Fri Jul 17 05:21:04 UTC 2020 I: starting to build murasaki/buster/arm64 on jenkins on '2020-07-17 05:20' Fri Jul 17 05:21:04 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_27/4008/console.log Fri Jul 17 05:21:04 UTC 2020 I: Downloading source for buster/murasaki=1.68.6-8 --2020-07-17 05:21:04-- http://deb.debian.org/debian/pool/main/m/murasaki/murasaki_1.68.6-8.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2233 (2.2K) Saving to: ‘murasaki_1.68.6-8.dsc’ 0K .. 100% 1.48M=0.001s 2020-07-17 05:21:04 (1.48 MB/s) - ‘murasaki_1.68.6-8.dsc’ saved [2233/2233] Fri Jul 17 05:21:04 UTC 2020 I: murasaki_1.68.6-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: murasaki Binary: murasaki, murasaki-mpi, murasaki-common Architecture: any all Version: 1.68.6-8 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/murasaki Vcs-Git: https://salsa.debian.org/med-team/murasaki.git Build-Depends: debhelper (>= 11~), 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: 398a53fe76476ec3c756754d13541dd25d98a58a 307745 murasaki_1.68.6.orig.tar.gz 54ef23b1e49028d148252b8843646a8ece97e9e2 8620 murasaki_1.68.6-8.debian.tar.xz Checksums-Sha256: ebb3f3df2c0b3dc9f43977685f6c5e37ea483fb4189f7d965acc634bd10aaefe 307745 murasaki_1.68.6.orig.tar.gz 18d5463472f5b64aba7376fb0158d92fd4d16a5d4be4b54e931cc9fd95ad9a89 8620 murasaki_1.68.6-8.debian.tar.xz Files: 25477c77aa21246d4a639527836e6c77 307745 murasaki_1.68.6.orig.tar.gz b5f1434bf5b1e6b2dbb0f9b57a26f709 8620 murasaki_1.68.6-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlu7RpMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtE6Cw//ZRv48rgqvye6UfNLjdCCMEOW2nTLNQDK SGSxViSKdmcCNiPetgxRQqJMeObOS+TWq30lATcc7teLDs+D9DPCiBABbmU10S7o D9RdkoUnGW4s0PbV8efEiyhB7TMp71DDjG0bdvDKWBMKJ4ZEcizfO5U1Uu6VJdJG A5mectsH8OhHY0892Y1mXPNrP0HvWxTAVs1ZKpqs4n95mdU6HZZx3W2rdbIGdOkv PFLQioSSVonY6qxdRySvHJcwX4TcsSj2mxOUAfpSyN5pSJGP3wrqzPB929/c6Aoz ALNM2GwB//tu4i9yrnyv+WNUy/zymPNSTTaT251YmuQ/36bqxESK/FCxhyFDROk5 ZljQAyFdDeebyQ2xoMEhkwyjc9HalqIR22clJZVzQyYymk56Jct3M9360dbfqsjt TW1oEZL/VLDx06On/b891Av20dqpXD5Z0XwEKtVcsw/j3kn3DDyhAYJ436sdQE7N nOhCpanaUcJcJAW/7Qx/9LBnj+MSlPAIxKVT2JKNiHBxJZWl9X2MwrKwMdtJkhmW IDvPHwAmqzghiDXCpnp02U8Ar4a7pHji96JAUVFvOyJ6TdNs/auvV84l0HpTvBQn S+zLqhX/9KtULh/omsn/vHwMXqJogA0KiWiJnne4TGwEnI15P3EveSd+IAzB3POb mXdqqJQ8jyU= =IIAP -----END PGP SIGNATURE----- Fri Jul 17 05:21:04 UTC 2020 I: Checking whether the package is not for us Fri Jul 17 05:21:04 UTC 2020 I: Starting 1st build on remote node codethink-sled15-arm64.debian.net. Fri Jul 17 05:21:04 UTC 2020 I: Preparing to do remote build '1' on codethink-sled15-arm64.debian.net. Fri Jul 17 05:24:38 UTC 2020 I: Deleting $TMPDIR on codethink-sled15-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Aug 18 23:44:11 -12 2021 I: pbuilder-time-stamp: 1629373451 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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: Copying source file I: copying [murasaki_1.68.6-8.dsc] I: copying [./murasaki_1.68.6.orig.tar.gz] I: copying [./murasaki_1.68.6-8.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Oct 7 23:59:15 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./murasaki_1.68.6-8.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_1.68.6-8.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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/31062/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='31062' 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.KZNuIZtP4e/pbuilderrc_ze31 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.KZNuIZtP4e/b1 --logfile b1/build.log murasaki_1.68.6-8.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled15-arm64 4.4.0-185-generic #215-Ubuntu SMP Mon Jun 8 21:55:24 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 18 02:48 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/31062/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), 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 ... 19168 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 (>= 11~); however: Package debhelper 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} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-filesystem-dev{a} libboost-filesystem1.67-dev{a} libboost-filesystem1.67.0{a} libboost-iostreams-dev{a} libboost-iostreams1.67-dev{a} libboost-regex-dev{a} libboost-regex1.67-dev{a} libboost-regex1.67.0{a} libboost-system1.67-dev{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libcrypto++-dev{a} libcrypto++6{a} libedit2{a} libelf1{a} libevent-2.1-6{a} libevent-core-2.1-6{a} libevent-pthreads-2.1-6{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc5{a} libibverbs-dev{a} libibverbs1{a} libicu-dev{a} libicu63{a} libjs-jquery{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{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} libpmix2{a} libpstreams-dev{a} libsigsegv2{a} libssl1.1{a} libterm-readkey-perl{a} libtext-wrapper-perl{a} libtool{a} libuchardet0{a} libxml2{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} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libglib2.0-data libgpm2 libmail-sendmail-perl lynx shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 84 newly installed, 0 to remove and 0 not upgraded. Need to get 50.1 MB of archives. After unpacking 315 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 libedit2 arm64 3.1-20181209-1 [91.2 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libkeyutils1 arm64 1.6-6 [14.9 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 libkrb5support0 arm64 1.17-3 [64.7 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 libk5crypto3 arm64 1.17-3 [122 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 libkrb5-3 arm64 1.17-3 [353 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libgssapi-krb5-2 arm64 1.17-3 [150 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 openssh-client arm64 1:7.9p1-10+deb10u2 [757 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 libnl-3-200 arm64 3.4.0-1 [54.9 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 libnl-route-3-200 arm64 3.4.0-1 [134 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libibverbs1 arm64 22.1-1 [47.8 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 ibverbs-providers arm64 22.1-1 [174 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 icu-devtools arm64 63.1-6+deb10u1 [179 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 libboost1.67-dev arm64 1.67.0-13+deb10u1 [8388 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 libboost-filesystem1.67.0 arm64 1.67.0-13+deb10u1 [257 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 libboost-system1.67-dev arm64 1.67.0-13+deb10u1 [231 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 libboost-filesystem1.67-dev arm64 1.67.0-13+deb10u1 [267 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 libboost-filesystem-dev arm64 1.67.0.1 [3684 B] Get: 52 http://deb.debian.org/debian buster/main arm64 libboost-regex1.67.0 arm64 1.67.0-13+deb10u1 [458 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 libicu-dev arm64 63.1-6+deb10u1 [9062 kB] Get: 54 http://deb.debian.org/debian buster/main arm64 libboost-regex1.67-dev arm64 1.67.0-13+deb10u1 [517 kB] Get: 55 http://deb.debian.org/debian buster/main arm64 libboost-iostreams1.67-dev arm64 1.67.0-13+deb10u1 [255 kB] Get: 56 http://deb.debian.org/debian buster/main arm64 libboost-iostreams-dev arm64 1.67.0.1 [3632 B] Get: 57 http://deb.debian.org/debian buster/main arm64 libboost-regex-dev arm64 1.67.0.1 [3916 B] Get: 58 http://deb.debian.org/debian buster/main arm64 libcrypto++6 arm64 5.6.4-8 [780 kB] Get: 59 http://deb.debian.org/debian buster/main arm64 libcrypto++-dev arm64 5.6.4-8 [1317 kB] Get: 60 http://deb.debian.org/debian buster/main arm64 libevent-2.1-6 arm64 2.1.8-stable-4 [150 kB] Get: 61 http://deb.debian.org/debian buster/main arm64 libevent-core-2.1-6 arm64 2.1.8-stable-4 [112 kB] Get: 62 http://deb.debian.org/debian buster/main arm64 libevent-pthreads-2.1-6 arm64 2.1.8-stable-4 [47.7 kB] Get: 63 http://deb.debian.org/debian buster/main arm64 libgfortran5 arm64 8.3.0-6 [298 kB] Get: 64 http://deb.debian.org/debian buster/main arm64 libltdl7 arm64 2.4.6-9 [389 kB] Get: 65 http://deb.debian.org/debian buster/main arm64 libnuma1 arm64 2.0.12-1 [25.6 kB] Get: 66 http://deb.debian.org/debian buster/main arm64 libhwloc5 arm64 1.11.12-3 [97.9 kB] Get: 67 http://deb.debian.org/debian buster/main arm64 libnuma-dev arm64 2.0.12-1 [40.0 kB] Get: 68 http://deb.debian.org/debian buster/main arm64 libltdl-dev arm64 2.4.6-9 [162 kB] Get: 69 http://deb.debian.org/debian buster/main arm64 libhwloc-dev arm64 1.11.12-3 [165 kB] Get: 70 http://deb.debian.org/debian buster/main arm64 libpciaccess0 arm64 0.14-1 [51.0 kB] Get: 71 http://deb.debian.org/debian buster/main arm64 ocl-icd-libopencl1 arm64 2.2.12-2 [37.4 kB] Get: 72 http://deb.debian.org/debian buster/main arm64 libhwloc-plugins arm64 1.11.12-3 [16.9 kB] Get: 73 http://deb.debian.org/debian buster/main arm64 libnl-3-dev arm64 3.4.0-1 [98.2 kB] Get: 74 http://deb.debian.org/debian buster/main arm64 libnl-route-3-dev arm64 3.4.0-1 [162 kB] Get: 75 http://deb.debian.org/debian buster/main arm64 libibverbs-dev arm64 22.1-1 [356 kB] Get: 76 http://deb.debian.org/debian buster/main arm64 libjs-jquery all 3.3.1~dfsg-3 [332 kB] Get: 77 http://deb.debian.org/debian buster/main arm64 libpmix2 arm64 3.1.2-3 [455 kB] Get: 78 http://deb.debian.org/debian buster/main arm64 libopenmpi3 arm64 3.1.3-11 [1996 kB] Get: 79 http://deb.debian.org/debian buster/main arm64 openmpi-common all 3.1.3-11 [165 kB] Get: 80 http://deb.debian.org/debian buster/main arm64 openmpi-bin arm64 3.1.3-11 [199 kB] Get: 81 http://deb.debian.org/debian buster/main arm64 libopenmpi-dev arm64 3.1.3-11 [974 kB] Get: 82 http://deb.debian.org/debian buster/main arm64 libpstreams-dev all 1.0.1-2 [129 kB] Get: 83 http://deb.debian.org/debian buster/main arm64 libterm-readkey-perl arm64 2.38-1 [27.0 kB] Get: 84 http://deb.debian.org/debian buster/main arm64 libtext-wrapper-perl all 1.05-2 [11.0 kB] Fetched 50.1 MB in 4s (13.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../11-libedit2_3.1-20181209-1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20181209-1) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../12-libkeyutils1_1.6-6_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6-6) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../13-libkrb5support0_1.17-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.17-3) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../14-libk5crypto3_1.17-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.17-3) ... Selecting previously unselected package libssl1.1:arm64. Preparing to unpack .../15-libssl1.1_1.1.1d-0+deb10u3_arm64.deb ... Unpacking libssl1.1:arm64 (1.1.1d-0+deb10u3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../16-libkrb5-3_1.17-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.17-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../17-libgssapi-krb5-2_1.17-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.17-3) ... Selecting previously unselected package openssh-client. Preparing to unpack .../18-openssh-client_1%3a7.9p1-10+deb10u2_arm64.deb ... Unpacking openssh-client (1:7.9p1-10+deb10u2) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../19-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../20-m4_1.4.18-2_arm64.deb ... Unpacking m4 (1.4.18-2) ... 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Preparing to unpack .../27-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../28-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../29-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../30-libelf1_0.176-1.1_arm64.deb ... Unpacking libelf1:arm64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../31-dwz_0.12-3_arm64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../32-libglib2.0-0_2.58.3-2+deb10u2_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:arm64. Preparing to unpack .../33-libicu63_63.1-6+deb10u1_arm64.deb ... Unpacking libicu63:arm64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../34-libxml2_2.9.4+dfsg1-7+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:arm64. Preparing to unpack .../35-libcroco3_0.6.12-3_arm64.deb ... Unpacking libcroco3:arm64 (0.6.12-3) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../36-libncurses6_6.1+20181013-2+deb10u2_arm64.deb ... Unpacking libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../37-gettext_0.19.8.1-9_arm64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../38-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 .../39-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../40-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package libnl-3-200:arm64. Preparing to unpack .../41-libnl-3-200_3.4.0-1_arm64.deb ... Unpacking libnl-3-200:arm64 (3.4.0-1) ... Selecting previously unselected package libnl-route-3-200:arm64. Preparing to unpack .../42-libnl-route-3-200_3.4.0-1_arm64.deb ... Unpacking libnl-route-3-200:arm64 (3.4.0-1) ... Selecting previously unselected package libibverbs1:arm64. Preparing to unpack .../43-libibverbs1_22.1-1_arm64.deb ... Unpacking libibverbs1:arm64 (22.1-1) ... Selecting previously unselected package ibverbs-providers:arm64. Preparing to unpack .../44-ibverbs-providers_22.1-1_arm64.deb ... Unpacking ibverbs-providers:arm64 (22.1-1) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../45-icu-devtools_63.1-6+deb10u1_arm64.deb ... Unpacking icu-devtools (63.1-6+deb10u1) ... Selecting previously unselected package libboost1.67-dev:arm64. Preparing to unpack .../46-libboost1.67-dev_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost1.67-dev:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-filesystem1.67.0:arm64. Preparing to unpack .../47-libboost-filesystem1.67.0_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-filesystem1.67.0:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-system1.67-dev:arm64. Preparing to unpack .../48-libboost-system1.67-dev_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-system1.67-dev:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-filesystem1.67-dev:arm64. Preparing to unpack .../49-libboost-filesystem1.67-dev_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-filesystem1.67-dev:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-filesystem-dev:arm64. Preparing to unpack .../50-libboost-filesystem-dev_1.67.0.1_arm64.deb ... Unpacking libboost-filesystem-dev:arm64 (1.67.0.1) ... Selecting previously unselected package libboost-regex1.67.0:arm64. Preparing to unpack .../51-libboost-regex1.67.0_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-regex1.67.0:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libicu-dev:arm64. Preparing to unpack .../52-libicu-dev_63.1-6+deb10u1_arm64.deb ... Unpacking libicu-dev:arm64 (63.1-6+deb10u1) ... Selecting previously unselected package libboost-regex1.67-dev:arm64. Preparing to unpack .../53-libboost-regex1.67-dev_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-regex1.67-dev:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-iostreams1.67-dev:arm64. Preparing to unpack .../54-libboost-iostreams1.67-dev_1.67.0-13+deb10u1_arm64.deb ... Unpacking libboost-iostreams1.67-dev:arm64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-iostreams-dev:arm64. Preparing to unpack .../55-libboost-iostreams-dev_1.67.0.1_arm64.deb ... Unpacking libboost-iostreams-dev:arm64 (1.67.0.1) ... Selecting previously unselected package libboost-regex-dev:arm64. Preparing to unpack .../56-libboost-regex-dev_1.67.0.1_arm64.deb ... Unpacking libboost-regex-dev:arm64 (1.67.0.1) ... Selecting previously unselected package libcrypto++6. Preparing to unpack .../57-libcrypto++6_5.6.4-8_arm64.deb ... Unpacking libcrypto++6 (5.6.4-8) ... Selecting previously unselected package libcrypto++-dev. Preparing to unpack .../58-libcrypto++-dev_5.6.4-8_arm64.deb ... Unpacking libcrypto++-dev (5.6.4-8) ... Selecting previously unselected package libevent-2.1-6:arm64. Preparing to unpack .../59-libevent-2.1-6_2.1.8-stable-4_arm64.deb ... Unpacking libevent-2.1-6:arm64 (2.1.8-stable-4) ... Selecting previously unselected package libevent-core-2.1-6:arm64. Preparing to unpack .../60-libevent-core-2.1-6_2.1.8-stable-4_arm64.deb ... Unpacking libevent-core-2.1-6:arm64 (2.1.8-stable-4) ... Selecting previously unselected package libevent-pthreads-2.1-6:arm64. Preparing to unpack .../61-libevent-pthreads-2.1-6_2.1.8-stable-4_arm64.deb ... Unpacking libevent-pthreads-2.1-6:arm64 (2.1.8-stable-4) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../62-libgfortran5_8.3.0-6_arm64.deb ... Unpacking libgfortran5:arm64 (8.3.0-6) ... Selecting previously unselected package libltdl7:arm64. Preparing to unpack .../63-libltdl7_2.4.6-9_arm64.deb ... Unpacking libltdl7:arm64 (2.4.6-9) ... Selecting previously unselected package libnuma1:arm64. Preparing to unpack .../64-libnuma1_2.0.12-1_arm64.deb ... Unpacking libnuma1:arm64 (2.0.12-1) ... Selecting previously unselected package libhwloc5:arm64. Preparing to unpack .../65-libhwloc5_1.11.12-3_arm64.deb ... Unpacking libhwloc5:arm64 (1.11.12-3) ... Selecting previously unselected package libnuma-dev:arm64. Preparing to unpack .../66-libnuma-dev_2.0.12-1_arm64.deb ... Unpacking libnuma-dev:arm64 (2.0.12-1) ... Selecting previously unselected package libltdl-dev:arm64. Preparing to unpack .../67-libltdl-dev_2.4.6-9_arm64.deb ... Unpacking libltdl-dev:arm64 (2.4.6-9) ... Selecting previously unselected package libhwloc-dev:arm64. Preparing to unpack .../68-libhwloc-dev_1.11.12-3_arm64.deb ... Unpacking libhwloc-dev:arm64 (1.11.12-3) ... Selecting previously unselected package libpciaccess0:arm64. Preparing to unpack .../69-libpciaccess0_0.14-1_arm64.deb ... Unpacking libpciaccess0:arm64 (0.14-1) ... Selecting previously unselected package ocl-icd-libopencl1:arm64. Preparing to unpack .../70-ocl-icd-libopencl1_2.2.12-2_arm64.deb ... Unpacking ocl-icd-libopencl1:arm64 (2.2.12-2) ... Selecting previously unselected package libhwloc-plugins:arm64. Preparing to unpack .../71-libhwloc-plugins_1.11.12-3_arm64.deb ... Unpacking libhwloc-plugins:arm64 (1.11.12-3) ... Selecting previously unselected package libnl-3-dev:arm64. Preparing to unpack .../72-libnl-3-dev_3.4.0-1_arm64.deb ... Unpacking libnl-3-dev:arm64 (3.4.0-1) ... Selecting previously unselected package libnl-route-3-dev:arm64. Preparing to unpack .../73-libnl-route-3-dev_3.4.0-1_arm64.deb ... Unpacking libnl-route-3-dev:arm64 (3.4.0-1) ... Selecting previously unselected package libibverbs-dev:arm64. Preparing to unpack .../74-libibverbs-dev_22.1-1_arm64.deb ... Unpacking libibverbs-dev:arm64 (22.1-1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../75-libjs-jquery_3.3.1~dfsg-3_all.deb ... Unpacking libjs-jquery (3.3.1~dfsg-3) ... Selecting previously unselected package libpmix2:arm64. 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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 1.68.6-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean dh_auto_clean make -j8 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 build dh build 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 -j8 "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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki_mpi.cc dinkymath.cc: In function 'std::__cxx11::string littleEndianStr(unsigned int, int)': dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] int last=0; ^~~~ dinkymath.cc: In function 'std::__cxx11::string littleEndianPat(unsigned int, int)': dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] int last=0; ^~~~ sequence.cc: In destructor 'Sequence::~Sequence()': sequence.cc:377:123: warning: throw will always call terminate() [-Wterminate] throw MurasakiException("Couldn't mark System V IPC shared memory region for deletion for sequence "+name+strerror(errno)); ^ sequence.cc:377:123: 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] memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]); ^ In file included from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/bits/stl_tree.h:63, from /usr/include/c++/8/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/8/bits/stl_pair.h:208:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here 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] memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]); ^ In file included from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/bits/stl_tree.h:63, from /usr/include/c++/8/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/8/bits/stl_pair.h:208:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here struct pair ^~~~ sequence.cc: In destructor 'BitSequence::~BitSequence()': sequence.cc:1394:133: warning: throw will always call terminate() [-Wterminate] throw MurasakiException("Couldn't detach System V shared memory region for "+(seq ? seq->filename:string("(anon)"))+strerror(errno)); ^ sequence.cc:1394:133: note: in C++11 destructors default to noexcept murasaki_mpi.cc: In function 'void mpi_types_init()': murasaki_mpi.cc:107:28: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.key,disp); ^ In file included from murasaki_mpi.cc:29: /usr/lib/aarch64-linux-gnu/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:107:28: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.key,disp); ^ In file included from murasaki_mpi.cc:29: /usr/lib/aarch64-linux-gnu/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:108:32: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.seqno,disp+1); ^ In file included from murasaki_mpi.cc:29: /usr/lib/aarch64-linux-gnu/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:108:32: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.seqno,disp+1); ^ In file included from murasaki_mpi.cc:29: /usr/lib/aarch64-linux-gnu/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:109:30: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.pos,disp+1); ^ In file included from murasaki_mpi.cc:29: /usr/lib/aarch64-linux-gnu/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:109:30: warning: 'int MPI_Address(void*, MPI_Aint*)' is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.pos,disp+1); ^ In file included from murasaki_mpi.cc:29: /usr/lib/aarch64-linux-gnu/openmpi/include/mpi.h:1186:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:112:61: warning: 'int MPI_Type_struct(int, int*, MPI_Aint*, ompi_datatype_t**, ompi_datatype_t**)' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(3,blocklen,disp,type,&MPI_HashMessage_type); ^ In file included from murasaki_mpi.cc:29: /usr/lib/aarch64-linux-gnu/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ murasaki_mpi.cc:112:61: warning: 'int MPI_Type_struct(int, int*, MPI_Aint*, ompi_datatype_t**, ompi_datatype_t**)' is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(3,blocklen,disp,type,&MPI_HashMessage_type); ^ In file included from murasaki_mpi.cc:29: /usr/lib/aarch64-linux-gnu/openmpi/include/mpi.h:1801:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ 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] int send_done; ^~~~~~~~~ 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] bool revZero=false; ^~~~~~~ murasaki_mpi.cc: In function 'word mpi_extract_checkSentQueue(std::vector >&, std::vector > >&, std::multimap&)': murasaki_mpi.cc:1025:18: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] 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] 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 = long unsigned int]': shmvector.hh:282:5: required from 'void ShmVector::resize(size_t) [with T = std::pair; size_t = long 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] memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/bits/stl_tree.h:63, from /usr/include/c++/8/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/8/bits/stl_pair.h:208:12: note: 'struct std::pair' declared here struct pair ^~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-compare.cc binseq.cc: In member function 'bool SequenceBinary::save(std::__cxx11::string)': binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] }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] memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region)); ^ In file included from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/ios:40, from /usr/include/c++/8/istream:38, from /usr/include/c++/8/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/8/bits/stl_pair.h:208:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 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] memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region)); ^ In file included from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/ios:40, from /usr/include/c++/8/istream:38, from /usr/include/c++/8/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/8/bits/stl_pair.h:208:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 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] memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region)); ^ In file included from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/ios:40, from /usr/include/c++/8/istream:38, from /usr/include/c++/8/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/8/bits/stl_pair.h:208:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here struct pair ^~~~ cgr.cc: In member function 'void Cgr::merge(Cgr&)': cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable] int redist=(unsigned long)(rez*rez)<=seedcount; ^~~~~~ cgr.cc: In member function 'bool Cgr::savePNG(std::__cxx11::string)': cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable] int res; ^~~ cgr.cc: In member function 'int PgmBuffer::loadPGM(std::__cxx11::string)': cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable] 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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-random.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-sample.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c testeco.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-or.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] 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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c geneparse.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-coverage.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::__cxx11::string)': getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=] }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] 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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread 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 -j8 "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 -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c timing.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c dinkymath.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c sequence.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c msethash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c options.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecohash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c ecolist.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c murasaki_mpi.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c arrayhash.cc dinkymath.cc: In function 'std::__cxx11::string littleEndianStr(unsigned int, int)': dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] int last=0; ^~~~ dinkymath.cc: In function 'std::__cxx11::string littleEndianPat(unsigned int, int)': dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] int last=0; ^~~~ 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] memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]); ^ In file included from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/bits/stl_tree.h:63, from /usr/include/c++/8/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/8/bits/stl_pair.h:208:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here 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] memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]); ^ In file included from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/bits/stl_tree.h:63, from /usr/include/c++/8/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/8/bits/stl_pair.h:208:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here struct pair ^~~~ 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] SeqPos shortest=0,shortlen=length(spaces[0]); ^~~~~~~~ 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] bool revZero=false; ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c seqread.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c scoring.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 = long unsigned int]': shmvector.hh:282:5: required from 'void ShmVector::resize(size_t) [with T = std::pair; size_t = long 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] memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/bits/stl_tree.h:63, from /usr/include/c++/8/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/8/bits/stl_pair.h:208:12: note: 'struct std::pair' declared here struct pair ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c openhash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c genopts.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c binseq.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-image.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr.cc binseq.cc: In member function 'bool SequenceBinary::save(std::__cxx11::string)': binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] }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] memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region)); ^ In file included from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/ios:40, from /usr/include/c++/8/istream:38, from /usr/include/c++/8/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/8/bits/stl_pair.h:208:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 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] memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region)); ^ In file included from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/ios:40, from /usr/include/c++/8/istream:38, from /usr/include/c++/8/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/8/bits/stl_pair.h:208:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 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] memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region)); ^ In file included from /usr/include/c++/8/bits/stl_algobase.h:64, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/ios:40, from /usr/include/c++/8/istream:38, from /usr/include/c++/8/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/8/bits/stl_pair.h:208:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here struct pair ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-compare.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] int redist=(unsigned long)(rez*rez)<=seedcount; ^~~~~~ cgr.cc: In member function 'bool Cgr::savePNG(std::__cxx11::string)': cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable] int res; ^~~ cgr.cc: In member function 'int PgmBuffer::loadPGM(std::__cxx11::string)': cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable] int wordwidth=1; ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-random.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c cgr-sample.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c testeco.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-compare.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c alignments.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] bool repeatmask=false,save=false; ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-or.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c geneparse.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-and.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-best.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c align-coverage.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c getsegments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -c mbfa.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread 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] bool seqStats=true; ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::__cxx11::string)': getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=] }catch(bad_lexical_cast e){ ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -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 -lcryptopp -pthread g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -DUSE_LIBCRYPTOPP -fno-strict-aliasing -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -lcryptopp -pthread 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 fakeroot debian/rules binary dh binary dh_testroot 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 71. 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 71. 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_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_strip dh_makeshlibs dh_shlibdeps 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-dbgsym' in '../murasaki-dbgsym_1.68.6-8_arm64.deb'. dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-8_arm64.deb'. dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-8_arm64.deb'. dpkg-deb: building package 'murasaki-common' in '../murasaki-common_1.68.6-8_all.deb'. dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-8_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../murasaki_1.68.6-8_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/31062 and its subdirectories I: Current time: Wed Aug 18 23:47:32 -12 2021 I: pbuilder-time-stamp: 1629373652 Fri Jul 17 05:24:39 UTC 2020 I: 1st build successful. Starting 2nd build on remote node codethink-sled14-arm64.debian.net. Fri Jul 17 05:24:39 UTC 2020 I: Preparing to do remote build '2' on codethink-sled14-arm64.debian.net. Fri Jul 17 05:29:17 UTC 2020 I: Deleting $TMPDIR on codethink-sled14-arm64.debian.net. Fri Jul 17 05:29:18 UTC 2020 I: murasaki_1.68.6-8_arm64.changes: Format: 1.8 Date: Mon, 08 Oct 2018 12:49:39 +0200 Source: murasaki Binary: murasaki murasaki-common murasaki-dbgsym murasaki-mpi murasaki-mpi-dbgsym Architecture: all arm64 Version: 1.68.6-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille 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 Closes: 910421 Changes: murasaki (1.68.6-8) unstable; urgency=medium . * Standards-Version: 4.2.1 * Provide copies of manpages instead of broken symlinks Closes: #910421 Checksums-Sha1: 6576edb20e4105057858207e21b0ce332e917519 144300 murasaki-common_1.68.6-8_all.deb 317327b47289e1c65e5e430a261884545844724b 15166504 murasaki-dbgsym_1.68.6-8_arm64.deb c5caa2f365e63ff2414d1902ca4108588e842e21 17070800 murasaki-mpi-dbgsym_1.68.6-8_arm64.deb 4dfcf5184c6c14391b082d3fd7da21bedafd8903 561112 murasaki-mpi_1.68.6-8_arm64.deb 0f968827206120c10c9abb1769de07b309c7b56b 7327 murasaki_1.68.6-8_arm64.buildinfo abc19ab0520ff6316e06be0a6690ee0a5f71859b 456056 murasaki_1.68.6-8_arm64.deb Checksums-Sha256: fe941606ec938090a3e21df4ee916ae0351226ef5b4e1e464f8d05ca12bd8ee3 144300 murasaki-common_1.68.6-8_all.deb 1428eb50a95edf4f432b2733004fb73a9a7719001ecb1e9b2de59aaee8fb9ed4 15166504 murasaki-dbgsym_1.68.6-8_arm64.deb b9cba298a2d31240d1d0bbc681c2f67db59b0b69a3aeb5fad6a2d164daaa8d5a 17070800 murasaki-mpi-dbgsym_1.68.6-8_arm64.deb 354e02bc7e020d4510f8f01d6e87fbddc9ba391d48c5fa01a654e20bcbe3d6d6 561112 murasaki-mpi_1.68.6-8_arm64.deb efdd009ca583a70943164ec860b8409b6438f1caf83be8b6d8f284e447b40cff 7327 murasaki_1.68.6-8_arm64.buildinfo 348724cb56dc0936fe206946dfa3c5c0d493651b8fa45a848228fc70ee2e8d7d 456056 murasaki_1.68.6-8_arm64.deb Files: 79ec3438f77885ef87c821ccc8e49bb6 144300 science optional murasaki-common_1.68.6-8_all.deb 03002e3ce58ad5acc0fbfa17612158b9 15166504 debug optional murasaki-dbgsym_1.68.6-8_arm64.deb 653674ddad7590de6e6d1220acc8a183 17070800 debug optional murasaki-mpi-dbgsym_1.68.6-8_arm64.deb 7989c4eb60736611958650686cf9456b 561112 science optional murasaki-mpi_1.68.6-8_arm64.deb b79d826f422a74999dc39afcea56d6d0 7327 science optional murasaki_1.68.6-8_arm64.buildinfo 69da2c748ca1cfce1939ddeb3becd830 456056 science optional murasaki_1.68.6-8_arm64.deb Fri Jul 17 05:29:26 UTC 2020 I: diffoscope 151 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.KZNuIZtP4e/murasaki_1.68.6-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.KZNuIZtP4e/murasaki_1.68.6-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.KZNuIZtP4e/murasaki_1.68.6-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.KZNuIZtP4e/b1/murasaki_1.68.6-8_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.KZNuIZtP4e/b2/murasaki_1.68.6-8_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.585s) 0.585s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.364s) 0.364s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Fri Jul 17 05:29:43 UTC 2020 I: diffoscope 151 found no differences in the changes files, and a .buildinfo file also exists. Fri Jul 17 05:29:43 UTC 2020 I: murasaki from buster built successfully and reproducibly on arm64. Fri Jul 17 05:29:44 UTC 2020 I: Submitting .buildinfo files to external archives: Fri Jul 17 05:29:44 UTC 2020 I: Submitting 12K b1/murasaki_1.68.6-8_arm64.buildinfo.asc Fri Jul 17 05:29:45 UTC 2020 I: Submitting 12K b2/murasaki_1.68.6-8_arm64.buildinfo.asc Fri Jul 17 05:29:47 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Jul 17 05:29:47 UTC 2020 I: Done submitting .buildinfo files. Fri Jul 17 05:29:47 UTC 2020 I: Removing signed murasaki_1.68.6-8_arm64.buildinfo.asc files: removed './b1/murasaki_1.68.6-8_arm64.buildinfo.asc' removed './b2/murasaki_1.68.6-8_arm64.buildinfo.asc'