Mon Jun 10 14:54:13 UTC 2024 I: starting to build murasaki/unstable/i386 on jenkins on '2024-06-10 14:53' Mon Jun 10 14:54:13 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_18/6894/console.log Mon Jun 10 14:54:13 UTC 2024 I: Downloading source for unstable/murasaki=1.68.6-13 --2024-06-10 14:54:13-- http://deb.debian.org/debian/pool/main/m/murasaki/murasaki_1.68.6-13.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2792 (2.7K) [text/prs.lines.tag] Saving to: ‘murasaki_1.68.6-13.dsc’ 0K .. 100% 366M=0s 2024-06-10 14:54:13 (366 MB/s) - ‘murasaki_1.68.6-13.dsc’ saved [2792/2792] Mon Jun 10 14:54:13 UTC 2024 I: murasaki_1.68.6-13.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: murasaki Binary: murasaki, murasaki-mpi, murasaki-common Architecture: any all Version: 1.68.6-13 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Nilesh Patra 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 9faf611f7851b6599d6242b8e05b0896988887fc 11204 murasaki_1.68.6-13.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 3a960dbbbda6e51d8a4b98c9889c8135b85a465a29c3c33a643d0528a7492128 11204 murasaki_1.68.6-13.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 445de24812178cef498ad9bd02b86b7c 11204 murasaki_1.68.6-13.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmEZYE8UHG5wYXRyYTk3 NEBnbWFpbC5jb20ACgkQALrnSzQzafEBZA/+JiiuRMk72tNtXdqXsruZn2As0AzG 1OUQVAlofluJXJg3BMVuDzVZT3/F1Jh1lpCR1NbSDlHzxN7f+8SEHzteeaYiTEge +V4b7MksGcRynuQqkJ7J6c1+5z2CQ5Bc9WqbZkwHVzLYDYTlWAnkyKncavS3wHvG NP+t8p73ylFTp7bRAipv/UlTBq1uouuDwxJnGyQHnQwvOgP9lJtBZnc0RrnzSxc3 CDn5PQaoXu4Efsrpvoq8bW8RtSsLMyMdy7Xk2G+DOh65GvIywBMjLc3KXPle/yeF 3cJ2KTG+aSvZy1CmuxQtCuPPSDW1kX/g6FlazuIrZP/Jya1k9nlxCOtsTu2jFe98 59YTRWyLS7iQCgesTQkAoULfzHH9Ujse+CICiJ3OBkLXSmxzNCM4xNY0iZA5m3We QWF0S5r9qxeU7V4OfFFZC4YSD0RvTpkSk13CFM8v3eMgbt9AzJCb/Sc9HIOmHvsJ nsL3Qbs5cyV/rPbWN4SI1EGqEdE2XeBKJu7cDlAaHp1fJ0zYCqPDD4FofOIUJpLA YxpC5HBvFv4hqKKCeUDQvpo4ZwYHIfhmrCboFAX1SR9HDVBL82JLXaw/+xXc9FjR OsuR8ZFLuHLilSjHLrHFzy1y+ssIzWyZ3HJHEpz1tJgf6p0iG6TBRjzL0B0NgcBm NGHCKTq6/ELzWCM= =c/ZJ -----END PGP SIGNATURE----- Mon Jun 10 14:54:13 UTC 2024 I: Checking whether the package is not for us Mon Jun 10 14:54:13 UTC 2024 I: Starting 1st build on remote node infom08-i386.debian.net. Mon Jun 10 14:54:13 UTC 2024 I: Preparing to do remote build '1' on infom08-i386.debian.net. Mon Jun 10 14:56:01 UTC 2024 I: Deleting $TMPDIR on infom08-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jul 13 09:17:11 -12 2025 I: pbuilder-time-stamp: 1752441431 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [murasaki_1.68.6-13.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_1.68.6-13.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Aug 15 18:43:27 2021 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./murasaki_1.68.6-13.dsc: no acceptable signature found 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_1.68.6-13.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc11.patch 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/1359/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='5ed8eccdf5014a4086354b1692f36fc9' 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='1359' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.VLZbqNLz/pbuilderrc_1ZKy --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VLZbqNLz/b1 --logfile b1/build.log murasaki_1.68.6-13.dsc' SUDO_GID='111' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom08-i386 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 5 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1359/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 ... 19700 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-13{a} gfortran-13-i686-linux-gnu{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-regex-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost1.83-dev{a} libbsd0{a} libcbor0.10{a} libcom-err2{a} libcrypto++-dev{a} libcrypto++8t64{a} libdebhelper-perl{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-13-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu-dev{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3t64{a} libpciaccess0{a} libpipeline1{a} libpsm-infinipath1{a} libpstreams-dev{a} librdmacm1t64{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 krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libmail-sendmail-perl lynx wget xauth 0 packages upgraded, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 72.6 MB of archives. After unpacking 424 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-4 [1194 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.1-8.1 [100 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 man-db i386 2.12.1-2 [1421 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 libbsd0 i386 0.12.2-1 [134 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 libedit2 i386 3.1-20240517-1 [97.6 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 libcbor0.10 i386 0.10.2-1.2 [30.8 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 libfido2-1 i386 1.14.0-1+b2 [87.4 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.20.1-6+b1 [36.1 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.1-1 [23.1 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.20.1-6+b1 [83.2 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] Get: 19 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.20.1-6+b1 [360 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.20.1-6+b1 [145 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 openssh-client i386 1:9.7p1-5 [991 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 autopoint all 0.21-14 [496 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-7 [517 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 33 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg-3 [704 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 debhelper all 13.15.3 [901 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.1.0-1 [733 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 libgfortran-13-dev i386 13.2.0-25 [783 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 gfortran-13-i686-linux-gnu i386 13.2.0-25 [11.2 MB] Get: 44 http://deb.debian.org/debian unstable/main i386 gfortran-13 i386 13.2.0-25 [12.8 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 libnl-3-200 i386 3.7.0-0.3 [61.8 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 libnl-route-3-200 i386 3.7.0-0.3 [193 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 libibverbs1 i386 52.0-1 [66.5 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 ibverbs-providers i386 52.0-1 [378 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 icu-devtools i386 72.1-4+b1 [216 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 libboost1.83-dev i386 1.83.0-3 [10.6 MB] Get: 51 http://deb.debian.org/debian unstable/main i386 libboost-atomic1.83.0 i386 1.83.0-3 [233 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 libboost-atomic1.83-dev i386 1.83.0-3 [235 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 libboost-filesystem1.83.0 i386 1.83.0-3 [286 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 libboost-system1.83.0 i386 1.83.0-3 [230 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 libboost-system1.83-dev i386 1.83.0-3 [231 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 libboost-filesystem1.83-dev i386 1.83.0-3 [302 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 libboost-filesystem-dev i386 1.83.0.2+b2 [3640 B] Get: 58 http://deb.debian.org/debian unstable/main i386 libboost-regex1.83.0 i386 1.83.0-3 [328 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 libicu-dev i386 72.1-4+b1 [10.6 MB] Get: 60 http://deb.debian.org/debian unstable/main i386 libboost-regex1.83-dev i386 1.83.0-3 [347 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 libboost-iostreams1.83-dev i386 1.83.0-3 [264 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 libboost-iostreams-dev i386 1.83.0.2+b2 [3588 B] Get: 63 http://deb.debian.org/debian unstable/main i386 libboost-regex-dev i386 1.83.0.2+b2 [3872 B] Get: 64 http://deb.debian.org/debian unstable/main i386 libcrypto++8t64 i386 8.9.0-1.1 [1197 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 libcrypto++-dev i386 8.9.0-1.1 [1896 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 libevent-2.1-7t64 i386 2.1.12-stable-10 [194 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libevent-core-2.1-7t64 i386 2.1.12-stable-10 [140 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 libevent-extra-2.1-7t64 i386 2.1.12-stable-10 [113 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libevent-pthreads-2.1-7t64 i386 2.1.12-stable-10 [54.1 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libevent-openssl-2.1-7t64 i386 2.1.12-stable-10 [61.7 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 libevent-dev i386 2.1.12-stable-10 [324 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libpsm-infinipath1 i386 3.3+20.604758e7-6.3 [177 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 librdmacm1t64 i386 52.0-1 [75.9 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 libfabric1 i386 1.17.0-3+b1 [540 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 libhwloc15 i386 2.10.0-1+b1 [175 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 libnuma1 i386 2.0.18-1 [23.5 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 libnuma-dev i386 2.0.18-1 [38.3 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libltdl7 i386 2.4.7-7+b1 [395 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 libltdl-dev i386 2.4.7-7+b1 [167 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 libhwloc-dev i386 2.10.0-1+b1 [268 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 libpciaccess0 i386 0.17-3+b1 [53.8 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.9-1+b1 [18.5 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.2-3+b1 [24.8 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.17.0-2 [148 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.7-1+b1 [822 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 libxnvctrl0 i386 535.171.04-1 [13.7 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 ocl-icd-libopencl1 i386 2.3.2-1+b1 [43.5 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 libhwloc-plugins i386 2.10.0-1+b1 [18.4 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libnl-3-dev i386 3.7.0-0.3 [105 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 libnl-route-3-dev i386 3.7.0-0.3 [223 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 libibverbs-dev i386 52.0-1 [698 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 libopenmpi3t64 i386 4.1.6-13.3 [2626 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 openmpi-common all 4.1.6-13.3 [169 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1 [915 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 openmpi-bin i386 4.1.6-13.3 [198 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 libopenmpi-dev i386 4.1.6-13.3 [1020 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 libpstreams-dev all 1.0.3-1 [134 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 libterm-readkey-perl i386 2.38-2+b3 [25.4 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 libtext-wrapper-perl all 1.05-4 [10.3 kB] Fetched 72.6 MB in 3s (23.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19700 files and directories currently installed.) Preparing to unpack .../000-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../001-libmagic-mgc_1%3a5.45-3_i386.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../002-libmagic1t64_1%3a5.45-3_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../003-file_1%3a5.45-3_i386.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../004-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../005-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../006-groff-base_1.23.0-4_i386.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../007-bsdextrautils_2.40.1-8.1_i386.deb ... Unpacking bsdextrautils (2.40.1-8.1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../008-libpipeline1_1.5.7-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-2) ... 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Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../015-libcom-err2_1.47.1-1_i386.deb ... Unpacking libcom-err2:i386 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../016-libk5crypto3_1.20.1-6+b1_i386.deb ... Unpacking libk5crypto3:i386 (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:i386. Preparing to unpack .../017-libkeyutils1_1.6.3-3_i386.deb ... Unpacking libkeyutils1:i386 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:i386. Preparing to unpack .../018-libkrb5-3_1.20.1-6+b1_i386.deb ... Unpacking libkrb5-3:i386 (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:i386. Preparing to unpack .../019-libgssapi-krb5-2_1.20.1-6+b1_i386.deb ... Unpacking libgssapi-krb5-2:i386 (1.20.1-6+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../020-openssh-client_1%3a9.7p1-5_i386.deb ... Unpacking openssh-client (1:9.7p1-5) ... Selecting previously unselected package m4. Preparing to unpack .../021-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../022-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../023-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../024-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../025-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../026-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. 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Selecting previously unselected package dwz. Preparing to unpack .../033-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../034-libicu72_72.1-4+b1_i386.deb ... Unpacking libicu72:i386 (72.1-4+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../035-libxml2_2.12.7+dfsg-3_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg-3) ... Selecting previously unselected package gettext. Preparing to unpack .../036-gettext_0.21-14+b1_i386.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../037-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../038-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. 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Unpacking libboost-atomic1.83.0:i386 (1.83.0-3) ... Selecting previously unselected package libboost-atomic1.83-dev:i386. Preparing to unpack .../051-libboost-atomic1.83-dev_1.83.0-3_i386.deb ... Unpacking libboost-atomic1.83-dev:i386 (1.83.0-3) ... Selecting previously unselected package libboost-filesystem1.83.0:i386. Preparing to unpack .../052-libboost-filesystem1.83.0_1.83.0-3_i386.deb ... Unpacking libboost-filesystem1.83.0:i386 (1.83.0-3) ... Selecting previously unselected package libboost-system1.83.0:i386. Preparing to unpack .../053-libboost-system1.83.0_1.83.0-3_i386.deb ... Unpacking libboost-system1.83.0:i386 (1.83.0-3) ... Selecting previously unselected package libboost-system1.83-dev:i386. Preparing to unpack .../054-libboost-system1.83-dev_1.83.0-3_i386.deb ... Unpacking libboost-system1.83-dev:i386 (1.83.0-3) ... Selecting previously unselected package libboost-filesystem1.83-dev:i386. Preparing to unpack .../055-libboost-filesystem1.83-dev_1.83.0-3_i386.deb ... Unpacking libboost-filesystem1.83-dev:i386 (1.83.0-3) ... Selecting previously unselected package libboost-filesystem-dev:i386. Preparing to unpack .../056-libboost-filesystem-dev_1.83.0.2+b2_i386.deb ... Unpacking libboost-filesystem-dev:i386 (1.83.0.2+b2) ... Selecting previously unselected package libboost-regex1.83.0:i386. Preparing to unpack .../057-libboost-regex1.83.0_1.83.0-3_i386.deb ... Unpacking libboost-regex1.83.0:i386 (1.83.0-3) ... Selecting previously unselected package libicu-dev:i386. Preparing to unpack .../058-libicu-dev_72.1-4+b1_i386.deb ... Unpacking libicu-dev:i386 (72.1-4+b1) ... Selecting previously unselected package libboost-regex1.83-dev:i386. Preparing to unpack .../059-libboost-regex1.83-dev_1.83.0-3_i386.deb ... Unpacking libboost-regex1.83-dev:i386 (1.83.0-3) ... Selecting previously unselected package libboost-iostreams1.83-dev:i386. Preparing to unpack .../060-libboost-iostreams1.83-dev_1.83.0-3_i386.deb ... Unpacking libboost-iostreams1.83-dev:i386 (1.83.0-3) ... Selecting previously unselected package libboost-iostreams-dev:i386. Preparing to unpack .../061-libboost-iostreams-dev_1.83.0.2+b2_i386.deb ... Unpacking libboost-iostreams-dev:i386 (1.83.0.2+b2) ... Selecting previously unselected package libboost-regex-dev:i386. Preparing to unpack .../062-libboost-regex-dev_1.83.0.2+b2_i386.deb ... Unpacking libboost-regex-dev:i386 (1.83.0.2+b2) ... Selecting previously unselected package libcrypto++8t64:i386. Preparing to unpack .../063-libcrypto++8t64_8.9.0-1.1_i386.deb ... Unpacking libcrypto++8t64:i386 (8.9.0-1.1) ... Selecting previously unselected package libcrypto++-dev:i386. Preparing to unpack .../064-libcrypto++-dev_8.9.0-1.1_i386.deb ... Unpacking libcrypto++-dev:i386 (8.9.0-1.1) ... Selecting previously unselected package libevent-2.1-7t64:i386. Preparing to unpack .../065-libevent-2.1-7t64_2.1.12-stable-10_i386.deb ... Unpacking libevent-2.1-7t64:i386 (2.1.12-stable-10) ... Selecting previously unselected package libevent-core-2.1-7t64:i386. Preparing to unpack .../066-libevent-core-2.1-7t64_2.1.12-stable-10_i386.deb ... Unpacking libevent-core-2.1-7t64:i386 (2.1.12-stable-10) ... Selecting previously unselected package libevent-extra-2.1-7t64:i386. Preparing to unpack .../067-libevent-extra-2.1-7t64_2.1.12-stable-10_i386.deb ... Unpacking libevent-extra-2.1-7t64:i386 (2.1.12-stable-10) ... Selecting previously unselected package libevent-pthreads-2.1-7t64:i386. Preparing to unpack .../068-libevent-pthreads-2.1-7t64_2.1.12-stable-10_i386.deb ... Unpacking libevent-pthreads-2.1-7t64:i386 (2.1.12-stable-10) ... Selecting previously unselected package libevent-openssl-2.1-7t64:i386. Preparing to unpack .../069-libevent-openssl-2.1-7t64_2.1.12-stable-10_i386.deb ... Unpacking libevent-openssl-2.1-7t64:i386 (2.1.12-stable-10) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../070-libevent-dev_2.1.12-stable-10_i386.deb ... Unpacking libevent-dev (2.1.12-stable-10) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../071-libpsm-infinipath1_3.3+20.604758e7-6.3_i386.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3) ... Selecting previously unselected package librdmacm1t64:i386. Preparing to unpack .../072-librdmacm1t64_52.0-1_i386.deb ... Unpacking librdmacm1t64:i386 (52.0-1) ... Selecting previously unselected package libfabric1:i386. Preparing to unpack .../073-libfabric1_1.17.0-3+b1_i386.deb ... Unpacking libfabric1:i386 (1.17.0-3+b1) ... Selecting previously unselected package libhwloc15:i386. Preparing to unpack .../074-libhwloc15_2.10.0-1+b1_i386.deb ... Unpacking libhwloc15:i386 (2.10.0-1+b1) ... Selecting previously unselected package libnuma1:i386. Preparing to unpack .../075-libnuma1_2.0.18-1_i386.deb ... Unpacking libnuma1:i386 (2.0.18-1) ... Selecting previously unselected package libnuma-dev:i386. Preparing to unpack .../076-libnuma-dev_2.0.18-1_i386.deb ... Unpacking libnuma-dev:i386 (2.0.18-1) ... Selecting previously unselected package libltdl7:i386. Preparing to unpack .../077-libltdl7_2.4.7-7+b1_i386.deb ... Unpacking libltdl7:i386 (2.4.7-7+b1) ... Selecting previously unselected package libltdl-dev:i386. Preparing to unpack .../078-libltdl-dev_2.4.7-7+b1_i386.deb ... Unpacking libltdl-dev:i386 (2.4.7-7+b1) ... Selecting previously unselected package libhwloc-dev:i386. Preparing to unpack .../079-libhwloc-dev_2.10.0-1+b1_i386.deb ... Unpacking libhwloc-dev:i386 (2.10.0-1+b1) ... Selecting previously unselected package libpciaccess0:i386. Preparing to unpack .../080-libpciaccess0_0.17-3+b1_i386.deb ... Unpacking libpciaccess0:i386 (0.17-3+b1) ... Selecting previously unselected package libxau6:i386. Preparing to unpack .../081-libxau6_1%3a1.0.9-1+b1_i386.deb ... Unpacking libxau6:i386 (1:1.0.9-1+b1) ... Selecting previously unselected package libxdmcp6:i386. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/murasaki-1.68.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../murasaki_1.68.6-13_source.changes dpkg-buildpackage: info: source package murasaki dpkg-buildpackage: info: source version 1.68.6-13 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 -j6 clean make[1]: Entering directory '/build/reproducible-path/murasaki-1.68.6' rm -rf *.o *~ .*~ core make -C src clean make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/murasaki-1.68.6/src' make[1]: Leaving directory '/build/reproducible-path/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/reproducible-path/murasaki-1.68.6' dh_auto_build -- USE_MPI=YES make -j6 "INSTALL=install --strip-program=true" USE_MPI=YES make[2]: Entering directory '/build/reproducible-path/murasaki-1.68.6' make -C src all make[3]: Entering directory '/build/reproducible-path/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 In file included from murasaki.h:24, from dinkymath.cc:27: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from dinkymath.h:24, from dinkymath.cc:26: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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; | ^~~~ In file included from murasaki.h:24, from sequence.cc:28: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from msethash.cc:25: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from options.h:28, from options.cc:26: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ sequence.cc: In destructor 'Sequence::~Sequence()': sequence.cc:377:9: 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:377:9: note: in C++11 destructors default to 'noexcept' In file included from murasaki.h:24, from murasaki.cc:37: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from murasaki.cc:29: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)': sequence.cc:1113:9: 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++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/bits/stl_tree.h:63: /usr/include/c++/13/bits/stl_pair.h:187:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here 187 | struct pair | ^~~~ sequence.cc:1114:9: 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]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here 187 | struct pair | ^~~~ sequence.cc: In destructor 'BitSequence::~BitSequence()': sequence.cc:1394:9: 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:1394:9: note: in C++11 destructors default to 'noexcept' 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.cc:41: hashing.h: In instantiation of 'SBox::SBox(int) [with T = short unsigned int]': sequence.cc:162:29: required from here hashing.h:56:21: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = short unsigned int*]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 56 | random_shuffle(boxes[b],boxes[b]+boxsize); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from /usr/include/boost/regex/v5/regex_workaround.hpp:23, from /usr/include/boost/regex/v5/regex.hpp:29, from /usr/include/boost/regex.hpp:34, from seqread.h:33, from binseq.hh:31, from sequence.h:32: /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here 4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ 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; | ^~~~~~~ murasaki.cc: In function 'bool convertPattern(std::string&)': murasaki.cc:1287:17: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 1287 | random_shuffle(randomStr.begin(),randomStr.end()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from /usr/include/boost/regex/v5/regex_workaround.hpp:23, from /usr/include/boost/regex/v5/regex.hpp:29, from /usr/include/boost/regex.hpp:34, from seqread.h:33, from binseq.hh:31, from sequence.h:32: /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here 4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ In file included from sequence.h:44: 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:1110:17: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair' declared here 187 | struct pair | ^~~~ In file included from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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 In file included from ecolist.h:23, from ecolist.cc:20: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ecolist.cc:467:26: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 467 | struct less_map : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from murasaki.h:24, from murasaki_mpi.cc:33: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/map:62, from /usr/lib/i386-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:42, from /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:2911, from murasaki_mpi.cc:29: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ murasaki_mpi.cc:89:29: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 89 | struct lt_mpi_worldMemory : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ murasaki_mpi.cc:95:29: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 95 | struct gt_mpi_worldMemory : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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; | ^~~~~~~~~ In file included from murasaki.h:24, from arrayhash.cc:28: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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 seqread.cc: In member function 'void SequenceByteReader::addRedirect(boost::cmatch)': seqread.cc:264:38: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 264 | stitchPath=stitchfile.branch_path(); | ~~~~~~~~~~~~~~~~~~~~~~^~ In file included from seqread.cc:35: /usr/include/boost/filesystem/path.hpp:1129:10: note: declared here 1129 | path branch_path() const { return parent_path(); } | ^~~~~~~~~~~ In file included from murasaki.h:24, from scoring.cc:27: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ murasaki_mpi.cc: In function 'void mpi_types_init()': murasaki_mpi.cc:107:18: warning: 'msg' may be used uninitialized [-Wmaybe-uninitialized] 107 | MPI_Get_address(&msg.key,disp); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /usr/lib/i386-linux-gnu/openmpi/include/mpi.h:1589:20: note: by argument 1 of type 'const void*' to 'int MPI_Get_address(const void*, MPI_Aint*)' declared here 1589 | OMPI_DECLSPEC int MPI_Get_address(const void *location, MPI_Aint *address); | ^~~~~~~~~~~~~~~ murasaki_mpi.cc:102:19: note: 'msg' declared here 102 | MPI_HashMessage msg; | ^~~ In file included from ecolist.h:23, from openhash.h:29, from openhash.cc:26: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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 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:158:9: 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++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/13/bits/stl_pair.h:187:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 187 | struct pair | ^~~~ binseq.cc:160:9: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 187 | struct pair | ^~~~ binseq.cc:162:9: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 187 | 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 cgr.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-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 'std::pair Cgr::sampleHighLow(double, double)': cgr.cc:339:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 339 | delete alt; | ^~~ cgr.cc:330:24: note: returned from 'void* operator new [](std::size_t)' 330 | pix *alt=new pix[size]; | ^ cgr.cc: In member function 'std::pair Cgr::sampleHighLow(int, int)': cgr.cc:354:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 354 | delete alt; | ^~~ cgr.cc:345:24: note: returned from 'void* operator new [](std::size_t)' 345 | pix *alt=new pix[size]; | ^ cgr.cc: In member function 'std::pair Cgr::findNiceRange()': cgr.cc:395:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 395 | delete alt; | ^~~ cgr.cc:376:24: note: returned from 'void* operator new [](std::size_t)' 376 | pix *alt=new pix[size]; | ^ 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 cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::string)': cgr.cc:547:7: warning: 'maxval' may be used uninitialized [-Wmaybe-uninitialized] 547 | switch(maxval){ | ^~~~~~ cgr.cc:494:8: note: 'maxval' was declared here 494 | gray maxval; | ^~~~~~ cgr.cc:557:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:493:7: note: 'width' was declared here 493 | int width,height; | ^~~~~ cgr.cc:557:31: warning: 'height' may be used uninitialized [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:493:13: note: 'height' was declared here 493 | int width,height; | ^~~~~~ cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)': cgr.cc:485:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:426:7: note: 'width' was declared here 426 | int width,height; | ^~~~~ cgr.cc:485:31: warning: 'height' may be used uninitialized [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:426:13: note: 'height' was declared here 426 | int width,height; | ^~~~~~ 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 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 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 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 In file included from ecolist.h:23, from testeco.cc:20: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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()))); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~ 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 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 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 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; | ^~~~~~~~ In file included from align-best.cc:33: In function 'std::ostream& Itree::operator<<(std::ostream&, const Interval<_IntType>&) [with _IntType = long int]', inlined from 'int main(int, char**)' at align-best.cc:173:35: itree.h:79:27: warning: array subscript -1 is outside array bounds of 'Itree::Interval [268435455]' [-Warray-bounds=] 79 | return os << "[" << i.start << "~" << i.stop << "]"; | ~~^~~~~ itree.h:79:45: warning: array subscript -1 is outside array bounds of 'Itree::Interval [268435455]' [-Warray-bounds=] 79 | return os << "[" << i.start << "~" << i.stop << "]"; | ~~^~~~ 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 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){ | ^ 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 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 ../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 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 ../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 ../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 ../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 ../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 make[3]: Leaving directory '/build/reproducible-path/murasaki-1.68.6/src' make[2]: Leaving directory '/build/reproducible-path/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/reproducible-path/murasaki-1.68.6' rm -rf *.o *~ .*~ core make -C src clean make[3]: Entering directory '/build/reproducible-path/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/reproducible-path/murasaki-1.68.6/src' make[2]: Leaving directory '/build/reproducible-path/murasaki-1.68.6' dh_auto_build -- USE_MPI=NO make -j6 "INSTALL=install --strip-program=true" USE_MPI=NO make[2]: Entering directory '/build/reproducible-path/murasaki-1.68.6' make -C src all make[3]: Entering directory '/build/reproducible-path/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 In file included from msethash.cc:25: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from murasaki.h:24, from dinkymath.cc:27: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from dinkymath.h:24, from dinkymath.cc:26: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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; | ^~~~ In file included from murasaki.h:24, from sequence.cc:28: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from options.h:28, from options.cc:26: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from murasaki.h:24, from murasaki.cc:37: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from murasaki.cc:29: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)': sequence.cc:1113:9: 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++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/bits/stl_tree.h:63: /usr/include/c++/13/bits/stl_pair.h:187:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here 187 | struct pair | ^~~~ sequence.cc:1114:9: 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]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here 187 | 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] 3332 | 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] 1008 | bool revZero=false; | ^~~~~~~ murasaki.cc: In function 'bool convertPattern(std::string&)': murasaki.cc:1287:17: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 1287 | random_shuffle(randomStr.begin(),randomStr.end()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from /usr/include/boost/regex/v5/regex_workaround.hpp:23, from /usr/include/boost/regex/v5/regex.hpp:29, from /usr/include/boost/regex.hpp:34, from seqread.h:33, from binseq.hh:31, from sequence.h:32: /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here 4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ In file included from sequence.cc:41: hashing.h: In instantiation of 'SBox::SBox(int) [with T = short unsigned int]': sequence.cc:162:29: required from here hashing.h:56:21: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = short unsigned int*]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 56 | random_shuffle(boxes[b],boxes[b]+boxsize); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from /usr/include/boost/regex/v5/regex_workaround.hpp:23, from /usr/include/boost/regex/v5/regex.hpp:29, from /usr/include/boost/regex.hpp:34, from seqread.h:33, from binseq.hh:31, from sequence.h:32: /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here 4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c ecolist.cc In file included from sequence.h:44: 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:1110:17: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair' declared here 187 | struct pair | ^~~~ In file included from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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 In file included from ecolist.h:23, from ecolist.cc:20: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ecolist.cc:467:26: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 467 | struct less_map : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from murasaki.h:24, from arrayhash.cc:28: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ seqread.cc: In member function 'void SequenceByteReader::addRedirect(boost::cmatch)': seqread.cc:264:38: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 264 | stitchPath=stitchfile.branch_path(); | ~~~~~~~~~~~~~~~~~~~~~~^~ In file included from seqread.cc:35: /usr/include/boost/filesystem/path.hpp:1129:10: note: declared here 1129 | path branch_path() const { return parent_path(); } | ^~~~~~~~~~~ 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 In file included from murasaki.h:24, from scoring.cc:27: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ecolist.h:23, from openhash.h:29, from openhash.cc:26: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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 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:158:9: 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++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/13/bits/stl_pair.h:187:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 187 | struct pair | ^~~~ binseq.cc:160:9: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 187 | struct pair | ^~~~ binseq.cc:162:9: 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)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 187 | 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] 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; | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-compare.cc cgr.cc: In member function 'std::pair Cgr::sampleHighLow(double, double)': cgr.cc:339:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 339 | delete alt; | ^~~ cgr.cc:330:24: note: returned from 'void* operator new [](std::size_t)' 330 | pix *alt=new pix[size]; | ^ cgr.cc: In member function 'std::pair Cgr::sampleHighLow(int, int)': cgr.cc:354:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 354 | delete alt; | ^~~ cgr.cc:345:24: note: returned from 'void* operator new [](std::size_t)' 345 | pix *alt=new pix[size]; | ^ cgr.cc: In member function 'std::pair Cgr::findNiceRange()': cgr.cc:395:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 395 | delete alt; | ^~~ cgr.cc:376:24: note: returned from 'void* operator new [](std::size_t)' 376 | pix *alt=new pix[size]; | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-random.cc cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::string)': cgr.cc:547:7: warning: 'maxval' may be used uninitialized [-Wmaybe-uninitialized] 547 | switch(maxval){ | ^~~~~~ cgr.cc:494:8: note: 'maxval' was declared here 494 | gray maxval; | ^~~~~~ cgr.cc:557:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:493:7: note: 'width' was declared here 493 | int width,height; | ^~~~~ cgr.cc:557:31: warning: 'height' may be used uninitialized [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:493:13: note: 'height' was declared here 493 | int width,height; | ^~~~~~ cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)': cgr.cc:485:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:426:7: note: 'width' was declared here 426 | int width,height; | ^~~~~ cgr.cc:485:31: warning: 'height' may be used uninitialized [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:426:13: note: 'height' was declared here 426 | int width,height; | ^~~~~~ 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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-compare.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 alignments.cc In file included from ecolist.h:23, from testeco.cc:20: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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 align-or.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c geneparse.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-and.cc 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 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; | ^~~~~~~~ In file included from align-best.cc:33: In function 'std::ostream& Itree::operator<<(std::ostream&, const Interval<_IntType>&) [with _IntType = long int]', inlined from 'int main(int, char**)' at align-best.cc:173:35: itree.h:79:27: warning: array subscript -1 is outside array bounds of 'Itree::Interval [268435455]' [-Warray-bounds=] 79 | return os << "[" << i.start << "~" << i.stop << "]"; | ~~^~~~~ itree.h:79:45: warning: array subscript -1 is outside array bounds of 'Itree::Interval [268435455]' [-Warray-bounds=] 79 | return os << "[" << i.start << "~" << i.stop << "]"; | ~~^~~~ 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 -c mbfa.cc 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 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 ../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 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 ../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 ../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 ../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 make[3]: Leaving directory '/build/reproducible-path/murasaki-1.68.6/src' make[2]: Leaving directory '/build/reproducible-path/murasaki-1.68.6' make[1]: Leaving directory '/build/reproducible-path/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/reproducible-path/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/reproducible-path/murasaki-1.68.6' dh_install -Nmurasaki -Nmurasaki-mpi dh_installdocs dh_installchangelogs debian/rules override_dh_installman-arch make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/murasaki-1.68.6' debian/rules override_dh_installman-indep make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/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/reproducible-path/murasaki-1.68.6' dh_fixperms -i chmod a+x debian/murasaki-common/usr/share/perl5/murasaki/config.pl make[1]: Leaving directory '/build/reproducible-path/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-mpi' in '../murasaki-mpi_1.68.6-13_i386.deb'. dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-13_i386.deb'. dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-13_i386.deb'. dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-13_i386.deb'. dpkg-deb: building package 'murasaki-common' in '../murasaki-common_1.68.6-13_all.deb'. dpkg-genbuildinfo --build=binary -O../murasaki_1.68.6-13_i386.buildinfo dpkg-genchanges --build=binary -O../murasaki_1.68.6-13_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1359 and its subdirectories I: Current time: Sun Jul 13 09:18:55 -12 2025 I: pbuilder-time-stamp: 1752441535 Mon Jun 10 14:56:01 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom07-i386.debian.net. Mon Jun 10 14:56:01 UTC 2024 I: Preparing to do remote build '2' on infom07-i386.debian.net. Mon Jun 10 15:00:51 UTC 2024 I: Deleting $TMPDIR on infom07-i386.debian.net. Mon Jun 10 15:00:52 UTC 2024 I: murasaki_1.68.6-13_i386.changes: Format: 1.8 Date: Mon, 16 Aug 2021 00:06:48 +0530 Source: murasaki Binary: murasaki murasaki-common murasaki-dbgsym murasaki-mpi murasaki-mpi-dbgsym Architecture: all i386 Version: 1.68.6-13 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 (1.68.6-13) unstable; urgency=medium . * d/p/gcc11.patch: Fix gcc-11 FTBFS * Add myself to uploaders Checksums-Sha1: 88598eb555953b1f3c38d075e6865b2c08aa45af 116840 murasaki-common_1.68.6-13_all.deb 235fc4ae7a29636beefa39429fa2dcbff8f2b036 14008880 murasaki-dbgsym_1.68.6-13_i386.deb a9a6066b66f8404b2271c3da4544e9fed0e1f40a 15203296 murasaki-mpi-dbgsym_1.68.6-13_i386.deb fe27b34caabbadad7ea5602418a9ba65e04127b4 756148 murasaki-mpi_1.68.6-13_i386.deb 3f0c14931a005cbab946c1d416515d70e4b63476 8434 murasaki_1.68.6-13_i386.buildinfo 0ad4646049b817c036d5b15f6debc5d70c6ddd4d 636352 murasaki_1.68.6-13_i386.deb Checksums-Sha256: a4f573e38b91606b2ca4bbf00e4c1219ea08608db5dc971ed8c666a297b3c0f6 116840 murasaki-common_1.68.6-13_all.deb 2aa38f66d5477edcd5ca19db33e03efb19b5f94587dca678dbe8df07ba6a8453 14008880 murasaki-dbgsym_1.68.6-13_i386.deb 9c71beb6f1178388990403149934d6c7c984957e22c75faa2b9779a36beff100 15203296 murasaki-mpi-dbgsym_1.68.6-13_i386.deb 929806d38d810b6808d2efdeb88abb88149323ebd2d6198f1a61d89dfc126314 756148 murasaki-mpi_1.68.6-13_i386.deb 88c9ccdb691f07f387419cccb2513395cf65e29a84040ca657adc9178e9f9945 8434 murasaki_1.68.6-13_i386.buildinfo b972c7994753c731f470b53ae89b2c969ed485fc902c88684c94c060f61bcf1a 636352 murasaki_1.68.6-13_i386.deb Files: abd71eab85ef42b1fc18b26381953366 116840 science optional murasaki-common_1.68.6-13_all.deb 2b11a84198b7547d74908d33549acfc7 14008880 debug optional murasaki-dbgsym_1.68.6-13_i386.deb 6530aea1968880d940427a1342f9a21c 15203296 debug optional murasaki-mpi-dbgsym_1.68.6-13_i386.deb 96fe382d9a716b1a6318367c8638f8b3 756148 science optional murasaki-mpi_1.68.6-13_i386.deb 26a3645815a96d4427bfe9a44aa06da3 8434 science optional murasaki_1.68.6-13_i386.buildinfo ae6e3e5ff6dbc51154fa5bcdd1392ef3 636352 science optional murasaki_1.68.6-13_i386.deb Mon Jun 10 15:00:53 UTC 2024 I: diffoscope 271 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_18-6894.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.VLZbqNLz/murasaki_1.68.6-13.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.VLZbqNLz/murasaki_1.68.6-13.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.VLZbqNLz/murasaki_1.68.6-13.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.VLZbqNLz/b1/murasaki_1.68.6-13_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.VLZbqNLz/b2/murasaki_1.68.6-13_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: 0.704s) 0.704s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.337s) 0.337s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1.068s CPU time consumed: 1.039s Mon Jun 10 15:00:55 UTC 2024 I: diffoscope 271 found no differences in the changes files, and a .buildinfo file also exists. Mon Jun 10 15:00:55 UTC 2024 I: murasaki from unstable built successfully and reproducibly on i386. Mon Jun 10 15:00:56 UTC 2024 I: Submitting .buildinfo files to external archives: Mon Jun 10 15:00:56 UTC 2024 I: Submitting 12K b1/murasaki_1.68.6-13_i386.buildinfo.asc Mon Jun 10 15:00:57 UTC 2024 I: Submitting 12K b2/murasaki_1.68.6-13_i386.buildinfo.asc Mon Jun 10 15:01:00 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jun 10 15:01:00 UTC 2024 I: Done submitting .buildinfo files. Mon Jun 10 15:01:00 UTC 2024 I: Removing signed murasaki_1.68.6-13_i386.buildinfo.asc files: removed './b1/murasaki_1.68.6-13_i386.buildinfo.asc' removed './b2/murasaki_1.68.6-13_i386.buildinfo.asc'