68.6-12_i386.buildinfo.asc Mon Jul 5 19:01:30 UTC 2021 I: Submitting 12K b2/murasaki_1.68.6-12_i386.buildinfo.asc Mon Jul 5 19:01:31 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jul 5 19:01:31 UTC 2021 I: Done submitting .buildinfo files. Mon Jul 5 19:01:31 UTC 2021 I: Removing signed murasaki_1.68.6-12_i386.buildinfo.asc files: removed './b1/murasaki_1.68.6-12_i386.buildinfo.asc' removed './b2/murasaki_1.68.6-12_i386.buildinfo.asc'