sbuild (Debian sbuild) 0.88.2 (16 January 2025) on carme.larted.org.uk +==============================================================================+ | murasaki 1.68.6-14 (amd64) Wed, 22 Jan 2025 00:15:13 +0000 | +==============================================================================+ Package: murasaki Version: 1.68.6-14 Source Version: 1.68.6-14 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Wed, 22 Jan 2025 00:15:13 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup murasaki_1.68.6-14 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup murasaki_1.68.6-14 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Wed, 22 Jan 2025 00:15:13 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3030 B] Get:2 http://deb.debian.org/debian unstable InRelease [205 kB] Get:1 file:/srv/reprepro perl-5.40 InRelease [3030 B] Get:3 file:/srv/reprepro perl-5.40/main amd64 Packages [8875 B] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-01-21-2012.31-F-2025-01-20-0805.29.pdiff [121 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-01-21-2012.31-F-2025-01-20-0805.29.pdiff [121 kB] Get:6 http://localhost:3142/debian sid InRelease [205 kB] Get:7 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2025-01-21-2012.31-F-2025-01-20-0805.29.pdiff [120 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2025-01-21-2012.31-F-2025-01-20-0805.29.pdiff [120 kB] Fetched 779 kB in 6s (134 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt libapt-pkg6.0t64 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2494 kB of archives. After this operation, 4096 B disk space will be freed. Get:1 http://deb.debian.org/debian unstable/main amd64 libapt-pkg6.0t64 amd64 2.9.24 [1114 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 apt amd64 2.9.24 [1380 kB] Fetched 2494 kB in 0s (117 MB/s) (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 ... 23043 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.24_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.24) over (2.9.23) ... Setting up libapt-pkg6.0t64:amd64 (2.9.24) ... (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 ... 23043 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.24_amd64.deb ... Unpacking apt (2.9.24) over (2.9.23) ... Setting up apt (2.9.24) ... Processing triggers for libc-bin (2.40-5) ... +------------------------------------------------------------------------------+ | Fetch source files Wed, 22 Jan 2025 00:15:22 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/murasaki_1.68.6-14.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Wed, 22 Jan 2025 00:15:22 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, mpi-default-dev, build-essential Filtered Build-Depends: debhelper-compat (= 13), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, mpi-default-dev, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/murasaki-xreV69/resolver-4pRF5o/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/murasaki-xreV69/resolver-4pRF5o/apt_archive ./ InRelease Get:2 copy:/build/murasaki-xreV69/resolver-4pRF5o/apt_archive ./ Release [609 B] Ign:3 copy:/build/murasaki-xreV69/resolver-4pRF5o/apt_archive ./ Release.gpg Get:4 copy:/build/murasaki-xreV69/resolver-4pRF5o/apt_archive ./ Sources [764 B] Get:5 copy:/build/murasaki-xreV69/resolver-4pRF5o/apt_archive ./ Packages [803 B] Fetched 2176 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils ca-certificates debhelper dh-autoreconf dh-strip-nondeterminism docutils-common dwz file gettext gettext-base gfortran-14 gfortran-14-x86-64-linux-gnu groff-base ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libboost-atomic1.83-dev libboost-atomic1.83.0 libboost-filesystem-dev libboost-filesystem1.83-dev libboost-filesystem1.83.0 libboost-iostreams-dev libboost-iostreams1.83-dev libboost-iostreams1.83.0 libboost-regex-dev libboost-regex1.83-dev libboost-regex1.83.0 libboost-system1.83-dev libboost-system1.83.0 libboost1.83-dev libcbor0.10 libcom-err2 libcrypto++-dev libcrypto++8t64 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-14-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libicu-dev libicu72 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm17t64 libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmunge2 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi40 libpciaccess0 libpipeline1 libpmix-dev libpmix2t64 libpsm-infinipath1 libpsm2-2 libpstreams-dev libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librdmacm1t64 libterm-readkey-perl libtext-wrapper-perl libtool libuchardet0 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libz3-4 m4 man-db media-types mpi-default-dev netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client openssl po-debconf python-babel-localedata python3 python3-alabaster python3-autocommand python3-babel python3-certifi python3-chardet python3-charset-normalizer python3-defusedxml python3-docutils python3-idna python3-imagesize python3-inflect python3-jaraco.context python3-jaraco.functools python3-jinja2 python3-markupsafe python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pygments python3-requests python3-roman python3-snowballstemmer python3-sphinx python3-typeguard python3-typing-extensions python3-urllib3 python3.13 python3.13-minimal sensible-utils sgml-base sphinx-common tzdata xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-14-multilib gfortran-14-doc libcoarrays-dev groff libboost1.83-doc libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-graph-parallel1.83-dev libboost-graph1.83-dev libboost-json1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev libboost-numpy1.83-dev libboost-program-options1.83-dev libboost-python1.83-dev libboost-random1.83-dev libboost-serialization1.83-dev libboost-stacktrace1.83-dev libboost-test1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user libhwloc-contrib-plugins icu-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils gcj-jdk m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl python3-doc python3-tk python3-venv python-charset-normalizer-doc docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base texlive-latex-recommended python-jinja2-doc python3-setuptools python-pygments-doc ttf-bitstream-vera python3-cryptography python3-openssl python3-socks python-requests-doc python3-stemmer dvipng dvisvgm fonts-freefont-otf imagemagick latexmk libjs-mathjax python3-sphinx-rtd-theme sphinx-doc tex-gyre texlive-fonts-extra texlive-fonts-recommended texlive-latex-extra texlive-plain-generic python3-brotli python3.13-venv python3.13-doc binfmt-support sgml-base-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libjson-xs-perl krb5-locales libcoarrays-openmpi-dev xauth libmail-sendmail-perl libpaper-utils python3-pil The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils ca-certificates debhelper dh-autoreconf dh-strip-nondeterminism docutils-common dwz file gettext gettext-base gfortran-14 gfortran-14-x86-64-linux-gnu groff-base ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libboost-atomic1.83-dev libboost-atomic1.83.0 libboost-filesystem-dev libboost-filesystem1.83-dev libboost-filesystem1.83.0 libboost-iostreams-dev libboost-iostreams1.83-dev libboost-iostreams1.83.0 libboost-regex-dev libboost-regex1.83-dev libboost-regex1.83.0 libboost-system1.83-dev libboost-system1.83.0 libboost1.83-dev libcbor0.10 libcom-err2 libcrypto++-dev libcrypto++8t64 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-14-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libicu-dev libicu72 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm17t64 libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmunge2 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi40 libpciaccess0 libpipeline1 libpmix-dev libpmix2t64 libpsm-infinipath1 libpsm2-2 libpstreams-dev libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librdmacm1t64 libterm-readkey-perl libtext-wrapper-perl libtool libuchardet0 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libz3-4 m4 man-db media-types mpi-default-dev netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client openssl po-debconf python-babel-localedata python3 python3-alabaster python3-autocommand python3-babel python3-certifi python3-chardet python3-charset-normalizer python3-defusedxml python3-docutils python3-idna python3-imagesize python3-inflect python3-jaraco.context python3-jaraco.functools python3-jinja2 python3-markupsafe python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pygments python3-requests python3-roman python3-snowballstemmer python3-sphinx python3-typeguard python3-typing-extensions python3-urllib3 python3.13 python3.13-minimal sbuild-build-depends-main-dummy sensible-utils sgml-base sphinx-common tzdata xml-core zlib1g-dev 0 upgraded, 168 newly installed, 0 to remove and 0 not upgraded. Need to get 152 MB of archives. After this operation, 771 MB of additional disk space will be used. Get:1 copy:/build/murasaki-xreV69/resolver-4pRF5o/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [928 B] Get:2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.1-3 [858 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.1-3 [2202 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-1 [259 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.1-3 [1973 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.1-3 [740 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get:12 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.0-2 [1422 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-1 [92.2 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.15.0-1+b1 [78.7 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:33 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:9.9p1-3 [991 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get:47 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-14 [837 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libgfortran-14-dev amd64 14.2.0-14 [881 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-14 [11.7 MB] Get:60 http://deb.debian.org/debian unstable/main amd64 gfortran-14 amd64 14.2.0-14 [13.5 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3+b1 [59.4 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3+b1 [182 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 55.0-1 [62.2 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 55.0-1 [351 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-6 [210 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-20+b1 [23.6 MB] Get:68 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get:69 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get:70 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 6.1.2+ds-1 [59.8 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.1.2-2 [535 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-5 [8877 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4 [10.6 MB] Get:77 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-4 [234 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-4 [235 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-4 [282 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-4 [230 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-4 [231 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-4 [298 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Get:84 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-4 [330 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-6 [10.4 MB] Get:86 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-4 [346 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-4 [254 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-4 [261 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get:90 http://deb.debian.org/debian unstable/main amd64 libboost-regex-dev amd64 1.83.0.2+b2 [3864 B] Get:91 http://deb.debian.org/debian unstable/main amd64 libcrypto++8t64 amd64 8.9.0-1.1+b1 [1170 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libcrypto++-dev amd64 8.9.0-1.1+b1 [1836 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 55.0-1 [70.2 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 1.17.0-3.1 [631 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.11.2-1 [164 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.18-1+b1 [36.6 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-2 [415 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.5.4-2 [165 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.11.2-1 [254 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b1 [14.2 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b2 [40.2 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.11.2-1 [18.1 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 55.0-1 [28.5 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 55.0-1 [43.3 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-0.3+b1 [100 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-0.3+b1 [200 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 55.0-1 [648 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.15-4+b1 [20.0 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 5.0.6-1 [652 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.6-3 [2360 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.6-3 [97.0 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get:135 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.1.3-4 [616 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get:137 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.16.0-1 [5696 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get:140 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:141 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:144 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:145 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get:146 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.16.0-1 [114 kB] Get:147 http://deb.debian.org/debian unstable/main amd64 python3-roman all 4.2-1 [10.4 kB] Get:148 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get:149 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get:150 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b2 [13.9 kB] Get:151 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.3-2 [120 kB] Get:152 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:153 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get:154 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2024.12.14+ds-1 [9624 B] Get:155 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get:156 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.8-2 [41.6 kB] Get:157 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.3.0-1 [114 kB] Get:158 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get:159 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get:160 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get:161 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.1.3-4 [468 kB] Get:162 http://deb.debian.org/debian unstable/main amd64 libpmix-dev amd64 5.0.6-1 [3962 kB] Get:163 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.6-3 [188 kB] Get:164 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.6-3 [1088 kB] Get:165 http://deb.debian.org/debian unstable/main amd64 libpstreams-dev all 1.0.3-1 [134 kB] Get:166 http://deb.debian.org/debian unstable/main amd64 libterm-readkey-perl amd64 2.38-2+b4 [24.6 kB] Get:167 http://deb.debian.org/debian unstable/main amd64 libtext-wrapper-perl all 1.05-4 [10.3 kB] Get:168 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.18 [3372 B] Preconfiguring packages ... Fetched 152 MB in 1s (144 MB/s) Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... 23043 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.1-3_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.1-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.1-3_amd64.deb ... Unpacking python3.13-minimal (3.13.1-3) ... Setting up libpython3.13-minimal:amd64 (3.13.1-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.1-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 23377 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-2_amd64.deb ... Unpacking python3-minimal (3.13.1-2) ... 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Selecting previously unselected package python3. (Reading database ... 24350 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.1-2_amd64.deb ... Unpacking python3 (3.13.1-2) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.4.0-2_amd64.deb ... Unpacking openssl (3.4.0-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20241223_all.deb ... Unpacking ca-certificates (20241223) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... 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Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libpciaccess0:amd64 (0.17-3+b3) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libboost1.83-dev:amd64 (1.83.0-4) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up libicu72:amd64 (72.1-6) ... Setting up bsdextrautils (2.40.4-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libcbor0.10:amd64 (0.10.2-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libboost-regex1.83.0:amd64 (1.83.0-4) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libedit2:amd64 (3.1-20250104-1) ... Setting up libboost-system1.83.0:amd64 (1.83.0-4) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libibumad3:amd64 (55.0-1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libibmad5:amd64 (55.0-1) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libtext-wrapper-perl (1.05-4) ... Setting up libboost-filesystem1.83.0:amd64 (1.83.0-4) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up python-babel-localedata (2.16.0-1) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Jan 22 00:15:41 UTC 2025. Universal Time is now: Wed Jan 22 00:15:41 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-4) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libmunge2:amd64 (0.5.15-4+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libboost-iostreams1.83.0:amd64 (1.83.0-4) ... Setting up libhwloc15:amd64 (2.11.2-1) ... Setting up libcrypto++8t64:amd64 (8.9.0-1.1+b1) ... Setting up autopoint (0.23.1-1) ... Setting up icu-devtools (72.1-6) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libltdl7:amd64 (2.5.4-2) ... Setting up libgfortran5:amd64 (14.2.0-14) ... Setting up libboost-atomic1.83-dev:amd64 (1.83.0-4) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libnuma1:amd64 (2.0.18-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libjson-perl (4.10000-1) ... Setting up libnl-3-200:amd64 (3.7.0-0.3+b1) ... Setting up libpsm2-2 (11.2.185-2.1) ... Setting up openmpi-common (5.0.6-3) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up netbase (6.4) ... Configuration file '/etc/protocols' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Configuration file '/etc/services' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libboost-system1.83-dev:amd64 (1.83.0-4) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libterm-readkey-perl (2.38-2+b4) ... Setting up libfido2-1:amd64 (1.15.0-1+b1) ... Setting up openssl (3.4.0-2) ... Setting up libdrm-common (2.4.123-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.1-3) ... Setting up libicu-dev:amd64 (72.1-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:amd64 (14.2.0-14) ... Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-2) ... Setting up python3.13 (3.13.1-3) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcrypto++-dev:amd64 (8.9.0-1.1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up python3 (3.13.1-2) ... Setting up libboost-filesystem1.83-dev:amd64 (1.83.0-4) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b2) ... Setting up gfortran-14-x86-64-linux-gnu (14.2.0-14) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.18-1+b1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3+b1) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:amd64 (2.5.4-2) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up python3-roman (4.2-1) ... Setting up python3-jinja2 (3.1.3-2) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:amd64 (1:17.0.6-20+b1) ... Setting up python3-certifi (2024.12.14+ds-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up libpstreams-dev (1.0.3-1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up python3-idna (3.8-2) ... Setting up libboost-regex1.83-dev:amd64 (1.83.0-4) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up libjs-sphinxdoc (8.1.3-4) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libnl-3-dev:amd64 (3.7.0-0.3+b1) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libhwloc-dev:amd64 (2.11.2-1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up gfortran-14 (14.2.0-14) ... Setting up libboost-regex-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-filesystem-dev:amd64 (1.83.0.2+b2) ... Setting up python3-imagesize (1.4.1-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up libibverbs1:amd64 (55.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up ibverbs-providers:amd64 (55.0-1) ... Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up libboost-iostreams1.83-dev:amd64 (1.83.0-4) ... Setting up openssh-client (1:9.9p1-3) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up libboost-iostreams-dev:amd64 (1.83.0.2+b2) ... Setting up libhwloc-plugins:amd64 (2.11.2-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnl-route-3-dev:amd64 (3.7.0-0.3+b1) ... Setting up python3-inflect (7.3.1-2) ... Setting up sphinx-common (8.1.3-4) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up libpmix2t64:amd64 (5.0.6-1) ... Setting up librdmacm1t64:amd64 (55.0-1) ... Setting up libhsakmt1:amd64 (6.1.2+ds-1) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up libfabric1:amd64 (1.17.0-3.1) ... Setting up python3-babel (2.16.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up debhelper (13.24.1) ... Setting up libibverbs-dev:amd64 (55.0-1) ... Setting up libhsa-runtime64-1:amd64 (6.1.2-2) ... Setting up libamdhip64-5 (5.7.1-5) ... Setting up libucx0:amd64 (1.17.0+ds-3) ... Setting up libopenmpi40:amd64 (5.0.6-3) ... Setting up openmpi-bin (5.0.6-3) ... update-alternatives: warning: update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Processing triggers for libc-bin (2.40-5) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-4) ... Setting up libpmix-dev:amd64 (5.0.6-1) ... Setting up libopenmpi-dev:amd64 (5.0.6-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.18) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. +------------------------------------------------------------------------------+ | Check architectures Wed, 22 Jan 2025 00:15:49 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Wed, 22 Jan 2025 00:15:50 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.11.10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1 (2024-11-23) amd64 (x86_64) Toolchain package versions: binutils_2.43.50.20250108-1 dpkg-dev_1.22.14 g++-13_13.3.0-12 g++-14_14.2.0-14 gcc-13_13.3.0-12 gcc-14_14.2.0-14 libc6-dev_2.40-5 libstdc++-13-dev_13.3.0-12 libstdc++-14-dev_14.2.0-14 libstdc++6_14.2.0-14 linux-libc-dev_6.12.10-1 Package versions: adduser_3.137 apt_2.9.24 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.23.1-1 autotools-dev_20220109.1 base-files_13.6 base-passwd_3.6.6 bash_5.2.37-1 binutils_2.43.50.20250108-1 binutils-common_2.43.50.20250108-1 binutils-x86-64-linux-gnu_2.43.50.20250108-1 bsdextrautils_2.40.4-1 bsdutils_1:2.40.4-1 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20241223 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-13_13.3.0-12 cpp-13-x86-64-linux-gnu_13.3.0-12 cpp-14_14.2.0-14 cpp-14-x86-64-linux-gnu_14.2.0-14 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-11 debconf_1.5.89 debhelper_13.24.1 debian-archive-keyring_2023.4 debianutils_5.21 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-1 diffutils_1:3.10-2 dirmngr_2.2.46-1+b1 docutils-common_0.21.2+dfsg-2 dpkg_1.22.14 dpkg-dev_1.22.14 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.45-3+b1 findutils_4.10.0-3 g++_4:14.2.0-1 g++-13_13.3.0-12 g++-13-x86-64-linux-gnu_13.3.0-12 g++-14_14.2.0-14 g++-14-x86-64-linux-gnu_14.2.0-14 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-13_13.3.0-12 gcc-13-base_13.3.0-12 gcc-13-x86-64-linux-gnu_13.3.0-12 gcc-14_14.2.0-14 gcc-14-base_14.2.0-14 gcc-14-x86-64-linux-gnu_14.2.0-14 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-1 gettext-base_0.23.1-1 gfortran-14_14.2.0-14 gfortran-14-x86-64-linux-gnu_14.2.0-14 gnupg_2.2.46-1 gnupg-l10n_2.2.46-1 gnupg-utils_2.2.46-1+b1 gpg_2.2.46-1+b1 gpg-agent_2.2.46-1+b1 gpg-wks-client_2.2.46-1+b1 gpgconf_2.2.46-1+b1 gpgsm_2.2.46-1+b1 gpgv_2.2.46-1+b1 grep_3.11-4 groff-base_1.23.0-7 gzip_1.13-1 hostname_3.25 ibverbs-providers_55.0-1 icu-devtools_72.1-6 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b2 libamdhip64-5_5.7.1-5 libapt-pkg6.0t64_2.9.24 libarchive-zip-perl_1.68-1 libasan8_14.2.0-14 libassuan0_2.5.6-1+b1 libassuan9_3.0.1-2 libatomic1_14.2.0-14 libattr1_1:2.5.2-2 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b1 libbinutils_2.43.50.20250108-1 libblkid1_2.40.4-1 libboost-atomic1.83-dev_1.83.0-4 libboost-atomic1.83.0_1.83.0-4 libboost-filesystem-dev_1.83.0.2+b2 libboost-filesystem1.83-dev_1.83.0-4 libboost-filesystem1.83.0_1.83.0-4 libboost-iostreams-dev_1.83.0.2+b2 libboost-iostreams1.83-dev_1.83.0-4 libboost-iostreams1.83.0_1.83.0-4 libboost-regex-dev_1.83.0.2+b2 libboost-regex1.83-dev_1.83.0-4 libboost-regex1.83.0_1.83.0-4 libboost-system1.83-dev_1.83.0-4 libboost-system1.83.0_1.83.0-4 libboost1.83-dev_1.83.0-4 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.40-5 libc-dev-bin_2.40-5 libc-l10n_2.40-5 libc6_2.40-5 libc6-dev_2.40-5 libcap-ng0_0.8.5-4 libcap2_1:2.66-5+b1 libcbor0.10_0.10.2-2 libcc1-0_14.2.0-14 libcom-err2_1.47.2-1 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libcrypto++-dev_8.9.0-1.1+b1 libcrypto++8t64_8.9.0-1.1+b1 libctf-nobfd0_2.43.50.20250108-1 libctf0_2.43.50.20250108-1 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.277 libdebhelper-perl_13.24.1 libdpkg-perl_1.22.14 libdrm-amdgpu1_2.4.123-1 libdrm-common_2.4.123-1 libdrm2_2.4.123-1 libeatmydata1_131-2+b1 libedit2_3.1-20250104-1 libelf1t64_0.192-4 libevent-2.1-7t64_2.1.12-stable-10+b1 libevent-core-2.1-7t64_2.1.12-stable-10+b1 libevent-dev_2.1.12-stable-10+b1 libevent-extra-2.1-7t64_2.1.12-stable-10+b1 libevent-openssl-2.1-7t64_2.1.12-stable-10+b1 libevent-pthreads-2.1-7t64_2.1.12-stable-10+b1 libexpat1_2.6.4-1 libfabric1_1.17.0-3.1 libffi8_3.4.6-1 libfido2-1_1.15.0-1+b1 libfile-stripnondeterminism-perl_1.14.1-1 libgcc-13-dev_13.3.0-12 libgcc-14-dev_14.2.0-14 libgcc-s1_14.2.0-14 libgcrypt20_1.11.0-7 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgfortran-14-dev_14.2.0-14 libgfortran5_14.2.0-14 libgmp10_2:6.3.0+dfsg-3 libgnutls30t64_3.8.8-2 libgomp1_14.2.0-14 libgpg-error0_1.51-3 libgprofng0_2.43.50.20250108-1 libgssapi-krb5-2_1.21.3-4 libhogweed6t64_3.10-1+b1 libhsa-runtime64-1_6.1.2-2 libhsakmt1_6.1.2+ds-1 libhwasan0_14.2.0-14 libhwloc-dev_2.11.2-1 libhwloc-plugins_2.11.2-1 libhwloc15_2.11.2-1 libibmad5_55.0-1 libibumad3_55.0-1 libibverbs-dev_55.0-1 libibverbs1_55.0-1 libicu-dev_72.1-6 libicu72_72.1-6 libidn2-0_2.3.7-2+b1 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libpam0g_1.5.3-7+b1 libpciaccess0_0.17-3+b3 libpcre2-8-0_10.44-5 libperl5.38t64_5.38.2-5 libperl5.40_5.40.1-1 libpipeline1_1.5.8-1 libpmix-dev_5.0.6-1 libpmix2t64_5.0.6-1 libpsm-infinipath1_3.3+20.604758e7-6.3 libpsm2-2_11.2.185-2.1 libpstreams-dev_1.0.3-1 libpython3-stdlib_3.13.1-2 libpython3.13-minimal_3.13.1-3 libpython3.13-stdlib_3.13.1-3 libquadmath0_14.2.0-14 librdmacm1t64_55.0-1 libreadline8t64_8.2-6 libsasl2-2_2.1.28+dfsg1-8+b1 libsasl2-modules-db_2.1.28+dfsg1-8+b1 libseccomp2_2.5.5-2 libselinux1_3.7-3+b1 libsemanage-common_3.7-2 libsemanage2_3.7-2+b1 libsepol2_3.7-1 libsframe1_2.43.50.20250108-1 libsmartcols1_2.40.4-1 libsqlite3-0_3.46.1-1 libssl3t64_3.4.0-2 libstdc++-13-dev_13.3.0-12 libstdc++-14-dev_14.2.0-14 libstdc++6_14.2.0-14 libsystemd0_257.2-2 libtasn1-6_4.19.0-3+b3 libterm-readkey-perl_2.38-2+b4 libtext-wrapper-perl_1.05-4 libtinfo6_6.5-2+b1 libtool_2.5.4-2 libtsan2_14.2.0-14 libubsan1_14.2.0-14 libuchardet0_0.0.8-1+b2 libucx0_1.17.0+ds-3 libudev1_257.2-2 libunistring5_1.3-1 libuuid1_2.40.4-1 libx11-6_2:1.8.10-2 libx11-data_2:1.8.10-2 libxau6_1:1.0.11-1 libxcb1_1.17.0-2+b1 libxdmcp6_1:1.1.5-1 libxext6_2:1.3.4-1+b3 libxml2_2.12.7+dfsg+really2.9.14-0.2+b1 libxnvctrl0_535.171.04-1+b1 libxxhash0_0.8.3-2 libz3-4_4.13.3-1 libzstd1_1.5.6+dfsg-2 linux-libc-dev_6.12.10-1 locales-all_2.40-5 login_1:4.16.0-2+really2.40.4-1 login.defs_1:4.16.0-7 m4_1.4.19-5 make_4.4.1-1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 media-types_10.1.0 mpi-default-dev_1.18 ncurses-base_6.5-2 ncurses-bin_6.5-2+b1 netbase_6.4 ocl-icd-libopencl1_2.3.2-1+b2 openmpi-bin_5.0.6-3 openmpi-common_5.0.6-3 openssh-client_1:9.9p1-3 openssl_3.4.0-2 openssl-provider-legacy_3.4.0-2 passwd_1:4.16.0-7 patch_2.7.6-7 perl_5.40.1-1 perl-base_5.40.1-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.1-1 pinentry-curses_1.3.1-2 po-debconf_1.0.21+nmu1 python-babel-localedata_2.16.0-1 python3_3.13.1-2 python3-alabaster_0.7.16-0.1 python3-autocommand_2.2.2-3 python3-babel_2.16.0-1 python3-certifi_2024.12.14+ds-1 python3-chardet_5.2.0+dfsg-2 python3-charset-normalizer_3.4.0-1+b1 python3-defusedxml_0.7.1-3 python3-docutils_0.21.2+dfsg-2 python3-idna_3.8-2 python3-imagesize_1.4.1-1 python3-inflect_7.3.1-2 python3-jaraco.context_6.0.0-1 python3-jaraco.functools_4.1.0-1 python3-jinja2_3.1.3-2 python3-markupsafe_2.1.5-1+b2 python3-minimal_3.13.1-2 python3-more-itertools_10.6.0-1 python3-packaging_24.2-1 python3-pkg-resources_75.6.0-1 python3-pygments_2.18.0+dfsg-2 python3-requests_2.32.3+dfsg-1 python3-roman_4.2-1 python3-snowballstemmer_2.2.0-4 python3-sphinx_8.1.3-4 python3-typeguard_4.4.1-1 python3-typing-extensions_4.12.2-2 python3-urllib3_2.3.0-1 python3.13_3.13.1-3 python3.13-minimal_3.13.1-3 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sgml-base_1.31 sphinx-common_8.1.3-4 sqv_1.2.1-5 sysvinit-utils_3.13-1 tar_1.35+dfsg-3.1 tzdata_2025a-1 usr-is-merged_39+nmu2 util-linux_2.40.4-1 xml-core_0.19 xz-utils_5.6.3-1+b1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Wed, 22 Jan 2025 00:15:50 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: murasaki Binary: murasaki, murasaki-mpi, murasaki-common Architecture: any all Version: 1.68.6-14 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Nilesh Patra Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Standards-Version: 4.7.0 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, libpstreams-dev, libterm-readkey-perl, libtext-wrapper-perl, mpi-default-dev Build-Depends: debhelper-compat (= 13), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, mpi-default-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 9403b175b189c614ea8a6347d0a4c3a50849806e 11224 murasaki_1.68.6-14.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 0237d35c8703611985593569214901098fe7d98e2281ccdbfe4e27962a59f7f8 11224 murasaki_1.68.6-14.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 96c84644f65aef0fcf53bc954300ab92 11224 murasaki_1.68.6-14.debian.tar.xz Dgit: c2a745a71b328a826d276147911f72bcffbe9e10 debian archive/debian/1.68.6-14 https://git.dgit.debian.org/murasaki -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmcvS7IUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdr/+w//VuLOkZpSAR7rJua9gATIo2zZ7mMe 9MiEnaErEoXzRFGQjRJjAFUmEHdfGauzJEm2DeT0DDtqcV+OEJZfu87uIaRjvnyv WLxIZ/TN1Z3PjFKLrO+KZll66wudugidu4LLJGdoXOOB4WKEV6mNZUDE6aIjEY2K CoJWmD5ir3uvDOs63rHzxFwpXDM/Yon+CoBwZcVOldYDyByyAkrh4KU7yrIaYLgH O5rfvACZjD7ZvYbxZ8773PgGch7Bwb2Q8iT2yuoc1fpbSX0py2yKQLfY3YCJAsQo /ryJCHFXkgpB/qFj+vFVkVR8QuboF1UwGlqxh5TTYGxy30klx48zV/12eRYpDKKQ mg4CNync1EJ6Ky1ky73V3R4sz4JRWShIb6dT2ObDq32VY0KQ918vVT7BoKU1mj8j 2hZ5K6vBmcP7evOTChak0NHI5bMwR8p07lHoGSyVpaDPTCqR/BZ3sWPbK7yCkSQw xvlSGRgiGwTSE4Uvv4RVpz3tBHIh0BBmgnGsPHdgd6J9f96CEcHVDEFTaoCm74XE WkjOaWsiaAsD022iNDhtIllwMSDDyNg6H8DGoqtz0XZY77D7jFUerh8IOXbd2S/c 0nTXHshaFPhPrgmJriJSlB0xeDh9/J1jjG/Bmq0kpyAHLgrUNCVXKeviHv6UK+S9 Xw1rwyKsv85WDmQ= =Sztt -----END PGP SIGNATURE----- gpgv: Signature made Sat Nov 9 11:46:58 2024 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./murasaki_1.68.6-14.dsc: no acceptable signature found dpkg-source: info: extracting murasaki in /build/murasaki-xreV69/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_1.68.6-14.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 Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Wed, 22 Jan 2025 00:15:50 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network murasaki_1.68.6-14 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network murasaki_1.68.6-14 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/murasaki-xreV69/murasaki-1.68.6 SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-ee4320a4-db7d-473c-8ff6-44a23c5cc2da SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package murasaki dpkg-buildpackage: info: source version 1.68.6-14 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j2 clean make[1]: Entering directory '/build/murasaki-xreV69/murasaki-1.68.6' rm -rf *.o *~ .*~ core make -C src clean make[2]: Entering directory '/build/murasaki-xreV69/murasaki-1.68.6/src' rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa make[2]: Leaving directory '/build/murasaki-xreV69/murasaki-1.68.6/src' make[1]: Leaving directory '/build/murasaki-xreV69/murasaki-1.68.6' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building murasaki using existing ./murasaki_1.68.6.orig-debian-tests-data.tar.gz dpkg-source: info: building murasaki using existing ./murasaki_1.68.6.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building murasaki in murasaki_1.68.6-14.debian.tar.xz dpkg-source: info: building murasaki in murasaki_1.68.6-14.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/murasaki-xreV69/murasaki-1.68.6' dh_auto_build -- USE_MPI=YES make -j2 "INSTALL=install --strip-program=true" USE_MPI=YES make[2]: Entering directory '/build/murasaki-xreV69/murasaki-1.68.6' make -C src all make[3]: Entering directory '/build/murasaki-xreV69/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 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from murasaki.cc:29: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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++/14/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++/14/bits/stl_algo.h:4492:5: note: declared here 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from dinkymath.h:24, from dinkymath.cc:26: /usr/include/c++/14/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; | ^~~~ 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 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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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’ 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++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/bits/stl_tree.h:63: /usr/include/c++/14/bits/stl_pair.h:284:12: note: ‘ShmVector >::val_type’ {aka ‘struct std::pair’} declared here 284 | 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++/14/bits/stl_pair.h:284:12: note: ‘ShmVector >::val_type’ {aka ‘struct std::pair’} declared here 284 | 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 162 | sbox=new SBoxT(hash_bits); | ^ 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++/14/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++/14/bits/stl_algo.h:4492:5: note: declared here 4492 | 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 = long unsigned int]’: shmvector.hh:282:5: required from ‘void ShmVector::resize(size_t) [with T = std::pair; size_t = long unsigned int]’ 282 | shmRealloc(c); | ^~~~~~~~~~ sequence.cc:1110:17: required from here 1110 | subSeqs.resize(binseq.regionSizes[0]); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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++/14/bits/stl_pair.h:284:12: note: ‘struct std::pair’ declared here 284 | 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 msethash.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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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 options.cc 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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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 ecohash.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecolist.cc 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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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 murasaki_mpi.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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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++/14/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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from murasaki_mpi.cc:30: /usr/include/c++/14/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 arrayhash.cc 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++/14/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++/14/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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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 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); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from murasaki_mpi.cc:29: /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:1677:20: note: by argument 1 of type ‘const void*’ to ‘int MPI_Get_address(const void*, MPI_Aint*)’ declared here 1677 | 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; | ^~~ 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(); } | ^~~~~~~~~~~ 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 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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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 openhash.cc 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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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 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++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/14/bits/stl_pair.h:284:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 284 | 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++/14/bits/stl_pair.h:284:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 284 | 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++/14/bits/stl_pair.h:284:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 284 | 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-image.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr.cc 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; | ^~~~~~~~~ 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]; | ^ cgr.cc: In member function ‘int PgmBuffer::loadBinaryPGM(std::string)’: 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 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 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 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 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; | ^~~~~~~~~~ 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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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 align-compare.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c alignments.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-or.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c geneparse.cc 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; | ^~~~~~~~ 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 -c mbfa.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../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-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 ../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 ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-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 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 make[3]: Leaving directory '/build/murasaki-xreV69/murasaki-1.68.6/src' make[2]: Leaving directory '/build/murasaki-xreV69/murasaki-1.68.6' for bin in geneparse mbfa murasaki cgr-* testeco align-* ; do \ mv ${bin} ${bin}-mpi ; \ done make clean make[2]: Entering directory '/build/murasaki-xreV69/murasaki-1.68.6' rm -rf *.o *~ .*~ core make -C src clean make[3]: Entering directory '/build/murasaki-xreV69/murasaki-1.68.6/src' rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa make[3]: Leaving directory '/build/murasaki-xreV69/murasaki-1.68.6/src' make[2]: Leaving directory '/build/murasaki-xreV69/murasaki-1.68.6' dh_auto_build -- USE_MPI=NO make -j2 "INSTALL=install --strip-program=true" USE_MPI=NO make[2]: Entering directory '/build/murasaki-xreV69/murasaki-1.68.6' make -C src all make[3]: Entering directory '/build/murasaki-xreV69/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 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from murasaki.cc:29: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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++/14/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++/14/bits/stl_algo.h:4492:5: note: declared here 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ 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++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from dinkymath.h:24, from dinkymath.cc:26: /usr/include/c++/14/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; | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c sequence.cc 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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/bits/stl_tree.h:63: /usr/include/c++/14/bits/stl_pair.h:284:12: note: ‘ShmVector >::val_type’ {aka ‘struct std::pair’} declared here 284 | 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++/14/bits/stl_pair.h:284:12: note: ‘ShmVector >::val_type’ {aka ‘struct std::pair’} declared here 284 | 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]); | ^~~~~~~~ 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 162 | sbox=new SBoxT(hash_bits); | ^ 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++/14/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++/14/bits/stl_algo.h:4492:5: note: declared here 4492 | 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 = long unsigned int]’: shmvector.hh:282:5: required from ‘void ShmVector::resize(size_t) [with T = std::pair; size_t = long unsigned int]’ 282 | shmRealloc(c); | ^~~~~~~~~~ sequence.cc:1110:17: required from here 1110 | subSeqs.resize(binseq.regionSizes[0]); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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++/14/bits/stl_pair.h:284:12: note: ‘struct std::pair’ declared here 284 | struct pair | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c msethash.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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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 options.cc 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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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 ecohash.cc 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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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 ecolist.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c murasaki_mpi.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c arrayhash.cc 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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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++/14/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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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 seqread.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c scoring.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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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 openhash.cc 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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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 genopts.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c binseq.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++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/14/bits/stl_pair.h:284:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 284 | 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++/14/bits/stl_pair.h:284:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 284 | 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++/14/bits/stl_pair.h:284:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 284 | struct pair | ^~~~ 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 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; | ^~~~~~~~~ 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]; | ^ cgr.cc: In member function ‘int PgmBuffer::loadBinaryPGM(std::string)’: 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-compare.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-random.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-sample.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c testeco.cc cgr-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; | ^~~~~~~~~~ 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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/14/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 align-compare.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c alignments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-or.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c geneparse.cc 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; | ^~~~~~~~ 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 ../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-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 ../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 ../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 ../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 ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-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 ../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 ../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/murasaki-xreV69/murasaki-1.68.6/src' make[2]: Leaving directory '/build/murasaki-xreV69/murasaki-1.68.6' make[1]: Leaving directory '/build/murasaki-xreV69/murasaki-1.68.6' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install-arch make[1]: Entering directory '/build/murasaki-xreV69/murasaki-1.68.6' dh_install -a # using wildcards in install files is practical but it duplicates some files find debian/murasaki/usr -name "*-mpi" -delete make[1]: Leaving directory '/build/murasaki-xreV69/murasaki-1.68.6' dh_install -Nmurasaki -Nmurasaki-mpi dh_installdocs dh_installchangelogs debian/rules override_dh_installman-arch make[1]: Entering directory '/build/murasaki-xreV69/murasaki-1.68.6' dh_installman -a mkdir -p debian/murasaki-mpi/usr/share/man/man1 for man in debian/murasaki/usr/share/man/man1/*.1 ; do \ cp -a ${man} debian/murasaki-mpi/usr/share/man/man1/`basename ${man} .1`-mpi.1 ; \ done make[1]: Leaving directory '/build/murasaki-xreV69/murasaki-1.68.6' debian/rules override_dh_installman-indep make[1]: Entering directory '/build/murasaki-xreV69/murasaki-1.68.6' dh_installman -i # create manpages for PL files mkdir -p debian/murasaki-common/usr/share/man/man1 for pscript in debian/murasaki-common/usr/lib/debian-med/bin/* ; do \ pod2man ${pscript} > debian/murasaki-common/usr/share/man/man1/`basename ${pscript}`.1 ; \ done pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/anchors2maf.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/anchors2osfinder.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/antisense.pl debian/murasaki-common/usr/lib/debian-med/bin/chromostitch.pl around line 134: '=item' outside of any '=over' debian/murasaki-common/usr/lib/debian-med/bin/chromostitch.pl around line 141: You forgot a '=back' before '=head1' POD document had syntax errors at /usr/bin/pod2man line 69. pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/dna2binary.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/dnashuffle.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/geneparse.pl debian/murasaki-common/usr/lib/debian-med/bin/getcds.pl around line 646: '=item' outside of any '=over' debian/murasaki-common/usr/lib/debian-med/bin/getcds.pl around line 646: =over without closing =back POD document had syntax errors at /usr/bin/pod2man line 69. pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/humantime.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/osfinder2anchors.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/randpat.pl find debian/murasaki-common/usr/share/man/man1 -empty -delete make[1]: Leaving directory '/build/murasaki-xreV69/murasaki-1.68.6' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms-indep make[1]: Entering directory '/build/murasaki-xreV69/murasaki-1.68.6' dh_fixperms -i chmod a+x debian/murasaki-common/usr/share/perl5/murasaki/config.pl make[1]: Leaving directory '/build/murasaki-xreV69/murasaki-1.68.6' dh_fixperms -Nmurasaki-common dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package murasaki-common: substitution variable ${misc:perl} used, but is not defined dpkg-gencontrol: warning: package murasaki-common: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-14_amd64.deb'. dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-14_amd64.deb'. dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-14_amd64.deb'. dpkg-deb: building package 'murasaki-common' in '../murasaki-common_1.68.6-14_all.deb'. dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-14_amd64.deb'. dpkg-genbuildinfo -O../murasaki_1.68.6-14_amd64.buildinfo dpkg-genchanges -O../murasaki_1.68.6-14_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2025-01-22T00:19:29Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Wed, 22 Jan 2025 00:19:30 +0000 | +------------------------------------------------------------------------------+ murasaki_1.68.6-14_amd64.changes: --------------------------------- Format: 1.8 Date: Sat, 09 Nov 2024 11:58:11 +0100 Source: murasaki Binary: murasaki murasaki-common murasaki-dbgsym murasaki-mpi murasaki-mpi-dbgsym Architecture: source all amd64 Version: 1.68.6-14 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: murasaki - homology detection tool across multiple large genomes murasaki-common - homology detection tool across multiple large genomes (common fil murasaki-mpi - homology detection tool across multiple large genomes (MPI-versio Closes: 1086908 Changes: murasaki (1.68.6-14) unstable; urgency=medium . * Team upload. * d/{,t}/control: migrate to mpi-default-*. (Closes: #1086908) * d/control: declare compliance to standards version 4.7.0. * d/patches/*: normalize dep3 headers. Most of the changes are normalisation of the Last-Update timestamp. * d/s/lintian-overrides: delete: override is now unused. 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86d62b8e3e304f8010dc752b9713090c 692752 science optional murasaki-mpi_1.68.6-14_amd64.deb ebc4986630e71c01403c297de2de788f 11041 science optional murasaki_1.68.6-14_amd64.buildinfo cceb8fd86d493cb92e36a9f5e7833f23 644676 science optional murasaki_1.68.6-14_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Wed, 22 Jan 2025 00:19:30 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: murasaki Binary: murasaki murasaki-common murasaki-dbgsym murasaki-mpi murasaki-mpi-dbgsym Architecture: all amd64 source Version: 1.68.6-14 Checksums-Md5: 659a4653a14dc91a52122a9376cf8653 1882 murasaki_1.68.6-14.dsc 664374b5ae5a73b7c6a60d94897f0fbf 117248 murasaki-common_1.68.6-14_all.deb f679a860bbe6f69e05797ed034b227a3 14983260 murasaki-dbgsym_1.68.6-14_amd64.deb 2aa370b4c7b26b815fbb4d188ac2453d 15627636 murasaki-mpi-dbgsym_1.68.6-14_amd64.deb 86d62b8e3e304f8010dc752b9713090c 692752 murasaki-mpi_1.68.6-14_amd64.deb cceb8fd86d493cb92e36a9f5e7833f23 644676 murasaki_1.68.6-14_amd64.deb Checksums-Sha1: fd06c90f19df03672704f0427fda02ad6bb78429 1882 murasaki_1.68.6-14.dsc 7a193e29d043975fa48833be51771b256add47ce 117248 murasaki-common_1.68.6-14_all.deb b33a22ae7287d5771fc1c1393c3d9068cb432fa5 14983260 murasaki-dbgsym_1.68.6-14_amd64.deb 6c200bbaa0d8e3467322fe0a28572db515417bda 15627636 murasaki-mpi-dbgsym_1.68.6-14_amd64.deb f197be34fd31e1800e87b04cdf43f12b1bd03306 692752 murasaki-mpi_1.68.6-14_amd64.deb 162f581d7a28636f6552e1435609100a4d1aa869 644676 murasaki_1.68.6-14_amd64.deb Checksums-Sha256: fc38b5a8b34cb15fc8a228b6119a46dd09a64bdd4e153d9df6351088678d3c7c 1882 murasaki_1.68.6-14.dsc 25116aa329953c93182e3407e2a0658f2706537a9ba49d29e4e9499ee977a008 117248 murasaki-common_1.68.6-14_all.deb 357e97947771b33d0b6d4697a79ea082e52460202247bc6af22c0b52e8489819 14983260 murasaki-dbgsym_1.68.6-14_amd64.deb 996453ce140c2bda67c10b123bb2a98addf4d204b2c168bab947a1ad1a9c2c9e 15627636 murasaki-mpi-dbgsym_1.68.6-14_amd64.deb 7e307332d69e2e10f95e1a8cc777ac818daa2e8e030563854cf15c3f697354bc 692752 murasaki-mpi_1.68.6-14_amd64.deb fa4265b50008b461a3adf73ca4ebeec26a17c96bd3c8a7223f011597651d228c 644676 murasaki_1.68.6-14_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 22 Jan 2025 00:19:29 +0000 Build-Path: /build/murasaki-xreV69/murasaki-1.68.6 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: adduser (= 3.137), autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.23.1-1), autotools-dev (= 20220109.1), base-files (= 13.6), base-passwd (= 3.6.6), bash (= 5.2.37-1), binutils (= 2.43.50.20250108-1), binutils-common (= 2.43.50.20250108-1), binutils-x86-64-linux-gnu (= 2.43.50.20250108-1), bsdextrautils (= 2.40.4-1), bsdutils (= 1:2.40.4-1), build-essential (= 12.12), bzip2 (= 1.0.8-6), ca-certificates (= 20241223), coreutils (= 9.5-1+b1), cpp (= 4:14.2.0-1), cpp-13 (= 13.3.0-12), cpp-13-x86-64-linux-gnu (= 13.3.0-12), cpp-14 (= 14.2.0-14), cpp-14-x86-64-linux-gnu (= 14.2.0-14), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-11), debconf (= 1.5.89), debhelper (= 13.24.1), debianutils (= 5.21), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-1), diffutils (= 1:3.10-2), docutils-common (= 0.21.2+dfsg-2), dpkg (= 1.22.14), dpkg-dev (= 1.22.14), dwz (= 0.15-1+b1), file (= 1:5.45-3+b1), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-14), g++-14-x86-64-linux-gnu (= 14.2.0-14), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-13 (= 13.3.0-12), gcc-13-base (= 13.3.0-12), gcc-13-x86-64-linux-gnu (= 13.3.0-12), gcc-14 (= 14.2.0-14), gcc-14-base (= 14.2.0-14), gcc-14-x86-64-linux-gnu (= 14.2.0-14), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-1), gettext-base (= 0.23.1-1), gfortran-14 (= 14.2.0-14), gfortran-14-x86-64-linux-gnu (= 14.2.0-14), grep (= 3.11-4), groff-base (= 1.23.0-7), gzip (= 1.13-1), hostname (= 3.25), ibverbs-providers (= 55.0-1), icu-devtools (= 72.1-6), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libamd-comgr2 (= 6.0+git20231212.4510c28+dfsg-3+b2), libamdhip64-5 (= 5.7.1-5), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-14), libatomic1 (= 14.2.0-14), libattr1 (= 1:2.5.2-2), libaudit-common (= 1:4.0.2-2), libaudit1 (= 1:4.0.2-2+b1), libbinutils (= 2.43.50.20250108-1), libblkid1 (= 2.40.4-1), libboost-atomic1.83-dev (= 1.83.0-4), libboost-atomic1.83.0 (= 1.83.0-4), libboost-filesystem-dev (= 1.83.0.2+b2), libboost-filesystem1.83-dev (= 1.83.0-4), libboost-filesystem1.83.0 (= 1.83.0-4), libboost-iostreams-dev (= 1.83.0.2+b2), libboost-iostreams1.83-dev (= 1.83.0-4), libboost-iostreams1.83.0 (= 1.83.0-4), libboost-regex-dev (= 1.83.0.2+b2), libboost-regex1.83-dev (= 1.83.0-4), libboost-regex1.83.0 (= 1.83.0-4), libboost-system1.83-dev (= 1.83.0-4), libboost-system1.83.0 (= 1.83.0-4), libboost1.83-dev (= 1.83.0-4), libbsd0 (= 0.12.2-2), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.40-5), libc-dev-bin (= 2.40-5), libc6 (= 2.40-5), libc6-dev (= 2.40-5), libcap-ng0 (= 0.8.5-4), libcap2 (= 1:2.66-5+b1), libcbor0.10 (= 0.10.2-2), libcc1-0 (= 14.2.0-14), libcom-err2 (= 1.47.2-1), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libcrypto++-dev (= 8.9.0-1.1+b1), libcrypto++8t64 (= 8.9.0-1.1+b1), libctf-nobfd0 (= 2.43.50.20250108-1), libctf0 (= 2.43.50.20250108-1), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.277), libdebhelper-perl (= 13.24.1), libdpkg-perl (= 1.22.14), libdrm-amdgpu1 (= 2.4.123-1), libdrm-common (= 2.4.123-1), libdrm2 (= 2.4.123-1), libedit2 (= 3.1-20250104-1), libelf1t64 (= 0.192-4), libevent-2.1-7t64 (= 2.1.12-stable-10+b1), libevent-core-2.1-7t64 (= 2.1.12-stable-10+b1), libevent-dev (= 2.1.12-stable-10+b1), libevent-extra-2.1-7t64 (= 2.1.12-stable-10+b1), libevent-openssl-2.1-7t64 (= 2.1.12-stable-10+b1), libevent-pthreads-2.1-7t64 (= 2.1.12-stable-10+b1), libexpat1 (= 2.6.4-1), libfabric1 (= 1.17.0-3.1), libffi8 (= 3.4.6-1), libfido2-1 (= 1.15.0-1+b1), libfile-stripnondeterminism-perl (= 1.14.1-1), libgcc-13-dev (= 13.3.0-12), libgcc-14-dev (= 14.2.0-14), libgcc-s1 (= 14.2.0-14), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgfortran-14-dev (= 14.2.0-14), libgfortran5 (= 14.2.0-14), libgmp10 (= 2:6.3.0+dfsg-3), libgomp1 (= 14.2.0-14), libgprofng0 (= 2.43.50.20250108-1), libgssapi-krb5-2 (= 1.21.3-4), libhsa-runtime64-1 (= 6.1.2-2), libhsakmt1 (= 6.1.2+ds-1), libhwasan0 (= 14.2.0-14), libhwloc-dev (= 2.11.2-1), libhwloc-plugins (= 2.11.2-1), libhwloc15 (= 2.11.2-1), libibmad5 (= 55.0-1), libibumad3 (= 55.0-1), libibverbs-dev (= 55.0-1), libibverbs1 (= 55.0-1), libicu-dev (= 72.1-6), libicu72 (= 72.1-6), libisl23 (= 0.27-1), libitm1 (= 14.2.0-14), libjansson4 (= 2.14-2+b3), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libjs-sphinxdoc (= 8.1.3-4), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libjson-perl (= 4.10000-1), libk5crypto3 (= 1.21.3-4), libkeyutils1 (= 1.6.3-4), libkrb5-3 (= 1.21.3-4), libkrb5support0 (= 1.21.3-4), libllvm17t64 (= 1:17.0.6-20+b1), liblsan0 (= 14.2.0-14), libltdl-dev (= 2.5.4-2), libltdl7 (= 2.5.4-2), liblzma5 (= 5.6.3-1+b1), libmagic-mgc (= 1:5.45-3+b1), libmagic1t64 (= 1:5.45-3+b1), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.40.4-1), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.1-1+b2), libmunge2 (= 0.5.15-4+b1), libncursesw6 (= 6.5-2+b1), libnl-3-200 (= 3.7.0-0.3+b1), libnl-3-dev (= 3.7.0-0.3+b1), libnl-route-3-200 (= 3.7.0-0.3+b1), libnl-route-3-dev (= 3.7.0-0.3+b1), libnuma-dev (= 2.0.18-1+b1), libnuma1 (= 2.0.18-1+b1), libopenmpi-dev (= 5.0.6-3), libopenmpi40 (= 5.0.6-3), libpam-modules (= 1.5.3-7+b1), libpam-modules-bin (= 1.5.3-7+b1), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7+b1), libpciaccess0 (= 0.17-3+b3), libpcre2-8-0 (= 10.44-5), libperl5.40 (= 5.40.1-1), libpipeline1 (= 1.5.8-1), libpmix-dev (= 5.0.6-1), libpmix2t64 (= 5.0.6-1), libpsm-infinipath1 (= 3.3+20.604758e7-6.3), libpsm2-2 (= 11.2.185-2.1), libpstreams-dev (= 1.0.3-1), libpython3-stdlib (= 3.13.1-2), libpython3.13-minimal (= 3.13.1-3), libpython3.13-stdlib (= 3.13.1-3), libquadmath0 (= 14.2.0-14), librdmacm1t64 (= 55.0-1), libreadline8t64 (= 8.2-6), libseccomp2 (= 2.5.5-2), libselinux1 (= 3.7-3+b1), libsemanage-common (= 3.7-2), libsemanage2 (= 3.7-2+b1), libsepol2 (= 3.7-1), libsframe1 (= 2.43.50.20250108-1), libsmartcols1 (= 2.40.4-1), libsqlite3-0 (= 3.46.1-1), libssl3t64 (= 3.4.0-2), libstdc++-14-dev (= 14.2.0-14), libstdc++6 (= 14.2.0-14), libsystemd0 (= 257.2-2), libterm-readkey-perl (= 2.38-2+b4), libtext-wrapper-perl (= 1.05-4), libtinfo6 (= 6.5-2+b1), libtool (= 2.5.4-2), libtsan2 (= 14.2.0-14), libubsan1 (= 14.2.0-14), libuchardet0 (= 0.0.8-1+b2), libucx0 (= 1.17.0+ds-3), libudev1 (= 257.2-2), libunistring5 (= 1.3-1), libuuid1 (= 2.40.4-1), libx11-6 (= 2:1.8.10-2), libx11-data (= 2:1.8.10-2), libxau6 (= 1:1.0.11-1), libxcb1 (= 1.17.0-2+b1), libxdmcp6 (= 1:1.1.5-1), libxext6 (= 2:1.3.4-1+b3), libxml2 (= 2.12.7+dfsg+really2.9.14-0.2+b1), libxnvctrl0 (= 535.171.04-1+b1), libz3-4 (= 4.13.3-1), libzstd1 (= 1.5.6+dfsg-2), linux-libc-dev (= 6.12.10-1), login.defs (= 1:4.16.0-7), m4 (= 1.4.19-5), make (= 4.4.1-1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), media-types (= 10.1.0), mpi-default-dev (= 1.18), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2+b1), netbase (= 6.4), ocl-icd-libopencl1 (= 2.3.2-1+b2), openmpi-bin (= 5.0.6-3), openmpi-common (= 5.0.6-3), openssh-client (= 1:9.9p1-3), openssl (= 3.4.0-2), openssl-provider-legacy (= 3.4.0-2), passwd (= 1:4.16.0-7), patch (= 2.7.6-7), perl (= 5.40.1-1), perl-base (= 5.40.1-1), perl-modules-5.40 (= 5.40.1-1), po-debconf (= 1.0.21+nmu1), python-babel-localedata (= 2.16.0-1), python3 (= 3.13.1-2), python3-alabaster (= 0.7.16-0.1), python3-autocommand (= 2.2.2-3), python3-babel (= 2.16.0-1), python3-certifi (= 2024.12.14+ds-1), python3-chardet (= 5.2.0+dfsg-2), python3-charset-normalizer (= 3.4.0-1+b1), python3-defusedxml (= 0.7.1-3), python3-docutils (= 0.21.2+dfsg-2), python3-idna (= 3.8-2), python3-imagesize (= 1.4.1-1), python3-inflect (= 7.3.1-2), python3-jaraco.context (= 6.0.0-1), python3-jaraco.functools (= 4.1.0-1), python3-jinja2 (= 3.1.3-2), python3-markupsafe (= 2.1.5-1+b2), python3-minimal (= 3.13.1-2), python3-more-itertools (= 10.6.0-1), python3-packaging (= 24.2-1), python3-pkg-resources (= 75.6.0-1), python3-pygments (= 2.18.0+dfsg-2), python3-requests (= 2.32.3+dfsg-1), python3-roman (= 4.2-1), python3-snowballstemmer (= 2.2.0-4), python3-sphinx (= 8.1.3-4), python3-typeguard (= 4.4.1-1), python3-typing-extensions (= 4.12.2-2), python3-urllib3 (= 2.3.0-1), python3.13 (= 3.13.1-3), python3.13-minimal (= 3.13.1-3), readline-common (= 8.2-6), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sgml-base (= 1.31), sphinx-common (= 8.1.3-4), sysvinit-utils (= 3.13-1), tar (= 1.35+dfsg-3.1), tzdata (= 2025a-1), util-linux (= 2.40.4-1), xml-core (= 0.19), xz-utils (= 5.6.3-1+b1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1731149891" +------------------------------------------------------------------------------+ | Package contents Wed, 22 Jan 2025 00:19:30 +0000 | +------------------------------------------------------------------------------+ murasaki-common_1.68.6-14_all.deb --------------------------------- new Debian package, version 2.0. size 117248 bytes: control archive=3224 bytes. 1282 bytes, 28 lines control 6185 bytes, 85 lines md5sums Package: murasaki-common Source: murasaki Version: 1.68.6-14 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 407 Depends: gnuplot | gnuplot5, libbio-perl-perl, r-cran-rocr, imagemagick Recommends: libterm-readkey-perl, libtext-wrapi18n-perl | libtext-wrapper-perl Section: science Priority: optional Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Description: homology detection tool across multiple large genomes (common files) Murasaki is a scalable and fast, language theory-based homology detection tool across multiple large genomes. It enable whole-genome scale multiple genome global alignments. Supports unlimited length gapped-seed patterns and unique TF-IDF based filtering. . Murasaki is an anchor alignment software, which is * exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 52 wall minutes)) * scalable (Arbitrarily parallelizable across multiple nodes using MPI. Even a single node with 16GB of ram can handle over 1Gbp of sequence.) * unlimited pattern length * repeat tolerant * intelligent noise reduction . This package contains all files that are common to the single core murasaki package and the multi core murasaki-mpi package. drwxr-xr-x root/root 0 2024-11-09 10:58 ./ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/lib/ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/lib/debian-med/ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/lib/debian-med/bin/ -rwxr-xr-x root/root 3948 2010-08-24 14:18 ./usr/lib/debian-med/bin/align2kog.pl -rwxr-xr-x root/root 5024 2010-08-24 14:18 ./usr/lib/debian-med/bin/analyze-pat.pl -rwxr-xr-x root/root 3917 2010-08-24 14:18 ./usr/lib/debian-med/bin/anchors2maf.pl -rwxr-xr-x root/root 5334 2010-08-24 14:18 ./usr/lib/debian-med/bin/anchors2osfinder.pl -rwxr-xr-x root/root 1973 2010-08-24 14:18 ./usr/lib/debian-med/bin/antisense.pl -rwxr-xr-x root/root 4401 2010-08-24 14:18 ./usr/lib/debian-med/bin/chromostitch.pl -rwxr-xr-x root/root 2745 2010-08-24 14:18 ./usr/lib/debian-med/bin/dna2binary.pl -rwxr-xr-x root/root 1939 2010-08-24 14:18 ./usr/lib/debian-med/bin/dnashuffle.pl -rwxr-xr-x root/root 2331 2010-08-24 14:18 ./usr/lib/debian-med/bin/faformat.pl -rwxr-xr-x root/root 55969 2024-11-09 10:58 ./usr/lib/debian-med/bin/filter.pl -rwxr-xr-x root/root 7335 2010-08-24 14:18 ./usr/lib/debian-med/bin/gatherstats.pl -rwxr-xr-x root/root 8380 2010-08-24 14:18 ./usr/lib/debian-med/bin/geneparse.pl -rwxr-xr-x root/root 21536 2010-08-24 14:18 ./usr/lib/debian-med/bin/getcds.pl -rwxr-xr-x root/root 3644 2010-08-24 14:18 ./usr/lib/debian-med/bin/getgene.pl -rwxr-xr-x root/root 5458 2010-08-24 14:18 ./usr/lib/debian-med/bin/histocomp.pl -rwxr-xr-x root/root 4341 2010-08-24 14:18 ./usr/lib/debian-med/bin/histoplot.pl -rwxr-xr-x root/root 7097 2010-08-24 14:18 ./usr/lib/debian-med/bin/homology-score.pl -rwxr-xr-x root/root 898 2010-08-24 14:18 ./usr/lib/debian-med/bin/humantime.pl -rwxr-xr-x root/root 4675 2010-08-24 14:18 ./usr/lib/debian-med/bin/interpolate.pl -rwxr-xr-x root/root 6016 2010-08-24 14:18 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14:18 ./usr/lib/debian-med/bin/randpat.pl -rwxr-xr-x root/root 3051 2010-08-24 14:18 ./usr/lib/debian-med/bin/rearrange.pl -rwxr-xr-x root/root 2794 2010-08-24 14:18 ./usr/lib/debian-med/bin/repeats2anchors.pl -rwxr-xr-x root/root 10809 2010-08-24 14:18 ./usr/lib/debian-med/bin/repeatviz.pl -rwxr-xr-x root/root 9502 2010-08-24 14:18 ./usr/lib/debian-med/bin/roc-at-cutoff.pl -rwxr-xr-x root/root 6378 2024-11-09 10:58 ./usr/lib/debian-med/bin/simpal.pl -rwxr-xr-x root/root 13783 2010-08-24 14:18 ./usr/lib/debian-med/bin/simplegraph.pl -rwxr-xr-x root/root 6884 2010-08-24 14:18 ./usr/lib/debian-med/bin/stat-histo.pl -rwxr-xr-x root/root 6875 2010-08-24 14:18 ./usr/lib/debian-med/bin/stat-vs-stat.pl -rwxr-xr-x root/root 14985 2024-11-09 10:58 ./usr/lib/debian-med/bin/substitch.pl drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/share/ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/share/doc/murasaki-common/ -rw-r--r-- root/root 238 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-rw-r--r-- root/root 1459 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki/Ticker.pm -rwxr-xr-x root/root 137 2024-11-09 10:58 ./usr/share/perl5/murasaki/config.pl murasaki-dbgsym_1.68.6-14_amd64.deb ----------------------------------- new Debian package, version 2.0. size 14983260 bytes: control archive=1188 bytes. 872 bytes, 12 lines control 1463 bytes, 14 lines md5sums Package: murasaki-dbgsym Source: murasaki Version: 1.68.6-14 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 16620 Depends: murasaki (= 1.68.6-14) Section: debug Priority: optional Description: debug symbols for murasaki Build-Ids: 0c75befef675ac3ed101c705fd1b36fa9b48d9e4 3c1c50568451fbaa77d4075f89bf970e08af5988 540eb4c4e2fc599efdc63567873b7af2a51a57d0 5dedb91ca81b6a2bfcb11fe963167df18d7947bc 5f72db57f9399cd62606dd71515412700d0d2bf5 871f0d1bef3f31fa4d340ccf11903170fe31d661 aaed9b1a4b66516b57d58979743746c7afaf875e c22796451a6c3566f4f74eb85d6648f4c0856769 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size 692752 bytes: control archive=1600 bytes. 1354 bytes, 28 lines control 1326 bytes, 20 lines md5sums Package: murasaki-mpi Source: murasaki Version: 1.68.6-14 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 4526 Depends: murasaki-common, libboost-filesystem1.83.0 (>= 1.83.0), libboost-iostreams1.83.0 (>= 1.83.0), libc6 (>= 2.38), libgcc-s1 (>= 3.0), libopenmpi40 (>= 5.0.6), libstdc++6 (>= 14) Section: science Priority: optional Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Description: homology detection tool across multiple large genomes (MPI-version) Murasaki is a scalable and fast, language theory-based homology detection tool across multiple large genomes. It enable whole-genome scale multiple genome global alignments. Supports unlimited length gapped-seed patterns and unique TF-IDF based filtering. . Murasaki is an anchor alignment software, which is * exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 52 wall minutes)) * scalable (Arbitrarily parallelizable across multiple nodes using MPI. Even a single node with 16GB of ram can handle over 1Gbp of sequence.) * unlimited pattern length * repeat tolerant * intelligent noise reduction . This package provides the MPI-enabled binary for murasaki. While this will speed up operation on multi-processor machines it will slow down on a single processor. drwxr-xr-x root/root 0 2024-11-09 10:58 ./ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/bin/ -rwxr-xr-x root/root 360952 2024-11-09 10:58 ./usr/bin/geneparse-mpi -rwxr-xr-x root/root 414072 2024-11-09 10:58 ./usr/bin/mbfa-mpi -rwxr-xr-x root/root 933000 2024-11-09 10:58 ./usr/bin/murasaki-mpi drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/lib/ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/lib/murasaki/ -rwxr-xr-x root/root 311592 2024-11-09 10:58 ./usr/lib/murasaki/align-and-mpi -rwxr-xr-x root/root 319816 2024-11-09 10:58 ./usr/lib/murasaki/align-best-mpi -rwxr-xr-x root/root 365408 2024-11-09 10:58 ./usr/lib/murasaki/align-compare-mpi -rwxr-xr-x root/root 471912 2024-11-09 10:58 ./usr/lib/murasaki/align-coverage-mpi -rwxr-xr-x root/root 311560 2024-11-09 10:58 ./usr/lib/murasaki/align-or-mpi -rwxr-xr-x root/root 92728 2024-11-09 10:58 ./usr/lib/murasaki/cgr-compare-mpi -rwxr-xr-x root/root 418264 2024-11-09 10:58 ./usr/lib/murasaki/cgr-image-mpi -rwxr-xr-x root/root 7138 2010-08-24 14:18 ./usr/lib/murasaki/cgr-image.pl-mpi -rwxr-xr-x root/root 105056 2024-11-09 10:58 ./usr/lib/murasaki/cgr-random-mpi -rwxr-xr-x root/root 414120 2024-11-09 10:58 ./usr/lib/murasaki/cgr-sample-mpi -rwxr-xr-x root/root 68000 2024-11-09 10:58 ./usr/lib/murasaki/testeco-mpi drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/share/ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/share/doc/murasaki-mpi/ -rw-r--r-- root/root 249 2024-11-09 10:58 ./usr/share/doc/murasaki-mpi/README.test -rw-r--r-- root/root 990 2024-11-09 10:58 ./usr/share/doc/murasaki-mpi/changelog.Debian.gz -rw-r--r-- root/root 2225 2024-11-09 10:58 ./usr/share/doc/murasaki-mpi/copyright drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/share/man/ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/share/man/man1/ -rw-r--r-- root/root 2518 2024-11-09 10:58 ./usr/share/man/man1/geneparse-mpi.1.gz -rw-r--r-- root/root 2721 2024-11-09 10:58 ./usr/share/man/man1/mbfa-mpi.1.gz -rw-r--r-- root/root 10888 2024-11-09 10:58 ./usr/share/man/man1/murasaki-mpi.1.gz murasaki_1.68.6-14_amd64.deb ---------------------------- new Debian package, version 2.0. size 644676 bytes: control archive=1440 bytes. 1124 bytes, 23 lines control 1182 bytes, 19 lines md5sums Package: murasaki Version: 1.68.6-14 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 4399 Depends: murasaki-common, libboost-filesystem1.83.0 (>= 1.83.0), libboost-iostreams1.83.0 (>= 1.83.0), libc6 (>= 2.38), libgcc-s1 (>= 3.0), libstdc++6 (>= 14) Section: science Priority: optional Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Description: homology detection tool across multiple large genomes Murasaki is a scalable and fast, language theory-based homology detection tool across multiple large genomes. It enable whole-genome scale multiple genome global alignments. Supports unlimited length gapped-seed patterns and unique TF-IDF based filtering. . Murasaki is an anchor alignment software, which is * exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 52 wall minutes)) * scalable (Arbitrarily parallelizable across multiple nodes using MPI. Even a single node with 16GB of ram can handle over 1Gbp of sequence.) * unlimited pattern length * repeat tolerant * intelligent noise reduction drwxr-xr-x root/root 0 2024-11-09 10:58 ./ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/bin/ -rwxr-xr-x root/root 360952 2024-11-09 10:58 ./usr/bin/geneparse -rwxr-xr-x root/root 414072 2024-11-09 10:58 ./usr/bin/mbfa -rwxr-xr-x root/root 810088 2024-11-09 10:58 ./usr/bin/murasaki drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/lib/ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/lib/murasaki/ -rwxr-xr-x root/root 311584 2024-11-09 10:58 ./usr/lib/murasaki/align-and -rwxr-xr-x root/root 319808 2024-11-09 10:58 ./usr/lib/murasaki/align-best -rwxr-xr-x root/root 365400 2024-11-09 10:58 ./usr/lib/murasaki/align-compare -rwxr-xr-x root/root 471912 2024-11-09 10:58 ./usr/lib/murasaki/align-coverage -rwxr-xr-x root/root 311552 2024-11-09 10:58 ./usr/lib/murasaki/align-or -rwxr-xr-x root/root 92720 2024-11-09 10:58 ./usr/lib/murasaki/cgr-compare -rwxr-xr-x root/root 418264 2024-11-09 10:58 ./usr/lib/murasaki/cgr-image -rwxr-xr-x root/root 105048 2024-11-09 10:58 ./usr/lib/murasaki/cgr-random -rwxr-xr-x root/root 414120 2024-11-09 10:58 ./usr/lib/murasaki/cgr-sample -rwxr-xr-x root/root 67992 2024-11-09 10:58 ./usr/lib/murasaki/testeco drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/share/ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/share/doc/murasaki/ -rw-r--r-- root/root 249 2024-11-09 10:58 ./usr/share/doc/murasaki/README.test -rw-r--r-- root/root 988 2024-11-09 10:58 ./usr/share/doc/murasaki/changelog.Debian.gz -rw-r--r-- root/root 2225 2024-11-09 10:58 ./usr/share/doc/murasaki/copyright drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/share/man/ drwxr-xr-x root/root 0 2024-11-09 10:58 ./usr/share/man/man1/ -rw-r--r-- root/root 2518 2024-11-09 10:58 ./usr/share/man/man1/geneparse.1.gz -rw-r--r-- root/root 2721 2024-11-09 10:58 ./usr/share/man/man1/mbfa.1.gz -rw-r--r-- root/root 10888 2024-11-09 10:58 ./usr/share/man/man1/murasaki.1.gz +------------------------------------------------------------------------------+ | Post Build Wed, 22 Jan 2025 00:19:31 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Wed, 22 Jan 2025 00:19:31 +0000 | +------------------------------------------------------------------------------+ Purging /build/murasaki-xreV69 Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Wed, 22 Jan 2025 00:19:32 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 291260 Build-Time: 219 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 27 Job: /srv/debomatic/incoming/murasaki_1.68.6-14.dsc Machine Architecture: amd64 Package: murasaki Package-Time: 256 Source-Version: 1.68.6-14 Space: 291260 Status: successful Version: 1.68.6-14 -------------------------------------------------------------------------------- Finished at 2025-01-22T00:19:29Z Build needed 00:04:16, 291260k disk space