sbuild (Debian sbuild) 0.90.2 (26 August 2025) on carme.larted.org.uk +==============================================================================+ | murasaki 1.68.6-15 (amd64) Sun, 28 Sep 2025 16:01:47 +0000 | +==============================================================================+ Package: murasaki Version: 1.68.6-15 Source Version: 1.68.6-15 Distribution: perl-5.42-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 Sun, 28 Sep 2025 16:01:47 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup murasaki_1.68.6-15 perl-5.42-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup murasaki_1.68.6-15 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sun, 28 Sep 2025 16:01:48 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B] Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://deb.debian.org/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Sun, 28 Sep 2025 16:01:49 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/murasaki_1.68.6-15.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 28 Sep 2025 16:01:50 +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-YRO0Zl/resolver-DOZRYh/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/murasaki-YRO0Zl/resolver-DOZRYh/apt_archive ./ InRelease Get:2 copy:/build/murasaki-YRO0Zl/resolver-DOZRYh/apt_archive ./ Release [609 B] Ign:3 copy:/build/murasaki-YRO0Zl/resolver-DOZRYh/apt_archive ./ Release.gpg Get:4 copy:/build/murasaki-YRO0Zl/resolver-DOZRYh/apt_archive ./ Sources [764 B] Get:5 copy:/build/murasaki-YRO0Zl/resolver-DOZRYh/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 debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran-15 gfortran-15-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 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libfuse3-4 libgfortran-15-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libicu-dev libicu76 libjs-jquery libjs-jquery-ui 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 libpmix2t64 libpsm2-2 libpstreams-dev librdmacm1t64 libterm-readkey-perl libtext-wrapper-perl libtool libuchardet0 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2-16 libxnvctrl0 libz3-4 libze1 m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf sensible-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n gfortran-15-multilib gfortran-15-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 fuse3 krb5-doc krb5-user libhwloc-contrib-plugins icu-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common krb5-locales libcoarrays-openmpi-dev xauth libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran-15 gfortran-15-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 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libfuse3-4 libgfortran-15-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libicu-dev libicu76 libjs-jquery libjs-jquery-ui 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 libpmix2t64 libpsm2-2 libpstreams-dev librdmacm1t64 libterm-readkey-perl libtext-wrapper-perl libtool libuchardet0 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2-16 libxnvctrl0 libz3-4 libze1 m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 121 newly installed, 0 to remove and 0 not upgraded. Need to get 199 MB/199 MB of archives. After this operation, 982 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.42/main amd64 libterm-readkey-perl amd64 2.38-2+b5 [24.6 kB] Get:2 copy:/build/murasaki-YRO0Zl/resolver-DOZRYh/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [928 B] Get:3 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.2-2 [98.1 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.16.0-2 [78.8 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:20 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:10.0p1-8 [986 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:34 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.28 [941 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libgfortran-15-dev amd64 15.2.0-4 [886 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-4 [78.8 MB] Get:44 http://deb.debian.org/debian unstable/main amd64 gfortran-15 amd64 15.2.0-4 [17.9 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.11.0-2 [67.1 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.11.0-2 [211 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 56.1-1+b1 [63.0 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 56.1-1+b1 [361 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libicu76 amd64 76.1-4 [9722 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 76.1-4 [215 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-22+b3 [23.6 MB] Get:53 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get:54 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.125-2 [8576 B] Get:55 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.125-2 [39.1 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.125-2 [23.2 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1 [22.2 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 6.2.4+ds-1 [61.1 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.1.2-3 [535 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-6 [8924 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-5 [10.6 MB] Get:62 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-5 [235 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-5 [236 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-5 [286 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-5 [231 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-5 [232 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-5 [302 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Get:69 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-5 [336 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 76.1-4 [10.8 MB] Get:71 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-5 [352 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-5 [256 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-5 [265 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get:75 http://deb.debian.org/debian unstable/main amd64 libboost-regex-dev amd64 1.83.0.2+b2 [3864 B] Get:76 http://deb.debian.org/debian unstable/main amd64 libcrypto++8t64 amd64 8.9.0-2 [1168 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libcrypto++-dev amd64 8.9.0-2 [1835 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 56.1-1+b1 [71.0 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 2.1.0-1.1 [706 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libfuse3-4 amd64 3.17.4-1 [99.2 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.12.2-1 [164 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.19-1 [36.5 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-5 [416 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.5.4-5 [168 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.12.2-1 [257 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b2 [14.2 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libze1 amd64 1.24.1-2 [514 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.3-1 [42.9 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.12.2-1 [23.5 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 56.1-1+b1 [30.1 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 56.1-1+b1 [44.9 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.11.0-2 [110 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.11.0-2 [235 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 56.1-1+b1 [659 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.16-1 [19.7 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 6.0.0+really5.0.8-1 [668 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.19.0+ds-1 [1336 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.8-10+b1 [2414 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.8-10 [97.5 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.8-10+b1 [190 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.8-10+b1 [1090 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libpstreams-dev all 1.0.3-1 [134 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libtext-wrapper-perl all 1.05-4 [10.3 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.19 [3432 B] Preconfiguring packages ... 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Setting up bsdextrautils (2.41.2-2) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libcbor0.10:amd64 (0.10.2-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libboost-regex1.83.0:amd64 (1.83.0-5) ... Setting up libdebhelper-perl (13.28) ... Setting up libedit2:amd64 (3.1-20250104-1) ... Setting up libboost-system1.83.0:amd64 (1.83.0-5) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libibumad3:amd64 (56.1-1+b1) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libibmad5:amd64 (56.1-1+b1) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libtext-wrapper-perl (1.05-4) ... Setting up libboost-filesystem1.83.0:amd64 (1.83.0-5) ... Setting up libze1:amd64 (1.24.1-2) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libboost-atomic1.83.0:amd64 (1.83.0-5) ... Setting up autotools-dev (20240727.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libmunge2:amd64 (0.5.16-1) ... Setting up libllvm17t64:amd64 (1:17.0.6-22+b3) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libboost-iostreams1.83.0:amd64 (1.83.0-5) ... Setting up libhwloc15:amd64 (2.12.2-1) ... Setting up libcrypto++8t64:amd64 (8.9.0-2) ... Setting up autopoint (0.23.1-2) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libltdl7:amd64 (2.5.4-5) ... Setting up libgfortran5:amd64 (15.2.0-4) ... Setting up libboost-atomic1.83-dev:amd64 (1.83.0-5) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libnuma1:amd64 (2.0.19-1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up ocl-icd-libopencl1:amd64 (2.3.3-1) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up libnl-3-200:amd64 (3.11.0-2) ... Setting up libpsm2-2 (11.2.185-2.1) ... Setting up openmpi-common (5.0.8-10) ... Setting up libx11-6:amd64 (2:1.8.12-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up libicu76:amd64 (76.1-4) ... Setting up libboost-system1.83-dev:amd64 (1.83.0-5) ... Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1) ... Setting up libfuse3-4:amd64 (3.17.4-1) ... Setting up libterm-readkey-perl (2.38-2+b5) ... Setting up libfido2-1:amd64 (1.16.0-2) ... Setting up libdrm-common (2.4.125-2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... 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 (8.9.0-2) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libboost-filesystem1.83-dev:amd64 (1.83.0-5) ... Setting up libgfortran-15-dev:amd64 (15.2.0-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.19-1) ... Setting up libnl-route-3-200:amd64 (3.11.0-2) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b2) ... Setting up dh-autoreconf (21) ... Setting up libltdl-dev:amd64 (2.5.4-5) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libpstreams-dev (1.0.3-1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up icu-devtools (76.1-4) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up libdrm2:amd64 (2.4.125-2) ... Setting up libnl-3-dev:amd64 (3.11.0-2) ... Setting up groff-base (1.23.0-9) ... Setting up libhwloc-dev:amd64 (2.12.2-1) ... Setting up libicu-dev:amd64 (76.1-4) ... Setting up libboost-filesystem-dev:amd64 (1.83.0.2+b2) ... Setting up libdrm-amdgpu1:amd64 (2.4.125-2) ... Setting up gfortran-15-x86-64-linux-gnu (15.2.0-4) ... Setting up libibverbs1:amd64 (56.1-1+b1) ... Setting up ibverbs-providers:amd64 (56.1-1+b1) ... Setting up openssh-client (1:10.0p1-8) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhwloc-plugins:amd64 (2.12.2-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnl-route-3-dev:amd64 (3.11.0-2) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up libboost-regex1.83-dev:amd64 (1.83.0-5) ... Setting up libpmix2t64:amd64 (6.0.0+really5.0.8-1) ... Setting up librdmacm1t64:amd64 (56.1-1+b1) ... Setting up libboost-regex-dev:amd64 (1.83.0.2+b2) ... Setting up libhsakmt1:amd64 (6.2.4+ds-1) ... Setting up gfortran-15 (15.2.0-4) ... Setting up libfabric1:amd64 (2.1.0-1.1) ... Setting up libboost-iostreams1.83-dev:amd64 (1.83.0-5) ... Setting up debhelper (13.28) ... Setting up libboost-iostreams-dev:amd64 (1.83.0.2+b2) ... Setting up libibverbs-dev:amd64 (56.1-1+b1) ... Setting up libhsa-runtime64-1:amd64 (6.1.2-3) ... Setting up libamdhip64-5:amd64 (5.7.1-6) ... Setting up libucx0:amd64 (1.19.0+ds-1) ... Setting up libopenmpi40:amd64 (5.0.8-10+b1) ... Setting up openmpi-bin (5.0.8-10+b1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: 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 Setting up libopenmpi-dev:amd64 (5.0.8-10+b1) ... 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 (1.19) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Check architectures Sun, 28 Sep 2025 16:02:07 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Sun, 28 Sep 2025 16:02:07 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.16.5+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.16.5-1 (2025-09-05) amd64 (x86_64) Toolchain package versions: binutils_2.45-7 dpkg-dev_1.22.21 g++-14_14.3.0-8 g++-15_15.2.0-4 gcc-14_14.3.0-8 gcc-15_15.2.0-4 libc6-dev_2.41-12 libstdc++-14-dev_14.3.0-8 libstdc++-15-dev_15.2.0-4 libstdc++6_15.2.0-4 linux-libc-dev_6.16.9-1 Package versions: adduser_3.153 apt_3.1.6 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.7 bash_5.3-1 binutils_2.45-7 binutils-common_2.45-7 binutils-gold_2.44-3 binutils-gold-x86-64-linux-gnu_2.44-3 binutils-x86-64-linux-gnu_2.45-7 bsdextrautils_2.41.2-2 bsdutils_1:2.41.2-2 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.7-3 cpp_4:15.2.0-4 cpp-14_14.3.0-8 cpp-14-x86-64-linux-gnu_14.3.0-8 cpp-15_15.2.0-4 cpp-15-x86-64-linux-gnu_15.2.0-4 cpp-x86-64-linux-gnu_4:15.2.0-4 dash_0.5.12-12 debconf_1.5.91 debhelper_13.28 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_21 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.10-4 dirmngr_2.4.8-3 dpkg_1.22.21 dpkg-dev_1.22.21 dwz_0.16-2 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:15.2.0-4 g++-14_14.3.0-8 g++-14-x86-64-linux-gnu_14.3.0-8 g++-15_15.2.0-4 g++-15-x86-64-linux-gnu_15.2.0-4 g++-x86-64-linux-gnu_4:15.2.0-4 gcc_4:15.2.0-4 gcc-14_14.3.0-8 gcc-14-base_14.3.0-8 gcc-14-x86-64-linux-gnu_14.3.0-8 gcc-15_15.2.0-4 gcc-15-base_15.2.0-4 gcc-15-x86-64-linux-gnu_15.2.0-4 gcc-x86-64-linux-gnu_4:15.2.0-4 gettext_0.23.1-2+b1 gettext-base_0.23.1-2+b1 gfortran-15_15.2.0-4 gfortran-15-x86-64-linux-gnu_15.2.0-4 gnupg_2.4.8-3 gnupg-l10n_2.4.8-3 gpg_2.4.8-3 gpg-agent_2.4.8-3 gpgconf_2.4.8-3 gpgsm_2.4.8-3 grep_3.12-1 groff-base_1.23.0-9 gzip_1.13-1 hostname_3.25 ibverbs-providers_56.1-1+b1 icu-devtools_76.1-4 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b2 libamdhip64-5_5.7.1-6 libapt-pkg7.0_3.1.6 libarchive-zip-perl_1.68-1 libasan8_15.2.0-4 libassuan9_3.0.2-2 libatomic1_15.2.0-4 libattr1_1:2.5.2-3 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1 libbinutils_2.45-7 libblkid1_2.41.2-2 libboost-atomic1.83-dev_1.83.0-5 libboost-atomic1.83.0_1.83.0-5 libboost-filesystem-dev_1.83.0.2+b2 libboost-filesystem1.83-dev_1.83.0-5 libboost-filesystem1.83.0_1.83.0-5 libboost-iostreams-dev_1.83.0.2+b2 libboost-iostreams1.83-dev_1.83.0-5 libboost-iostreams1.83.0_1.83.0-5 libboost-regex-dev_1.83.0.2+b2 libboost-regex1.83-dev_1.83.0-5 libboost-regex1.83.0_1.83.0-5 libboost-system1.83-dev_1.83.0-5 libboost-system1.83.0_1.83.0-5 libboost1.83-dev_1.83.0-5 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.41-12 libc-dev-bin_2.41-12 libc-l10n_2.41-12 libc6_2.41-12 libc6-dev_2.41-12 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-10+b1 libcbor0.10_0.10.2-2 libcc1-0_15.2.0-4 libcom-err2_1.47.2-3+b3 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libcrypto++-dev_8.9.0-2 libcrypto++8t64_8.9.0-2 libctf-nobfd0_2.45-7 libctf0_2.45-7 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.280 libdebhelper-perl_13.28 libdpkg-perl_1.22.21 libdrm-amdgpu1_2.4.125-2 libdrm-common_2.4.125-2 libdrm2_2.4.125-2 libeatmydata1_131-2+b1 libedit2_3.1-20250104-1 libelf1t64_0.193-3 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 libfabric1_2.1.0-1.1 libffi8_3.5.2-2 libfido2-1_1.16.0-2 libfile-stripnondeterminism-perl_1.15.0-1 libfuse3-4_3.17.4-1 libgcc-14-dev_14.3.0-8 libgcc-15-dev_15.2.0-4 libgcc-s1_15.2.0-4 libgcrypt20_1.11.2-2 libgdbm-compat4t64_1.26-1 libgdbm6t64_1.26-1 libgfortran-15-dev_15.2.0-4 libgfortran5_15.2.0-4 libgmp10_2:6.3.0+dfsg-5 libgnutls30t64_3.8.10-2 libgomp1_15.2.0-4 libgpg-error0_1.55-2 libgprofng0_2.45-7 libgssapi-krb5-2_1.21.3-5 libhogweed6t64_3.10.2-1 libhsa-runtime64-1_6.1.2-3 libhsakmt1_6.2.4+ds-1 libhwasan0_15.2.0-4 libhwloc-dev_2.12.2-1 libhwloc-plugins_2.12.2-1 libhwloc15_2.12.2-1 libibmad5_56.1-1+b1 libibumad3_56.1-1+b1 libibverbs-dev_56.1-1+b1 libibverbs1_56.1-1+b1 libicu-dev_76.1-4 libicu76_76.1-4 libidn2-0_2.3.8-4 libisl23_0.27-1 libitm1_15.2.0-4 libjansson4_2.14-2+b3 libjs-jquery_3.7.1+dfsg+~3.5.33-1 libjs-jquery-ui_1.13.2+dfsg-1 libk5crypto3_1.21.3-5 libkeyutils1_1.6.3-6 libkrb5-3_1.21.3-5 libkrb5support0_1.21.3-5 libksba8_1.6.7-2+b1 liblastlog2-2_2.41.2-2 libldap2_2.6.10+dfsg-1+b1 libllvm17t64_1:17.0.6-22+b3 liblsan0_15.2.0-4 libltdl-dev_2.5.4-5 libltdl7_2.5.4-5 liblz4-1_1.10.0-4 liblzma5_5.8.1-1.1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41.2-2 libmpc3_1.3.1-2 libmpfr6_4.2.2-2 libmunge2_0.5.16-1 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.2-1 libnl-3-200_3.11.0-2 libnl-3-dev_3.11.0-2 libnl-route-3-200_3.11.0-2 libnl-route-3-dev_3.11.0-2 libnpth0t64_1.8-3 libnuma-dev_2.0.19-1 libnuma1_2.0.19-1 libopenmpi-dev_5.0.8-10+b1 libopenmpi40_5.0.8-10+b1 libp11-kit0_0.25.9-2 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpciaccess0_0.17-3+b3 libpcre2-8-0_10.46-1 libperl5.40_5.40.1-6 libperl5.42_5.42.0-2 libpipeline1_1.5.8-1 libpmix2t64_6.0.0+really5.0.8-1 libpsm2-2_11.2.185-2.1 libpstreams-dev_1.0.3-1 libquadmath0_15.2.0-4 librdmacm1t64_56.1-1+b1 libreadline8t64_8.3-3 libsasl2-2_2.1.28+dfsg1-9 libsasl2-modules-db_2.1.28+dfsg1-9 libseccomp2_2.6.0-2 libselinux1_3.8.1-1 libsemanage-common_3.8.1-1 libsemanage2_3.8.1-1 libsepol2_3.8.1-1 libsframe2_2.45-7 libsmartcols1_2.41.2-2 libsqlite3-0_3.46.1-8 libssl3t64_3.5.3-1 libstdc++-14-dev_14.3.0-8 libstdc++-15-dev_15.2.0-4 libstdc++6_15.2.0-4 libsystemd0_258-1 libtasn1-6_4.20.0-2 libterm-readkey-perl_2.38-2+b5 libtext-wrapper-perl_1.05-4 libtinfo6_6.5+20250216-2 libtool_2.5.4-5 libtsan2_15.2.0-4 libubsan1_15.2.0-4 libuchardet0_0.0.8-2 libucx0_1.19.0+ds-1 libudev1_258-1 libunistring5_1.3-2 libuuid1_2.41.2-2 libx11-6_2:1.8.12-1 libx11-data_2:1.8.12-1 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 libxml2-16_2.14.5+dfsg-0.2 libxnvctrl0_535.171.04-1+b2 libxxhash0_0.8.3-2 libz3-4_4.13.3-1 libze1_1.24.1-2 libzstd1_1.5.7+dfsg-1.1 linux-libc-dev_6.16.9-1 locales-all_2.41-12 login.defs_1:4.18.0-1 m4_1.4.20-1 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 mpi-default-dev_1.19 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 ocl-icd-libopencl1_2.3.3-1 openmpi-bin_5.0.8-10+b1 openmpi-common_5.0.8-10 openssh-client_1:10.0p1-8 openssl-provider-legacy_3.5.3-1 passwd_1:4.18.0-1 patch_2.8-2 perl_5.42.0-2 perl-base_5.42.0-2 perl-modules-5.40_5.40.1-6 perl-modules-5.42_5.42.0-2 pinentry-curses_1.3.2-3 po-debconf_1.0.21+nmu1 readline-common_8.3-3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.26 sqv_1.3.0-3 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 util-linux_2.41.2-2 xz-utils_5.8.1-1.1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Sun, 28 Sep 2025 16:02:07 +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: 1.68.6-15 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Standards-Version: 4.7.2 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 7cdd0e37a07e49ba7f4aa3eee5d25c341d4e4bb4 11588 murasaki_1.68.6-15.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 cb26683ab97418c34c29f0b99ebca4d60cb10091d488afad2734a89177736be3 11588 murasaki_1.68.6-15.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 f5847bec8ff043c175ca67745865576b 11588 murasaki_1.68.6-15.debian.tar.xz -----BEGIN PGP SIGNATURE----- iIgEARYKADAWIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCaNkAPxIcbmlsZXNoQGRl Ymlhbi5vcmcACgkQKieQS9ckPtoWJAD9FrvD/n/xBKZ3Oj/7UBwZBbZtptZ+HvG9 aljj8XNQJFoBAM+c3F1uO145HulvJf80dzJ7w0TJ7EO6uPBQ0nM7vrcD =G7k5 -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./murasaki_1.68.6-15.dsc: no acceptable signature found dpkg-source: info: extracting murasaki in /build/murasaki-YRO0Zl/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_1.68.6-15.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 dpkg-source: info: applying boost-1.88.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Sun, 28 Sep 2025 16:02:07 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network murasaki_1.68.6-15 perl-5.42-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network murasaki_1.68.6-15 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent 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-YRO0Zl/murasaki-1.68.6 SCHROOT_ALIAS_NAME=perl-5.42-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.42-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.42-amd64-debomatic-dc4282c6-f3e5-47e4-be0e-cce71a710eb9 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 1.68.6-15 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra 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-YRO0Zl/murasaki-1.68.6' rm -rf *.o *~ .*~ core make -C src clean make[2]: Entering directory '/build/murasaki-YRO0Zl/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-YRO0Zl/murasaki-1.68.6/src' make[1]: Leaving directory '/build/murasaki-YRO0Zl/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_1.68.6-15.debian.tar.xz dpkg-source: info: building murasaki in murasaki_1.68.6-15.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-YRO0Zl/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-YRO0Zl/murasaki-1.68.6' make -C src all make[3]: Entering directory '/build/murasaki-YRO0Zl/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from murasaki.cc:29: /usr/include/c++/15/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++/15/algorithm:63, 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++/15/bits/stl_algo.h:4537:5: note: declared here 4537 | 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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from dinkymath.h:24, from dinkymath.cc:26: /usr/include/c++/15/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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/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++/15/bits/stl_algobase.h:64, from /usr/include/c++/15/bits/stl_tree.h:65: /usr/include/c++/15/bits/stl_pair.h:302:12: note: ‘ShmVector >::val_type’ {aka ‘struct std::pair’} declared here 302 | 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++/15/bits/stl_pair.h:302:12: note: ‘ShmVector >::val_type’ {aka ‘struct std::pair’} declared here 302 | 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++/15/algorithm:63, 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++/15/bits/stl_algo.h:4537:5: note: declared here 4537 | 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++/15/bits/stl_pair.h:302:12: note: ‘struct std::pair’ declared here 302 | 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 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 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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/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 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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecolist.cc 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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/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++/15/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 mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c arrayhash.cc In file included from 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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from murasaki_mpi.cc:30: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ murasaki_mpi.cc:89:29: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 89 | struct lt_mpi_worldMemory : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/15/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++/15/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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/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; | ^~~ 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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/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++/15/bits/stl_algobase.h:64, from /usr/include/c++/15/string:53, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/15/bits/stl_pair.h:302:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 302 | 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++/15/bits/stl_pair.h:302:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 302 | 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++/15/bits/stl_pair.h:302:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 302 | 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; | ^~~~~~~~~ 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 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-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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/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; | ^~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c mbfa.cc getsegments.cc: In function ‘size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::string)’: getsegments.cc:153:29: warning: catching polymorphic type ‘class boost::bad_lexical_cast’ by value [-Wcatch-value=] 153 | }catch(bad_lexical_cast e){ | ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../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-YRO0Zl/murasaki-1.68.6/src' make[2]: Leaving directory '/build/murasaki-YRO0Zl/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-YRO0Zl/murasaki-1.68.6' rm -rf *.o *~ .*~ core make -C src clean make[3]: Entering directory '/build/murasaki-YRO0Zl/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-YRO0Zl/murasaki-1.68.6/src' make[2]: Leaving directory '/build/murasaki-YRO0Zl/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-YRO0Zl/murasaki-1.68.6' make -C src all make[3]: Entering directory '/build/murasaki-YRO0Zl/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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from murasaki.cc:29: /usr/include/c++/15/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++/15/algorithm:63, 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++/15/bits/stl_algo.h:4537:5: note: declared here 4537 | 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++/15/string:51, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from dinkymath.h:24, from dinkymath.cc:26: /usr/include/c++/15/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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/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++/15/bits/stl_algobase.h:64, from /usr/include/c++/15/bits/stl_tree.h:65: /usr/include/c++/15/bits/stl_pair.h:302:12: note: ‘ShmVector >::val_type’ {aka ‘struct std::pair’} declared here 302 | 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++/15/bits/stl_pair.h:302:12: note: ‘ShmVector >::val_type’ {aka ‘struct std::pair’} declared here 302 | 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++/15/algorithm:63, 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++/15/bits/stl_algo.h:4537:5: note: declared here 4537 | 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++/15/bits/stl_pair.h:302:12: note: ‘struct std::pair’ declared here 302 | 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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/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 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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from options.h:28, from options.cc:26: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/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 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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/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++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c murasaki_mpi.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c arrayhash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c seqread.cc In file included from 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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/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 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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/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++/15/bits/stl_algobase.h:64, from /usr/include/c++/15/string:53, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/istream:42, from /usr/include/c++/15/fstream:42, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/15/bits/stl_pair.h:302:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 302 | 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++/15/bits/stl_pair.h:302:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 302 | 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++/15/bits/stl_pair.h:302:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 302 | 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 cgr-sample.cc: In function ‘int main(int, char**)’: cgr-sample.cc:54:8: warning: variable ‘repeatmask’ set but not used [-Wunused-but-set-variable] 54 | bool repeatmask=false,save=false; | ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c testeco.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-compare.cc In file included from 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++/15/bits/stl_tree.h:67, from /usr/include/c++/15/set:64, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/15/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 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; | ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c mbfa.cc getsegments.cc: In function ‘size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::string)’: getsegments.cc:153:29: warning: catching polymorphic type ‘class boost::bad_lexical_cast’ by value [-Wcatch-value=] 153 | }catch(bad_lexical_cast e){ | ^ 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-YRO0Zl/murasaki-1.68.6/src' make[2]: Leaving directory '/build/murasaki-YRO0Zl/murasaki-1.68.6' make[1]: Leaving directory '/build/murasaki-YRO0Zl/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-YRO0Zl/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-YRO0Zl/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-YRO0Zl/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-YRO0Zl/murasaki-1.68.6' debian/rules override_dh_installman-indep make[1]: Entering directory '/build/murasaki-YRO0Zl/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 32. 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 32. 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-YRO0Zl/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-YRO0Zl/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-YRO0Zl/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_1.68.6-15_amd64.deb'. dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-15_amd64.deb'. dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-15_amd64.deb'. dpkg-deb: building package 'murasaki-common' in '../murasaki-common_1.68.6-15_all.deb'. dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-15_amd64.deb'. dpkg-genbuildinfo -O../murasaki_1.68.6-15_amd64.buildinfo dpkg-genchanges -O../murasaki_1.68.6-15_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 2025-09-28T16:04:52Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 28 Sep 2025 16:04:52 +0000 | +------------------------------------------------------------------------------+ murasaki_1.68.6-15_amd64.changes: --------------------------------- Format: 1.8 Date: Sat, 27 Sep 2025 15:09:06 +0530 Source: murasaki Binary: murasaki murasaki-common murasaki-dbgsym murasaki-mpi murasaki-mpi-dbgsym Architecture: source all amd64 Version: 1.68.6-15 Distribution: perl-5.42-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: murasaki - homology detection tool across multiple large genomes murasaki-common - homology detection tool across multiple large genomes (common fil murasaki-mpi - homology detection tool across multiple large genomes (MPI-versio Closes: 1110615 Changes: murasaki (1.68.6-15) unstable; urgency=medium . * Team Upload. * Add patch to fix FTBFS with boost 1.88 (Closes: #1110615) * Drop myself from uploaders * Bump Standards-Version to 4.7.2 (no changes needed) Checksums-Sha1: 915ba2153564309e93965cc8e359702a7fdf4afc 1848 murasaki_1.68.6-15.dsc 35c63bcd3ffd51fcb5b16004a41b79cf7774cbb9 11580 murasaki_1.68.6-15.debian.tar.xz 7e288ea059f37d325a31181fc5dbd855ced6e685 118544 murasaki-common_1.68.6-15_all.deb 160210a55426b706ecec89125797bd10a72f09c8 15083448 murasaki-dbgsym_1.68.6-15_amd64.deb 603ebe4078aeabcd3a563bf6e0d4bb12daa938e3 15761756 murasaki-mpi-dbgsym_1.68.6-15_amd64.deb 083ce297c0259158649ff6393515f5beb328d8e3 695532 murasaki-mpi_1.68.6-15_amd64.deb b8774c0bb5efe7c805c37412795dbc9d2cf267f9 9264 murasaki_1.68.6-15_amd64.buildinfo 8a5eb3309775b46e3b9708fd235b75837a178658 647320 murasaki_1.68.6-15_amd64.deb Checksums-Sha256: c5d66bb38c52c5e2e6aaff018ae78138ca9babdef734cdccf9ec390a7905bd4f 1848 murasaki_1.68.6-15.dsc 9f4a926c559b63520e4e23d5b0353a8d764d412bc6f39ca57e44779248e8fc27 11580 murasaki_1.68.6-15.debian.tar.xz 0bfb8e8f6c7576be98fb997a124f8b41729c52d545d525abb47e65bdb880a682 118544 murasaki-common_1.68.6-15_all.deb 8a857811857f606328d92474606cde320718190eb76347e0c3a5061f62072293 15083448 murasaki-dbgsym_1.68.6-15_amd64.deb 7871723b01fcb6f338acab357366df7b6ea96407ee7b98cfc6a1a47bedf48a11 15761756 murasaki-mpi-dbgsym_1.68.6-15_amd64.deb 3347073e3de3641f6a42b7a0d74c487b286b9f18ea51b8aeda5fad92ed45b66b 695532 murasaki-mpi_1.68.6-15_amd64.deb 8076861c2fb9d71781792b434c1c26da146d3e1fb6ea68ed40a353fb4efd5eb8 9264 murasaki_1.68.6-15_amd64.buildinfo 799ca781fb9b24b481d04a0852d0fa80ddfb97c2ea909163c701ef95caa69250 647320 murasaki_1.68.6-15_amd64.deb Files: 90aba58141e366de9187584c69885027 1848 science optional murasaki_1.68.6-15.dsc 46483ae4e0c3fa182521d63767f89c2f 11580 science optional murasaki_1.68.6-15.debian.tar.xz 4389ed0d3199bea7a024842fc30f02bd 118544 science optional murasaki-common_1.68.6-15_all.deb 43d4679a21c77baceb0af4a8ab47413a 15083448 debug optional murasaki-dbgsym_1.68.6-15_amd64.deb a0025d369cb921a995bc5e921d0ed8a1 15761756 debug optional murasaki-mpi-dbgsym_1.68.6-15_amd64.deb 1eca5cae773e4644576d55f4f1aedf0c 695532 science optional murasaki-mpi_1.68.6-15_amd64.deb 60c7932e2505e9515f0702674b1a0d91 9264 science optional murasaki_1.68.6-15_amd64.buildinfo d25122ca72f1d8b4238b99d75859d7b8 647320 science optional murasaki_1.68.6-15_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sun, 28 Sep 2025 16:04:52 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: murasaki Binary: murasaki murasaki-common murasaki-dbgsym murasaki-mpi murasaki-mpi-dbgsym Architecture: all amd64 source Version: 1.68.6-15 Checksums-Md5: 90aba58141e366de9187584c69885027 1848 murasaki_1.68.6-15.dsc 4389ed0d3199bea7a024842fc30f02bd 118544 murasaki-common_1.68.6-15_all.deb 43d4679a21c77baceb0af4a8ab47413a 15083448 murasaki-dbgsym_1.68.6-15_amd64.deb a0025d369cb921a995bc5e921d0ed8a1 15761756 murasaki-mpi-dbgsym_1.68.6-15_amd64.deb 1eca5cae773e4644576d55f4f1aedf0c 695532 murasaki-mpi_1.68.6-15_amd64.deb d25122ca72f1d8b4238b99d75859d7b8 647320 murasaki_1.68.6-15_amd64.deb Checksums-Sha1: 915ba2153564309e93965cc8e359702a7fdf4afc 1848 murasaki_1.68.6-15.dsc 7e288ea059f37d325a31181fc5dbd855ced6e685 118544 murasaki-common_1.68.6-15_all.deb 160210a55426b706ecec89125797bd10a72f09c8 15083448 murasaki-dbgsym_1.68.6-15_amd64.deb 603ebe4078aeabcd3a563bf6e0d4bb12daa938e3 15761756 murasaki-mpi-dbgsym_1.68.6-15_amd64.deb 083ce297c0259158649ff6393515f5beb328d8e3 695532 murasaki-mpi_1.68.6-15_amd64.deb 8a5eb3309775b46e3b9708fd235b75837a178658 647320 murasaki_1.68.6-15_amd64.deb Checksums-Sha256: c5d66bb38c52c5e2e6aaff018ae78138ca9babdef734cdccf9ec390a7905bd4f 1848 murasaki_1.68.6-15.dsc 0bfb8e8f6c7576be98fb997a124f8b41729c52d545d525abb47e65bdb880a682 118544 murasaki-common_1.68.6-15_all.deb 8a857811857f606328d92474606cde320718190eb76347e0c3a5061f62072293 15083448 murasaki-dbgsym_1.68.6-15_amd64.deb 7871723b01fcb6f338acab357366df7b6ea96407ee7b98cfc6a1a47bedf48a11 15761756 murasaki-mpi-dbgsym_1.68.6-15_amd64.deb 3347073e3de3641f6a42b7a0d74c487b286b9f18ea51b8aeda5fad92ed45b66b 695532 murasaki-mpi_1.68.6-15_amd64.deb 799ca781fb9b24b481d04a0852d0fa80ddfb97c2ea909163c701ef95caa69250 647320 murasaki_1.68.6-15_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 28 Sep 2025 16:04:51 +0000 Build-Path: /build/murasaki-YRO0Zl/murasaki-1.68.6 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: adduser (= 3.153), autoconf (= 2.72-3.1), automake (= 1:1.17-4), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.7), bash (= 5.3-1), binutils (= 2.45-7), binutils-common (= 2.45-7), binutils-x86-64-linux-gnu (= 2.45-7), bsdextrautils (= 2.41.2-2), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.7-3), cpp (= 4:15.2.0-4), cpp-14 (= 14.3.0-8), cpp-14-x86-64-linux-gnu (= 14.3.0-8), cpp-15 (= 15.2.0-4), cpp-15-x86-64-linux-gnu (= 15.2.0-4), cpp-x86-64-linux-gnu (= 4:15.2.0-4), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.28), debianutils (= 5.23.2), dh-autoreconf (= 21), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.10-4), dpkg (= 1.22.21), dpkg-dev (= 1.22.21), dwz (= 0.16-2), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:15.2.0-4), g++-15 (= 15.2.0-4), g++-15-x86-64-linux-gnu (= 15.2.0-4), g++-x86-64-linux-gnu (= 4:15.2.0-4), gcc (= 4:15.2.0-4), gcc-14 (= 14.3.0-8), gcc-14-base (= 14.3.0-8), gcc-14-x86-64-linux-gnu (= 14.3.0-8), gcc-15 (= 15.2.0-4), gcc-15-base (= 15.2.0-4), gcc-15-x86-64-linux-gnu (= 15.2.0-4), gcc-x86-64-linux-gnu (= 4:15.2.0-4), gettext (= 0.23.1-2+b1), gettext-base (= 0.23.1-2+b1), gfortran-15 (= 15.2.0-4), gfortran-15-x86-64-linux-gnu (= 15.2.0-4), grep (= 3.12-1), groff-base (= 1.23.0-9), gzip (= 1.13-1), hostname (= 3.25), ibverbs-providers (= 56.1-1+b1), icu-devtools (= 76.1-4), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libamd-comgr2 (= 6.0+git20231212.4510c28+dfsg-3+b2), libamdhip64-5 (= 5.7.1-6), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-4), libatomic1 (= 15.2.0-4), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1), libbinutils (= 2.45-7), libblkid1 (= 2.41.2-2), libboost-atomic1.83-dev (= 1.83.0-5), libboost-atomic1.83.0 (= 1.83.0-5), libboost-filesystem-dev (= 1.83.0.2+b2), libboost-filesystem1.83-dev (= 1.83.0-5), libboost-filesystem1.83.0 (= 1.83.0-5), libboost-iostreams-dev (= 1.83.0.2+b2), libboost-iostreams1.83-dev (= 1.83.0-5), libboost-iostreams1.83.0 (= 1.83.0-5), libboost-regex-dev (= 1.83.0.2+b2), libboost-regex1.83-dev (= 1.83.0-5), libboost-regex1.83.0 (= 1.83.0-5), libboost-system1.83-dev (= 1.83.0-5), libboost-system1.83.0 (= 1.83.0-5), libboost1.83-dev (= 1.83.0-5), libbsd0 (= 0.12.2-2), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.41-12), libc-dev-bin (= 2.41-12), libc6 (= 2.41-12), libc6-dev (= 2.41-12), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-10+b1), libcbor0.10 (= 0.10.2-2), libcc1-0 (= 15.2.0-4), libcom-err2 (= 1.47.2-3+b3), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libcrypto++-dev (= 8.9.0-2), libcrypto++8t64 (= 8.9.0-2), libctf-nobfd0 (= 2.45-7), libctf0 (= 2.45-7), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.280), libdebhelper-perl (= 13.28), libdpkg-perl (= 1.22.21), libdrm-amdgpu1 (= 2.4.125-2), libdrm-common (= 2.4.125-2), libdrm2 (= 2.4.125-2), libedit2 (= 3.1-20250104-1), libelf1t64 (= 0.193-3), 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), libfabric1 (= 2.1.0-1.1), libffi8 (= 3.5.2-2), libfido2-1 (= 1.16.0-2), libfile-stripnondeterminism-perl (= 1.15.0-1), libfuse3-4 (= 3.17.4-1), libgcc-14-dev (= 14.3.0-8), libgcc-15-dev (= 15.2.0-4), libgcc-s1 (= 15.2.0-4), libgdbm-compat4t64 (= 1.26-1), libgdbm6t64 (= 1.26-1), libgfortran-15-dev (= 15.2.0-4), libgfortran5 (= 15.2.0-4), libgmp10 (= 2:6.3.0+dfsg-5), libgomp1 (= 15.2.0-4), libgprofng0 (= 2.45-7), libgssapi-krb5-2 (= 1.21.3-5), libhsa-runtime64-1 (= 6.1.2-3), libhsakmt1 (= 6.2.4+ds-1), libhwasan0 (= 15.2.0-4), libhwloc-dev (= 2.12.2-1), libhwloc-plugins (= 2.12.2-1), libhwloc15 (= 2.12.2-1), libibmad5 (= 56.1-1+b1), libibumad3 (= 56.1-1+b1), libibverbs-dev (= 56.1-1+b1), libibverbs1 (= 56.1-1+b1), libicu-dev (= 76.1-4), libicu76 (= 76.1-4), libisl23 (= 0.27-1), libitm1 (= 15.2.0-4), libjansson4 (= 2.14-2+b3), libjs-jquery (= 3.7.1+dfsg+~3.5.33-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libk5crypto3 (= 1.21.3-5), libkeyutils1 (= 1.6.3-6), libkrb5-3 (= 1.21.3-5), libkrb5support0 (= 1.21.3-5), libllvm17t64 (= 1:17.0.6-22+b3), liblsan0 (= 15.2.0-4), libltdl-dev (= 2.5.4-5), libltdl7 (= 2.5.4-5), liblzma5 (= 5.8.1-1.1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41.2-2), libmpc3 (= 1.3.1-2), libmpfr6 (= 4.2.2-2), libmunge2 (= 0.5.16-1), libnl-3-200 (= 3.11.0-2), libnl-3-dev (= 3.11.0-2), libnl-route-3-200 (= 3.11.0-2), libnl-route-3-dev (= 3.11.0-2), libnuma-dev (= 2.0.19-1), libnuma1 (= 2.0.19-1), libopenmpi-dev (= 5.0.8-10+b1), libopenmpi40 (= 5.0.8-10+b1), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpciaccess0 (= 0.17-3+b3), libpcre2-8-0 (= 10.46-1), libperl5.42 (= 5.42.0-2), libpipeline1 (= 1.5.8-1), libpmix2t64 (= 6.0.0+really5.0.8-1), libpsm2-2 (= 11.2.185-2.1), libpstreams-dev (= 1.0.3-1), libquadmath0 (= 15.2.0-4), librdmacm1t64 (= 56.1-1+b1), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsemanage-common (= 3.8.1-1), libsemanage2 (= 3.8.1-1), libsepol2 (= 3.8.1-1), libsframe2 (= 2.45-7), libsmartcols1 (= 2.41.2-2), libssl3t64 (= 3.5.3-1), libstdc++-14-dev (= 14.3.0-8), libstdc++-15-dev (= 15.2.0-4), libstdc++6 (= 15.2.0-4), libsystemd0 (= 258-1), libterm-readkey-perl (= 2.38-2+b5), libtext-wrapper-perl (= 1.05-4), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-5), libtsan2 (= 15.2.0-4), libubsan1 (= 15.2.0-4), libuchardet0 (= 0.0.8-2), libucx0 (= 1.19.0+ds-1), libudev1 (= 258-1), libunistring5 (= 1.3-2), libuuid1 (= 2.41.2-2), libx11-6 (= 2:1.8.12-1), libx11-data (= 2:1.8.12-1), 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), libxml2-16 (= 2.14.5+dfsg-0.2), libxnvctrl0 (= 535.171.04-1+b2), libz3-4 (= 4.13.3-1), libze1 (= 1.24.1-2), libzstd1 (= 1.5.7+dfsg-1.1), linux-libc-dev (= 6.16.9-1), login.defs (= 1:4.18.0-1), m4 (= 1.4.20-1), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), mpi-default-dev (= 1.19), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), ocl-icd-libopencl1 (= 2.3.3-1), openmpi-bin (= 5.0.8-10+b1), openmpi-common (= 5.0.8-10), openssh-client (= 1:10.0p1-8), openssl-provider-legacy (= 3.5.3-1), passwd (= 1:4.18.0-1), patch (= 2.8-2), perl (= 5.42.0-2), perl-base (= 5.42.0-2), perl-modules-5.42 (= 5.42.0-2), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.26), sysvinit-utils (= 3.14-4), tar (= 1.35+dfsg-3.1), util-linux (= 2.41.2-2), xz-utils (= 5.8.1-1.1), 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="1758965946" +------------------------------------------------------------------------------+ | Package contents Sun, 28 Sep 2025 16:04:52 +0000 | +------------------------------------------------------------------------------+ murasaki-common_1.68.6-15_all.deb --------------------------------- new Debian package, version 2.0. size 118544 bytes: control archive=3228 bytes. 1282 bytes, 28 lines control 6185 bytes, 85 lines md5sums Package: murasaki-common Source: murasaki Version: 1.68.6-15 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 413 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 2025-09-27 09:39 ./ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/debian-med/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./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 2025-09-27 09:39 ./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 ./usr/lib/debian-med/bin/kogalign.pl -rwxr-xr-x root/root 5770 2010-08-24 14:18 ./usr/lib/debian-med/bin/lav2murasaki.pl -rwxr-xr-x root/root 8150 2010-08-24 14:18 ./usr/lib/debian-med/bin/maf2anchors.pl -rwxr-xr-x root/root 4012 2010-08-24 14:18 ./usr/lib/debian-med/bin/mauve2anchors.pl -rwxr-xr-x root/root 5185 2010-08-24 14:18 ./usr/lib/debian-med/bin/mauveAlignment2anchors.pl -rwxr-xr-x root/root 2931 2010-08-24 14:18 ./usr/lib/debian-med/bin/mbgd-to-kog.pl -rwxr-xr-x root/root 1473 2010-08-24 14:18 ./usr/lib/debian-med/bin/mfasplit.pl -rwxr-xr-x root/root 3708 2010-08-24 14:18 ./usr/lib/debian-med/bin/names2kog.pl -rwxr-xr-x root/root 4090 2010-08-24 14:18 ./usr/lib/debian-med/bin/osfinder2anchors.pl -rwxr-xr-x root/root 2734 2010-08-24 14:18 ./usr/lib/debian-med/bin/overlay.pl -rwxr-xr-x root/root 3765 2010-08-24 14:18 ./usr/lib/debian-med/bin/phAlignment2anchors.pl -rwxr-xr-x root/root 6152 2025-09-27 09:39 ./usr/lib/debian-med/bin/qlob.pl -rwxr-xr-x root/root 1952 2010-08-24 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 2025-09-27 09:39 ./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 2025-09-27 09:39 ./usr/lib/debian-med/bin/substitch.pl drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/doc/murasaki-common/ -rw-r--r-- root/root 238 2025-09-27 09:39 ./usr/share/doc/murasaki-common/README.Debian -rw-r--r-- root/root 1063 2025-09-27 09:39 ./usr/share/doc/murasaki-common/changelog.Debian.gz -rw-r--r-- root/root 2225 2025-09-27 09:39 ./usr/share/doc/murasaki-common/copyright drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/lintian/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 70 2025-09-27 09:39 ./usr/share/lintian/overrides/murasaki-common drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/man/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/man/man1/ -rw-r--r-- root/root 1048 2025-09-27 09:39 ./usr/share/man/man1/align2kog.pl.1.gz -rw-r--r-- root/root 1030 2025-09-27 09:39 ./usr/share/man/man1/analyze-pat.pl.1.gz -rw-r--r-- root/root 1269 2025-09-27 09:39 ./usr/share/man/man1/chromostitch.pl.1.gz -rw-r--r-- root/root 1109 2025-09-27 09:39 ./usr/share/man/man1/faformat.pl.1.gz -rw-r--r-- root/root 3109 2025-09-27 09:39 ./usr/share/man/man1/filter.pl.1.gz -rw-r--r-- root/root 1101 2025-09-27 09:39 ./usr/share/man/man1/gatherstats.pl.1.gz -rw-r--r-- root/root 1809 2025-09-27 09:39 ./usr/share/man/man1/getcds.pl.1.gz -rw-r--r-- root/root 1041 2025-09-27 09:39 ./usr/share/man/man1/getgene.pl.1.gz -rw-r--r-- root/root 1101 2025-09-27 09:39 ./usr/share/man/man1/histocomp.pl.1.gz -rw-r--r-- root/root 1481 2025-09-27 09:39 ./usr/share/man/man1/histoplot.pl.1.gz -rw-r--r-- root/root 1096 2025-09-27 09:39 ./usr/share/man/man1/homology-score.pl.1.gz -rw-r--r-- root/root 1063 2025-09-27 09:39 ./usr/share/man/man1/interpolate.pl.1.gz -rw-r--r-- root/root 1026 2025-09-27 09:39 ./usr/share/man/man1/kogalign.pl.1.gz -rw-r--r-- root/root 1208 2025-09-27 09:39 ./usr/share/man/man1/lav2murasaki.pl.1.gz -rw-r--r-- root/root 1357 2025-09-27 09:39 ./usr/share/man/man1/maf2anchors.pl.1.gz -rw-r--r-- root/root 998 2025-09-27 09:39 ./usr/share/man/man1/mauve2anchors.pl.1.gz -rw-r--r-- root/root 1112 2025-09-27 09:39 ./usr/share/man/man1/mauveAlignment2anchors.pl.1.gz -rw-r--r-- root/root 1020 2025-09-27 09:39 ./usr/share/man/man1/mbgd-to-kog.pl.1.gz -rw-r--r-- root/root 951 2025-09-27 09:39 ./usr/share/man/man1/mfasplit.pl.1.gz -rw-r--r-- root/root 1134 2025-09-27 09:39 ./usr/share/man/man1/names2kog.pl.1.gz -rw-r--r-- root/root 1229 2025-09-27 09:39 ./usr/share/man/man1/overlay.pl.1.gz -rw-r--r-- root/root 997 2025-09-27 09:39 ./usr/share/man/man1/phAlignment2anchors.pl.1.gz -rw-r--r-- root/root 1409 2025-09-27 09:39 ./usr/share/man/man1/qlob.pl.1.gz -rw-r--r-- root/root 1031 2025-09-27 09:39 ./usr/share/man/man1/rearrange.pl.1.gz -rw-r--r-- root/root 975 2025-09-27 09:39 ./usr/share/man/man1/repeats2anchors.pl.1.gz -rw-r--r-- root/root 1595 2025-09-27 09:39 ./usr/share/man/man1/repeatviz.pl.1.gz -rw-r--r-- root/root 1479 2025-09-27 09:39 ./usr/share/man/man1/roc-at-cutoff.pl.1.gz -rw-r--r-- root/root 1152 2025-09-27 09:39 ./usr/share/man/man1/simpal.pl.1.gz -rw-r--r-- root/root 1427 2025-09-27 09:39 ./usr/share/man/man1/simplegraph.pl.1.gz -rw-r--r-- root/root 1374 2025-09-27 09:39 ./usr/share/man/man1/stat-histo.pl.1.gz -rw-r--r-- root/root 1466 2025-09-27 09:39 ./usr/share/man/man1/stat-vs-stat.pl.1.gz -rw-r--r-- root/root 1510 2025-09-27 09:39 ./usr/share/man/man1/substitch.pl.1.gz drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/perl5/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/perl5/murasaki/ -rw-r--r-- root/root 3047 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki.pm drwxr-xr-x root/root 0 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki/ -rw-r--r-- root/root 8037 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki/KOG.pm -rw-r--r-- root/root 7146 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki/OrthoConsistency.pm -rw-r--r-- root/root 4383 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki/OrthoList.pm -rw-r--r-- root/root 8019 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki/OrthoPairs.pm -rw-r--r-- root/root 2893 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki/SeqFeatures.pm -rw-r--r-- root/root 1459 2010-08-24 14:18 ./usr/share/perl5/murasaki/Murasaki/Ticker.pm -rwxr-xr-x root/root 137 2025-09-27 09:39 ./usr/share/perl5/murasaki/config.pl murasaki-dbgsym_1.68.6-15_amd64.deb ----------------------------------- new Debian package, version 2.0. size 15083448 bytes: control archive=1188 bytes. 872 bytes, 12 lines control 1463 bytes, 14 lines md5sums Package: murasaki-dbgsym Source: murasaki Version: 1.68.6-15 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 16689 Depends: murasaki (= 1.68.6-15) Section: debug Priority: optional Description: debug symbols for murasaki Build-Ids: 02fcf96efe99be98aff1a74626bd71703f4a49b1 427420bc749be83cb34572df97922a1725b0a815 54fc39ff3170b8ad5e8dcbe86f605e79a22182b2 7548d14ef6c03fa73f925ab39d57fb1fbcf0a4b4 7de04439bdda2780ba1b0ddede6274ba04d77f28 9ff0970bf44a12b5b088e754a664b3f1753d74e4 a24d9f67aa5572ac0d8bba49d82a0c405cb35d99 b0f0e6cde02192918b2de3c1cba45402ccf4e261 b7a7ce0bb372a0c39890c7836910fa5ec4e3b53d e15ecc29b55dddbe157fcef47ac007da31e4d93a eec33d6386bcc57bf090360294bc44050d7cf3be f6e5cc2e21c527f0dde89771f5b1f6b707de2532 fe667b54201abf4f3f40462436cf97ccf71d2895 drwxr-xr-x root/root 0 2025-09-27 09:39 ./ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/debug/.build-id/02/ -rw-r--r-- root/root 3907320 2025-09-27 09:39 ./usr/lib/debug/.build-id/02/fcf96efe99be98aff1a74626bd71703f4a49b1.debug drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/debug/.build-id/42/ -rw-r--r-- root/root 954728 2025-09-27 09:39 ./usr/lib/debug/.build-id/42/7420bc749be83cb34572df97922a1725b0a815.debug drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/debug/.build-id/54/ 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./usr/lib/debug/.build-id/fe/667b54201abf4f3f40462436cf97ccf71d2895.debug drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 856288 2025-09-27 09:39 ./usr/lib/debug/.dwz/x86_64-linux-gnu/murasaki.debug drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-09-27 09:39 ./usr/share/doc/murasaki-dbgsym -> murasaki murasaki-mpi-dbgsym_1.68.6-15_amd64.deb --------------------------------------- new Debian package, version 2.0. size 15761756 bytes: control archive=1196 bytes. 884 bytes, 12 lines control 1467 bytes, 14 lines md5sums Package: murasaki-mpi-dbgsym Source: murasaki Version: 1.68.6-15 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 17356 Depends: murasaki-mpi (= 1.68.6-15) Section: debug Priority: optional Description: debug 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./usr/lib/debug/.build-id/e1/5ecc29b55dddbe157fcef47ac007da31e4d93a.debug drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/debug/.build-id/e4/ -rw-r--r-- root/root 1285800 2025-09-27 09:39 ./usr/lib/debug/.build-id/e4/a7888792147643bd762a733408063fb2f5514c.debug drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/debug/.build-id/ec/ -rw-r--r-- root/root 975720 2025-09-27 09:39 ./usr/lib/debug/.build-id/ec/9aa9df0838efd1a029295e5e449dfbcfe2d070.debug drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 856488 2025-09-27 09:39 ./usr/lib/debug/.dwz/x86_64-linux-gnu/murasaki-mpi.debug drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-09-27 09:39 ./usr/share/doc/murasaki-mpi-dbgsym -> murasaki-mpi murasaki-mpi_1.68.6-15_amd64.deb -------------------------------- new Debian package, version 2.0. size 695532 bytes: control archive=1592 bytes. 1354 bytes, 28 lines control 1326 bytes, 20 lines md5sums Package: murasaki-mpi Source: murasaki Version: 1.68.6-15 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 4555 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 (>= 5.0.8), 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 2025-09-27 09:39 ./ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/bin/ -rwxr-xr-x root/root 365048 2025-09-27 09:39 ./usr/bin/geneparse-mpi -rwxr-xr-x root/root 409976 2025-09-27 09:39 ./usr/bin/mbfa-mpi -rwxr-xr-x root/root 933000 2025-09-27 09:39 ./usr/bin/murasaki-mpi drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/murasaki/ -rwxr-xr-x root/root 319784 2025-09-27 09:39 ./usr/lib/murasaki/align-and-mpi -rwxr-xr-x root/root 323912 2025-09-27 09:39 ./usr/lib/murasaki/align-best-mpi -rwxr-xr-x root/root 373600 2025-09-27 09:39 ./usr/lib/murasaki/align-compare-mpi -rwxr-xr-x root/root 476008 2025-09-27 09:39 ./usr/lib/murasaki/align-coverage-mpi -rwxr-xr-x root/root 315656 2025-09-27 09:39 ./usr/lib/murasaki/align-or-mpi -rwxr-xr-x root/root 92728 2025-09-27 09:39 ./usr/lib/murasaki/cgr-compare-mpi -rwxr-xr-x root/root 422360 2025-09-27 09:39 ./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 2025-09-27 09:39 ./usr/lib/murasaki/cgr-random-mpi -rwxr-xr-x root/root 410024 2025-09-27 09:39 ./usr/lib/murasaki/cgr-sample-mpi -rwxr-xr-x root/root 68000 2025-09-27 09:39 ./usr/lib/murasaki/testeco-mpi drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/doc/murasaki-mpi/ -rw-r--r-- root/root 249 2025-09-27 09:39 ./usr/share/doc/murasaki-mpi/README.test -rw-r--r-- root/root 1062 2025-09-27 09:39 ./usr/share/doc/murasaki-mpi/changelog.Debian.gz -rw-r--r-- root/root 2225 2025-09-27 09:39 ./usr/share/doc/murasaki-mpi/copyright drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/man/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/man/man1/ -rw-r--r-- root/root 2518 2025-09-27 09:39 ./usr/share/man/man1/geneparse-mpi.1.gz -rw-r--r-- root/root 2721 2025-09-27 09:39 ./usr/share/man/man1/mbfa-mpi.1.gz -rw-r--r-- root/root 10888 2025-09-27 09:39 ./usr/share/man/man1/murasaki-mpi.1.gz murasaki_1.68.6-15_amd64.deb ---------------------------- new Debian package, version 2.0. size 647320 bytes: control archive=1440 bytes. 1124 bytes, 23 lines control 1182 bytes, 19 lines md5sums Package: murasaki Version: 1.68.6-15 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 4436 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 2025-09-27 09:39 ./ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/bin/ -rwxr-xr-x root/root 365048 2025-09-27 09:39 ./usr/bin/geneparse -rwxr-xr-x root/root 409976 2025-09-27 09:39 ./usr/bin/mbfa -rwxr-xr-x root/root 818280 2025-09-27 09:39 ./usr/bin/murasaki drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/lib/murasaki/ -rwxr-xr-x root/root 319776 2025-09-27 09:39 ./usr/lib/murasaki/align-and -rwxr-xr-x root/root 323904 2025-09-27 09:39 ./usr/lib/murasaki/align-best -rwxr-xr-x root/root 373592 2025-09-27 09:39 ./usr/lib/murasaki/align-compare -rwxr-xr-x root/root 476008 2025-09-27 09:39 ./usr/lib/murasaki/align-coverage -rwxr-xr-x root/root 315648 2025-09-27 09:39 ./usr/lib/murasaki/align-or -rwxr-xr-x root/root 92720 2025-09-27 09:39 ./usr/lib/murasaki/cgr-compare -rwxr-xr-x root/root 422360 2025-09-27 09:39 ./usr/lib/murasaki/cgr-image -rwxr-xr-x root/root 105048 2025-09-27 09:39 ./usr/lib/murasaki/cgr-random -rwxr-xr-x root/root 410024 2025-09-27 09:39 ./usr/lib/murasaki/cgr-sample -rwxr-xr-x root/root 67992 2025-09-27 09:39 ./usr/lib/murasaki/testeco drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/doc/murasaki/ -rw-r--r-- root/root 249 2025-09-27 09:39 ./usr/share/doc/murasaki/README.test -rw-r--r-- root/root 1059 2025-09-27 09:39 ./usr/share/doc/murasaki/changelog.Debian.gz -rw-r--r-- root/root 2225 2025-09-27 09:39 ./usr/share/doc/murasaki/copyright drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/man/ drwxr-xr-x root/root 0 2025-09-27 09:39 ./usr/share/man/man1/ -rw-r--r-- root/root 2518 2025-09-27 09:39 ./usr/share/man/man1/geneparse.1.gz -rw-r--r-- root/root 2721 2025-09-27 09:39 ./usr/share/man/man1/mbfa.1.gz -rw-r--r-- root/root 10888 2025-09-27 09:39 ./usr/share/man/man1/murasaki.1.gz +------------------------------------------------------------------------------+ | Post Build Sun, 28 Sep 2025 16:04:53 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 28 Sep 2025 16:04:53 +0000 | +------------------------------------------------------------------------------+ Purging /build/murasaki-YRO0Zl Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 28 Sep 2025 16:04:54 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 293712 Build-Time: 165 Distribution: perl-5.42-throwaway Host Architecture: amd64 Install-Time: 17 Job: /srv/debomatic/incoming/murasaki_1.68.6-15.dsc Machine Architecture: amd64 Package: murasaki Package-Time: 185 Source-Version: 1.68.6-15 Space: 293712 Status: successful Version: 1.68.6-15 -------------------------------------------------------------------------------- Finished at 2025-09-28T16:04:52Z Build needed 00:03:05, 293712k disk space