sbuild (Debian sbuild) 0.91.9 (05 May 2026) on carme.larted.org.uk +==============================================================================+ | murasaki 1.68.6-17 (amd64) Mon, 29 Jun 2026 09:38:09 +0000 | +==============================================================================+ Package: murasaki Version: 1.68.6-17 Source Version: 1.68.6-17 Distribution: perl-5.44-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 Mon, 29 Jun 2026 09:38:11 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup murasaki_1.68.6-17 perl-5.44-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup murasaki_1.68.6-17 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Mon, 29 Jun 2026 09:38:12 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Get:2 http://deb.debian.org/debian unstable InRelease [193 kB] Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Get:3 http://deb.debian.org/debian sid InRelease [193 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:5 http://deb.debian.org/debian sid/main Sources.diff/Index [63.6 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 Packages T-2026-06-29-0800.45-F-2026-06-29-0800.45.pdiff [9895 B] Get:6 http://deb.debian.org/debian unstable/main amd64 Packages T-2026-06-29-0800.45-F-2026-06-29-0800.45.pdiff [9895 B] Get:7 http://deb.debian.org/debian sid/main Sources T-2026-06-29-0800.45-F-2026-06-29-0800.45.pdiff [11.0 kB] Get:7 http://deb.debian.org/debian sid/main Sources T-2026-06-29-0800.45-F-2026-06-29-0800.45.pdiff [11.0 kB] Fetched 534 kB in 3s (196 kB/s) 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 Mon, 29 Jun 2026 09:38:16 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/murasaki_1.68.6-17.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 29 Jun 2026 09:38:17 +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-rAzmfo/resolver-j5yS3m/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/murasaki-rAzmfo/resolver-j5yS3m/apt_archive ./ InRelease Get:2 copy:/build/murasaki-rAzmfo/resolver-j5yS3m/apt_archive ./ Release [609 B] Ign:3 copy:/build/murasaki-rAzmfo/resolver-j5yS3m/apt_archive ./ Release.gpg Get:4 copy:/build/murasaki-rAzmfo/resolver-j5yS3m/apt_archive ./ Sources [764 B] Get:5 copy:/build/murasaki-rAzmfo/resolver-j5yS3m/apt_archive ./ Packages [803 B] Fetched 2176 B in 0s (209 kB/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... Solving dependencies... 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 intltool-debian libamd-comgr3 libamdhip64-6 libarchive-zip-perl libboost-atomic1.90-dev libboost-atomic1.90.0 libboost-filesystem-dev libboost-filesystem1.90-dev libboost-filesystem1.90.0 libboost-iostreams-dev libboost-iostreams1.90-dev libboost-iostreams1.90.0 libboost-random1.90-dev libboost-random1.90.0 libboost-regex-dev libboost-regex1.90-dev libboost-regex1.90.0 libboost1.90-dev libbsd0 libcbor0.10 libclang-common-21-dev 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 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm21 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 libprrte-bin libprrte-dev libprrte3 libpsm2-2 libpstreams-dev librdmacm1t64 libsystemd-shared libterm-readkey-perl libtext-wrapper-perl libtool libtss2-esys-3.0.2-0t64 libtss2-mu-4.0.1-0t64 libtss2-rc0t64 libtss2-sys1t64 libtss2-tcti-cmd0t64 libtss2-tcti-device0t64 libtss2-tcti-mssim0t64 libtss2-tcti-swtpm0t64 libucc1 libuchardet0 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2-16 libxnvctrl0 libz3-4 libze1 m4 man-db mount mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf sensible-utils systemd systemd-tpm tpm-udev 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 libboost1.90-doc libboost-chrono1.90-dev libboost-container1.90-dev libboost-context1.90-dev libboost-contract1.90-dev libboost-coroutine1.90-dev libboost-date-time1.90-dev libboost-exception1.90-dev libboost-fiber1.90-dev libboost-graph-parallel1.90-dev libboost-graph1.90-dev libboost-json1.90-dev libboost-locale1.90-dev libboost-log1.90-dev libboost-math1.90-dev libboost-mpi-python1.90-dev libboost-mpi1.90-dev libboost-nowide1.90-dev libboost-numpy1.90-dev libboost-program-options1.90-dev libboost-python1.90-dev libboost-serialization1.90-dev libboost-stacktrace1.90-dev libboost-test1.90-dev libboost-thread1.90-dev libboost-timer1.90-dev libboost-type-erasure1.90-dev libboost-url1.90-dev libboost-wave1.90-dev libboost1.90-tools-dev libmpfrc++-dev libntl-dev fuse3 krb5-doc krb5-user libhwloc-contrib-plugins libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils libarchive13t64 libcurl4t64 libdw1t64 libfdisk1 libmicrohttpd12t64 libpwquality1 libqrencode4 m4-doc apparmor less www-browser nfs-common opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl systemd-container systemd-homed systemd-imds systemd-userdbd systemd-boot systemd-report systemd-resolved systemd-repart polkitd Recommended packages: curl | wget | lynx python3:any libclang-rt-21-dev libarchive-cpio-perl javascript-common krb5-locales libcoarrays-openmpi-dev libpmix-dev libapparmor1 libbpf1 libcryptsetup12 libkmod2 xauth libmail-sendmail-perl default-dbus-system-bus | dbus-system-bus linux-sysctl-defaults login systemd-timesyncd | time-daemon systemd-cryptsetup 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 intltool-debian libamd-comgr3 libamdhip64-6 libarchive-zip-perl libboost-atomic1.90-dev libboost-atomic1.90.0 libboost-filesystem-dev libboost-filesystem1.90-dev libboost-filesystem1.90.0 libboost-iostreams-dev libboost-iostreams1.90-dev libboost-iostreams1.90.0 libboost-random1.90-dev libboost-random1.90.0 libboost-regex-dev libboost-regex1.90-dev libboost-regex1.90.0 libboost1.90-dev libbsd0 libcbor0.10 libclang-common-21-dev 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 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm21 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 libprrte-bin libprrte-dev libprrte3 libpsm2-2 libpstreams-dev librdmacm1t64 libsystemd-shared libterm-readkey-perl libtext-wrapper-perl libtool libtss2-esys-3.0.2-0t64 libtss2-mu-4.0.1-0t64 libtss2-rc0t64 libtss2-sys1t64 libtss2-tcti-cmd0t64 libtss2-tcti-device0t64 libtss2-tcti-mssim0t64 libtss2-tcti-swtpm0t64 libucc1 libuchardet0 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2-16 libxnvctrl0 libz3-4 libze1 m4 man-db mount mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf sbuild-build-depends-main-dummy sensible-utils systemd systemd-tpm tpm-udev zlib1g-dev 0 upgraded, 136 newly installed, 0 to remove and 0 not upgraded. Need to get 132 MB/132 MB of archives. After this operation, 682 MB of additional disk space will be used. Get:1 copy:/build/murasaki-rAzmfo/resolver-j5yS3m/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [928 B] Get:2 file:/srv/reprepro perl-5.44/main amd64 libterm-readkey-perl amd64 2.38-2+b5 [24.7 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 mount amd64 2.42.2-1 [165 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 261.1-2 [2567 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 tpm-udev all 4.1.3-6 [27.4 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libtss2-mu-4.0.1-0t64 amd64 4.1.3-6 [77.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libtss2-tcti-cmd0t64 amd64 4.1.3-6 [34.4 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libtss2-tcti-device0t64 amd64 4.1.3-6 [35.7 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libtss2-tcti-mssim0t64 amd64 4.1.3-6 [35.7 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libtss2-tcti-swtpm0t64 amd64 4.1.3-6 [35.8 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libtss2-sys1t64 amd64 4.1.3-6 [55.3 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libtss2-esys-3.0.2-0t64 amd64 4.1.3-6 [172 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 libtss2-rc0t64 amd64 4.1.3-6 [31.0 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 systemd-tpm amd64 261.1-2 [157 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 systemd amd64 261.1-2 [3335 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-1 [332 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.2-1 [100.0 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-3 [132 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20260512-1 [93.6 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2.1+b1 [28.6 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.17.0-1 [80.6 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Get:34 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-3 [335 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:10.3p1-5 [1006 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-1 [820 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.2 [77.1 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:48 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.3+dfsg-1 [642 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-1 [2660 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.2 [933 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 16.1.0-2 [877 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libgfortran-15-dev amd64 15.3.0-1 [877 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.3.0-1 [12.8 MB] Get:58 http://deb.debian.org/debian unstable/main amd64 gfortran-15 amd64 15.3.0-1 [22.2 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.12.0-2+b1 [62.2 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.12.0-2+b1 [200 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 63.0-1.1+b3 [63.2 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 63.0-1.1+b3 [383 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1.1 [8644 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libllvm21 amd64 1:21.1.8-7+b4 [28.2 MB] Get:65 http://deb.debian.org/debian unstable/main amd64 libclang-common-21-dev amd64 1:21.1.8-7+b4 [768 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libamd-comgr3 amd64 7.0.2+dfsg-3 [13.9 MB] Get:67 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.134-2 [7840 B] Get:68 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.134-2 [38.5 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.134-2 [23.3 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1+b2 [22.0 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.4.3+dfsg-5 [678 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libamdhip64-6 amd64 6.4.3-5 [9385 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libboost1.90-dev amd64 1.90.0-6 [11.3 MB] Get:74 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.90.0 amd64 1.90.0-6 [227 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.90-dev amd64 1.90.0-6 [228 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.90.0 amd64 1.90.0-6 [276 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.90-dev amd64 1.90.0-6 [293 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem-dev amd64 1.90.0.2 [2896 B] Get:79 http://deb.debian.org/debian unstable/main amd64 libboost-random1.90.0 amd64 1.90.0-6 [230 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libboost-random1.90-dev amd64 1.90.0-6 [232 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.90.0 amd64 1.90.0-6 [327 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.90-dev amd64 1.90.0-6 [343 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.90.0 amd64 1.90.0-6 [245 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.90-dev amd64 1.90.0-6 [253 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams-dev amd64 1.90.0.2 [2844 B] Get:86 http://deb.debian.org/debian unstable/main amd64 libboost-regex-dev amd64 1.90.0.2 [3124 B] Get:87 http://deb.debian.org/debian unstable/main amd64 libcrypto++8t64 amd64 8.9.0-2+b2 [1178 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libcrypto++-dev amd64 8.9.0-2+b2 [1842 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b2 [184 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b2 [134 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b2 [108 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b2 [54.3 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b2 [61.3 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10+b2 [308 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 63.0-1.1+b3 [72.0 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 2.1.0-1.1+b2 [716 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libfuse3-4 amd64 3.18.2-2 [103 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.14.0-2 [166 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.19-1+b2 [36.2 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-11 [416 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.5.4-11 [168 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.14.0-2 [260 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b4 [52.1 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1+b2 [20.7 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-2+b1 [28.2 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b2 [144 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.13-1 [346 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.13-1 [829 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b4 [50.7 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b3 [14.1 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libze1 amd64 1.28.2-2 [795 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.4-1+b1 [42.8 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.14.0-2 [21.7 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 63.0-1.1+b3 [28.8 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 63.0-1.1+b3 [43.5 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.12.0-2+b1 [105 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.12.0-2+b1 [220 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 63.0-1.1+b3 [695 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.18-1 [18.8 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 6.0.0+really5.0.9-3+b2 [670 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.21.0-1 [977 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 libucc1 amd64 1.8.0-2 [345 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.10-1 [2018 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.10-1 [30.3 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 libprrte3 amd64 3.0.13-3 [451 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 libprrte-dev amd64 3.0.13-3 [3654 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 libprrte-bin amd64 3.0.13-3 [51.9 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.10-1 [154 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.10-1 [1028 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 libpstreams-dev all 1.0.4-2 [146 kB] Get:135 http://deb.debian.org/debian unstable/main amd64 libtext-wrapper-perl all 1.05-4 [10.3 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.20 [3504 B] Preconfiguring packages ... 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Setting up autoconf (2.73-2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-3) ... Setting up libnuma1:amd64 (2.0.19-1+b2) ... Setting up dwz (0.16-4) ... Setting up mount (2.42.2-1) ... Setting up sensible-utils (0.0.26) ... Setting up ocl-icd-libopencl1:amd64 (2.3.4-1+b1) ... Setting up libuchardet0:amd64 (0.0.8-2+b2) ... Setting up libnl-3-200:amd64 (3.12.0-2+b1) ... Setting up libpsm2-2 (11.2.185-2.1) ... Setting up openmpi-common (5.0.10-1) ... Setting up libboost1.90-dev:amd64 (1.90.0-6) ... Setting up libx11-6:amd64 (2:1.8.13-1) ... Setting up libboost-atomic1.90.0:amd64 (1.90.0-6) ... Setting up libkrb5-3:amd64 (1.22.1-3) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Setting up libboost-regex1.90.0:amd64 (1.90.0-6) ... Setting up libclang-common-21-dev:amd64 (1:21.1.8-7+b4) ... Setting up libboost-filesystem1.90.0:amd64 (1.90.0-6) ... Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1) ... Setting up libfuse3-4:amd64 (3.18.2-2) ... Setting up libterm-readkey-perl (2.38-2+b5) ... Setting up libfido2-1:amd64 (1.17.0-1) ... Setting up libboost-random1.90.0:amd64 (1.90.0-6) ... Setting up libbsd0:amd64 (0.12.2-3) ... Setting up libdrm-common (2.4.134-2) ... Setting up libboost-iostreams1.90.0:amd64 (1.90.0-6) ... Setting up automake (1:1.18.1-4) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.1-1) ... Setting up gettext (1.0-1) ... Setting up libtool (2.5.4-11) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Setting up libedit2:amd64 (3.1-20260512-1) ... Setting up libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Setting up libcrypto++-dev:amd64 (8.9.0-2+b2) ... Setting up libxext6:amd64 (2:1.3.4-1+b4) ... Setting up libgfortran-15-dev:amd64 (15.3.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.19-1+b2) ... Setting up libnl-route-3-200:amd64 (3.12.0-2+b1) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b3) ... Setting up dh-autoreconf (22) ... Setting up libltdl-dev:amd64 (2.5.4-11) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm21:amd64 (1:21.1.8-7+b4) ... Setting up libpstreams-dev (1.0.4-2) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-3) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Setting up dh-strip-nondeterminism (1.15.1-1) ... Setting up libdrm2:amd64 (2.4.134-2) ... Setting up libnl-3-dev:amd64 (3.12.0-2+b1) ... Setting up libboost-regex1.90-dev:amd64 (1.90.0-6) ... Setting up groff-base (1.24.1-1) ... Setting up libamd-comgr3:amd64 (7.0.2+dfsg-3) ... Setting up libboost-atomic1.90-dev:amd64 (1.90.0-6) ... Setting up libhwloc-dev:amd64 (2.14.0-2) ... Setting up libboost-random1.90-dev:amd64 (1.90.0-6) ... Setting up libboost-regex-dev:amd64 (1.90.0.2) ... Setting up libdrm-amdgpu1:amd64 (2.4.134-2) ... Setting up gfortran-15-x86-64-linux-gnu (15.3.0-1) ... Setting up libboost-filesystem1.90-dev:amd64 (1.90.0-6) ... Setting up po-debconf (1.0.22) ... Setting up libboost-iostreams1.90-dev:amd64 (1.90.0-6) ... Setting up libboost-iostreams-dev:amd64 (1.90.0.2) ... Setting up libhwloc-plugins:amd64 (2.14.0-2) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' → '/usr/lib/systemd/system/man-db.timer'. Setting up libnl-route-3-dev:amd64 (3.12.0-2+b1) ... Setting up libevent-dev (2.1.12-stable-10+b2) ... Setting up libpmix2t64:amd64 (6.0.0+really5.0.9-3+b2) ... Setting up libhsa-runtime64-1:amd64 (6.4.3+dfsg-5) ... Setting up libboost-filesystem-dev:amd64 (1.90.0.2) ... Setting up gfortran-15 (15.3.0-1) ... Setting up debhelper (14.2) ... Setting up libamdhip64-6:amd64 (6.4.3-5) ... Setting up libprrte3:amd64 (3.0.13-3) ... Setting up libprrte-dev:amd64 (3.0.13-3) ... Setting up libprrte-bin (3.0.13-3) ... Setting up libucx0:amd64 (1.21.0-1) ... Setting up libtss2-tcti-cmd0t64:amd64 (4.1.3-6) ... Setting up libtss2-rc0t64:amd64 (4.1.3-6) ... Setting up libtss2-mu-4.0.1-0t64:amd64 (4.1.3-6) ... Setting up libtss2-tcti-device0t64:amd64 (4.1.3-6) ... Setting up libtss2-tcti-mssim0t64:amd64 (4.1.3-6) ... Setting up libtss2-tcti-swtpm0t64:amd64 (4.1.3-6) ... Setting up systemd-tpm (261.1-2) ... Setting up systemd (261.1-2) ... Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' → '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' → '/usr/lib/systemd/system/systemd-pstore.service'. Created symlink '/etc/systemd/system/autovt@.service' → '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' → '/usr/lib/systemd/system/getty@.service'. Initializing machine ID from random generator. Setting up tpm-udev (4.1.3-6) ... Created symlink '/etc/systemd/system/paths.target.wants/tpm-udev.path' → '/usr/lib/systemd/system/tpm-udev.path'. /var/lib/dpkg/info/tpm-udev.postinst: 52: udevadm: not found Setting up libibverbs1:amd64 (63.0-1.1+b3) ... Creating group 'rdma' with GID 993. Setting up ibverbs-providers:amd64 (63.0-1.1+b3) ... Setting up openssh-client (1:10.3p1-5) ... Created symlink '/etc/systemd/user/sockets.target.wants/ssh-agent.socket' → '/usr/lib/systemd/user/ssh-agent.socket'. Setting up libibverbs-dev:amd64 (63.0-1.1+b3) ... Setting up libtss2-sys1t64:amd64 (4.1.3-6) ... Setting up libucc1:amd64 (1.8.0-2) ... Setting up libtss2-esys-3.0.2-0t64:amd64 (4.1.3-6) ... Setting up librdmacm1t64:amd64 (63.0-1.1+b3) ... Setting up libfabric1:amd64 (2.1.0-1.1+b2) ... Setting up libopenmpi40:amd64 (5.0.10-1) ... Setting up openmpi-bin (5.0.10-1) ... 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) does not exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev (5.0.10-1) ... 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 (1.20) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.42-17) ... +------------------------------------------------------------------------------+ | Check architectures Mon, 29 Jun 2026 09:38:36 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Mon, 29 Jun 2026 09:38:36 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.46.50.20260617-1 dpkg-dev_1.23.7 g++-15_15.3.0-1 gcc-15_15.3.0-1 libc6-dev_2.42-17 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 linux-libc-dev_7.0.13-1 Package versions: apt_3.3.1 autoconf_2.73-2 automake_1:1.18.1-4 autopoint_1.0-1 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 binutils_2.46.50.20260617-1 binutils-common_2.46.50.20260617-1 binutils-x86-64-linux-gnu_2.46.50.20260617-1 bsdextrautils_2.42.2-1 build-essential_12.12 bzip2_1.0.8-6+b2 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.3.0-1 cpp-15-x86-64-linux-gnu_15.3.0-1 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_14.2 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_22 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-5 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 eatmydata_131-2 file_1:5.47-4 findutils_4.10.0-4 g++_4:15.2.0-5+b1 g++-15_15.3.0-1 g++-15-x86-64-linux-gnu_15.3.0-1 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.3.0-1 gcc-15-base_15.3.0-1 gcc-15-x86-64-linux-gnu_15.3.0-1 gcc-16-base_16.1.0-2 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_1.0-1 gettext-base_1.0-1 gfortran-15_15.3.0-1 gfortran-15-x86-64-linux-gnu_15.3.0-1 gnupg_2.4.9-5 gnupg-l10n_2.4.9-5 gpg_2.4.9-5 gpg-agent_2.4.9-5 gpgconf_2.4.9-5 gpgsm_2.4.9-5 grep_3.12-1 groff-base_1.24.1-1 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libcap-ng0_0.9.3-1 libcbor0.10_0.10.2-2.1+b1 libcc1-0_16.1.0-2 libclang-common-21-dev_1:21.1.8-7+b4 libcom-err2_1.47.4-1 libcrypt1_1:4.5.1-1+b1 libcrypto++-dev_8.9.0-2+b2 libcrypto++8t64_8.9.0-2+b2 libctf-nobfd0_2.46.50.20260617-1 libctf0_2.46.50.20260617-1 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.2 libdpkg-perl_1.23.7 libdrm-amdgpu1_2.4.134-2 libdrm-common_2.4.134-2 libdrm2_2.4.134-2 libeatmydata1_131-2+b2 libedit2_3.1-20260512-1 libelf1t64_0.195-1 libevent-2.1-7t64_2.1.12-stable-10+b2 libevent-core-2.1-7t64_2.1.12-stable-10+b2 libevent-dev_2.1.12-stable-10+b2 libevent-extra-2.1-7t64_2.1.12-stable-10+b2 libevent-openssl-2.1-7t64_2.1.12-stable-10+b2 libevent-pthreads-2.1-7t64_2.1.12-stable-10+b2 libfabric1_2.1.0-1.1+b2 libffi8_3.5.2-4 libfido2-1_1.17.0-1 libfile-stripnondeterminism-perl_1.15.1-1 libfuse3-4_3.18.2-2 libgcc-15-dev_15.3.0-1 libgcc-s1_16.1.0-2 libgcrypt20_1.12.2-1 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgfortran-15-dev_15.3.0-1 libgfortran5_16.1.0-2 libgmp10_2:6.3.0+dfsg-5+b2 libgnutls30t64_3.8.13-1 libgomp1_16.1.0-2 libgpg-error0_1.61-3 libgprofng0_2.46.50.20260617-1 libgssapi-krb5-2_1.22.1-3 libhogweed6t64_3.10.2-1+b1 libhsa-runtime64-1_6.4.3+dfsg-5 libhwasan0_16.1.0-2 libhwloc-dev_2.14.0-2 libhwloc-plugins_2.14.0-2 libhwloc15_2.14.0-2 libibmad5_63.0-1.1+b3 libibumad3_63.0-1.1+b3 libibverbs-dev_63.0-1.1+b3 libibverbs1_63.0-1.1+b3 libidn2-0_2.3.8-5 libisl23_0.27-2 libitm1_16.1.0-2 libjansson4_2.15.0-1 libjs-jquery_3.7.1+dfsg+~3.5.33-1 libjs-jquery-ui_1.13.2+dfsg-1 libk5crypto3_1.22.1-3 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-3 libkrb5support0_1.22.1-3 libksba8_1.8.0-3 libldap2_2.6.13+dfsg-1+b1 libllvm21_1:21.1.8-7+b4 liblsan0_16.1.0-2 libltdl-dev_2.5.4-11 libltdl7_2.5.4-11 liblz4-1_1.10.0-10 liblzma5_5.8.3-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmount1_2.42.2-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libmunge2_0.5.18-1 libncursesw6_6.6+20251231-1+b1 libnettle8t64_3.10.2-1+b1 libnl-3-200_3.12.0-2+b1 libnl-3-dev_3.12.0-2+b1 libnl-route-3-200_3.12.0-2+b1 libnl-route-3-dev_3.12.0-2+b1 libnpth0t64_1.8-3+b2 libnuma-dev_2.0.19-1+b2 libnuma1_2.0.19-1+b2 libopenmpi-dev_5.0.10-1 libopenmpi40_5.0.10-1 libp11-kit0_0.26.2-3 libpam-modules_1.7.0-6 libpam-modules-bin_1.7.0-6 libpam-runtime_1.7.0-6 libpam0g_1.7.0-6 libpciaccess0_0.17-3+b4 libpcre2-8-0_10.46-1+b2 libperl5.40_5.40.1-8 libperl5.44_5.44.0~rc1-1 libpipeline1_1.5.8-3 libpmix2t64_6.0.0+really5.0.9-3+b2 libprrte-bin_3.0.13-3 libprrte-dev_3.0.13-3 libprrte3_3.0.13-3 libpsm2-2_11.2.185-2.1 libpstreams-dev_1.0.4-2 libquadmath0_16.1.0-2 librdmacm1t64_63.0-1.1+b3 libreadline8t64_8.3-4 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.0-2+b1 libselinux1_3.10-1 libsframe3_2.46.50.20260617-1 libsmartcols1_2.42.2-1 libsqlite3-0_3.53.3-1 libssl3t64_3.6.3-1 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 libsystemd-shared_261.1-2 libsystemd0_261.1-2 libtasn1-6_4.21.0-2+b1 libterm-readkey-perl_2.38-2+b5 libtext-wrapper-perl_1.05-4 libtinfo6_6.6+20251231-1+b1 libtool_2.5.4-11 libtsan2_16.1.0-2 libtss2-esys-3.0.2-0t64_4.1.3-6 libtss2-mu-4.0.1-0t64_4.1.3-6 libtss2-rc0t64_4.1.3-6 libtss2-sys1t64_4.1.3-6 libtss2-tcti-cmd0t64_4.1.3-6 libtss2-tcti-device0t64_4.1.3-6 libtss2-tcti-mssim0t64_4.1.3-6 libtss2-tcti-swtpm0t64_4.1.3-6 libubsan1_16.1.0-2 libucc1_1.8.0-2 libuchardet0_0.0.8-2+b2 libucx0_1.21.0-1 libudev1_261.1-2 libunistring5_1.4.2-1 libuuid1_2.42.2-1 libx11-6_2:1.8.13-1 libx11-data_2:1.8.13-1 libxau6_1:1.0.11-1+b2 libxcb1_1.17.0-2+b2 libxdmcp6_1:1.1.5-2+b1 libxext6_2:1.3.4-1+b4 libxml2-16_2.15.3+dfsg-1 libxnvctrl0_535.171.04-1+b3 libxxhash0_0.8.3-2+b2 libz3-4_4.13.3-1.1 libze1_1.28.2-2 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.0.13-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 mount_2.42.2-1 mpi-default-dev_1.20 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1+b1 ocl-icd-libopencl1_2.3.4-1+b1 openmpi-bin_5.0.10-1 openmpi-common_5.0.10-1 openssh-client_1:10.3p1-5 openssl-provider-legacy_3.6.3-1 patch_2.8-2 perl_5.44.0~rc1-1 perl-base_5.44.0~rc1-1 perl-modules-5.40_5.40.1-8 perl-modules-5.44_5.44.0~rc1-1 pinentry-curses_1.3.2-4 po-debconf_1.0.22 readline-common_8.3-4 rpcsvc-proto_1.4.4-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.4.0-1 systemd_261.1-2 systemd-tpm_261.1-2 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 tpm-udev_4.1.3-6 util-linux_2.42.2-1 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Mon, 29 Jun 2026 09:38:36 +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: 1.68.6-17 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Standards-Version: 4.7.3 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 3d5008d7337a8e8621423aaf77148dc79d07f501 12264 murasaki_1.68.6-17.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 d4bf5115156f51f6e49822b76436aa7a565e496fb8b499da21f01434a424ad81 12264 murasaki_1.68.6-17.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 430c2ccacdf0858a3503e87a8a6993c6 12264 murasaki_1.68.6-17.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmmZ8ccRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFxEhAAjPfwConF7MlP+djvAhLkKoRovI8MOj1V 60K5X3bNbvpAS692TON8NrkUPqZknVgoHk8VHK45oWPMqRpBU48nSZ2NTnefq0a/ vsJwEErHIJJ4k+cyvl8/hCLP4ls6Z20NgoRo1HQa2PT0siRgCdqw+fiwL6mETfkS MmZhUvke74L3JmjVdHZOOfvWRhWp4lRwfRDjRj8STqSpS8+2+ZhcTE2PqhMkz1ii 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dpkg-source: info: extracting murasaki in /build/murasaki-rAzmfo/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_1.68.6-17.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 dpkg-source: info: applying buildflags.patch dpkg-source: info: applying libboost1.90.patch clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Time Build Commands Mon, 29 Jun 2026 09:38:38 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network murasaki_1.68.6-17 perl-5.44-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network murasaki_1.68.6-17 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/murasaki-rAzmfo/murasaki-1.68.6 SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-1c7693c4-56d5-4b2d-9aa1-748fa59aa4d1 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 1.68.6-17 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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-rAzmfo/murasaki-1.68.6' rm -rf *.o *~ .*~ core make -C src clean make[2]: Entering directory '/build/murasaki-rAzmfo/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-rAzmfo/murasaki-1.68.6/src' make[1]: Leaving directory '/build/murasaki-rAzmfo/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_1.68.6-17.debian.tar.xz dpkg-source: info: building murasaki in ../murasaki_1.68.6-17.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-rAzmfo/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-rAzmfo/murasaki-1.68.6' make -C src all make[3]: Entering directory '/build/murasaki-rAzmfo/murasaki-1.68.6/src' mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | 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:24, from /usr/include/boost/regex/v5/regex.hpp:29, from /usr/include/boost/regex.hpp:31, 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:134:12: note: declared here 134 | 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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | 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:24, from /usr/include/boost/regex/v5/regex.hpp:29, from /usr/include/boost/regex.hpp:31, 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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | 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:134:12: note: declared here 134 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | 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:134:12: note: declared here 134 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | 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:134:12: note: declared here 134 | 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:134:12: note: declared here 134 | 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:134:12: note: declared here 134 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr.cc cgr.cc: In member function ‘void Cgr::merge(Cgr&)’: cgr.cc:140:7: warning: variable ‘redist’ set but not used [-Wunused-but-set-variable] 140 | int redist=(unsigned long)(rez*rez)<=seedcount; | ^~~~~~ cgr.cc: In member function ‘bool Cgr::savePNG(std::string)’: cgr.cc:288:7: warning: variable ‘res’ set but not used [-Wunused-but-set-variable] 288 | int res; | ^~~ cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::string)’: cgr.cc:435:7: warning: variable ‘wordwidth’ set but not used [-Wunused-but-set-variable] 435 | int wordwidth=1; | ^~~~~~~~~ cgr.cc: In member function ‘std::pair Cgr::sampleHighLow(double, double)’: cgr.cc:339:10: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 339 | delete alt; | ^~~ cgr.cc:330:24: note: returned from ‘void* operator new [](std::size_t)’ 330 | pix *alt=new pix[size]; | ^ cgr.cc: In member function ‘std::pair Cgr::sampleHighLow(int, int)’: cgr.cc:354:10: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 354 | delete alt; | ^~~ cgr.cc:345:24: note: returned from ‘void* operator new [](std::size_t)’ 345 | pix *alt=new pix[size]; | ^ cgr.cc: In member function ‘std::pair Cgr::findNiceRange()’: cgr.cc:395:10: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 395 | delete alt; | ^~~ cgr.cc:376:24: note: returned from ‘void* operator new [](std::size_t)’ 376 | pix *alt=new pix[size]; | ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-compare.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c getsegments.cc align-coverage.cc: In function ‘int main(int, char**)’: align-coverage.cc:148:10: warning: variable ‘seqStats’ set but not used [-Wunused-but-set-variable] 148 | bool seqStats=true; | ^~~~~~~~ getsegments.cc: In function ‘size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::string)’: getsegments.cc:153:29: warning: catching polymorphic type ‘class boost::bad_lexical_cast’ by value [-Wcatch-value=] 153 | }catch(bad_lexical_cast e){ | ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c mbfa.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/murasaki-rAzmfo/murasaki-1.68.6/src' make[2]: Leaving directory '/build/murasaki-rAzmfo/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-rAzmfo/murasaki-1.68.6' rm -rf *.o *~ .*~ core make -C src clean make[3]: Entering directory '/build/murasaki-rAzmfo/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-rAzmfo/murasaki-1.68.6/src' make[2]: Leaving directory '/build/murasaki-rAzmfo/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-rAzmfo/murasaki-1.68.6' make -C src all make[3]: Entering directory '/build/murasaki-rAzmfo/murasaki-1.68.6/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c murasaki.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c timing.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | 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:24, from /usr/include/boost/regex/v5/regex.hpp:29, from /usr/include/boost/regex.hpp:31, 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:134:12: note: declared here 134 | 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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | 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:24, from /usr/include/boost/regex/v5/regex.hpp:29, from /usr/include/boost/regex.hpp:31, 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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c msethash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | 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:134:12: note: declared here 134 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | 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:134:12: note: declared here 134 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c murasaki_mpi.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c arrayhash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c genopts.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c cgr-image.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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]; | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c cgr-compare.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c cgr-random.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c testeco.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:134:12: note: declared here 134 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c alignments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c align-or.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c geneparse.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c align-and.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c align-best.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c align-coverage.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c getsegments.cc align-coverage.cc: In function ‘int main(int, char**)’: align-coverage.cc:148:10: warning: variable ‘seqStats’ set but not used [-Wunused-but-set-variable] 148 | bool seqStats=true; | ^~~~~~~~ getsegments.cc: In function ‘size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::string)’: getsegments.cc:153:29: warning: catching polymorphic type ‘class boost::bad_lexical_cast’ by value [-Wcatch-value=] 153 | }catch(bad_lexical_cast e){ | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c mbfa.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/murasaki-rAzmfo/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/murasaki-rAzmfo/murasaki-1.68.6/src' make[2]: Leaving directory '/build/murasaki-rAzmfo/murasaki-1.68.6' make[1]: Leaving directory '/build/murasaki-rAzmfo/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-rAzmfo/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-rAzmfo/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-rAzmfo/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-rAzmfo/murasaki-1.68.6' debian/rules override_dh_installman-indep make[1]: Entering directory '/build/murasaki-rAzmfo/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-rAzmfo/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-rAzmfo/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-rAzmfo/murasaki-1.68.6' dh_fixperms -Nmurasaki-common dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package murasaki-common: substitution variable ${misc:perl} used, but is not defined dpkg-gencontrol: warning: package murasaki-common: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-17_amd64.deb'. dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-17_amd64.deb'. dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-17_amd64.deb'. dpkg-deb: building package 'murasaki-common' in '../murasaki-common_1.68.6-17_all.deb'. dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-17_amd64.deb'. dpkg-genbuildinfo -O../murasaki_1.68.6-17_amd64.buildinfo dpkg-genchanges -O../murasaki_1.68.6-17_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 2026-06-29T09:43:12Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 29 Jun 2026 09:43:12 +0000 | +------------------------------------------------------------------------------+ murasaki_1.68.6-17_amd64.changes: --------------------------------- Format: 1.8 Date: Sat, 21 Feb 2026 18:48:42 +0100 Source: murasaki Binary: murasaki murasaki-common murasaki-dbgsym murasaki-mpi murasaki-mpi-dbgsym Architecture: source all amd64 Version: 1.68.6-17 Distribution: perl-5.44-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: murasaki - homology detection tool across multiple large genomes murasaki-common - homology detection tool across multiple large genomes (common fil murasaki-mpi - homology detection tool across multiple large genomes (MPI-versio Closes: 1128133 Changes: murasaki (1.68.6-17) unstable; urgency=medium . * Port to boost 1.90 Closes: #1128133 * d/watch: version=5 * Standards-Version: 4.7.3 (routine-update) * Remove Priority field to comply with Debian Policy 4.7.3 (routine- update) Checksums-Sha1: baf63ad8c78d38ea5d7b4385af853b823a3e9482 1848 murasaki_1.68.6-17.dsc 3d5008d7337a8e8621423aaf77148dc79d07f501 12264 murasaki_1.68.6-17.debian.tar.xz 200f21a167599acfd70fac1159f90f6e4e09c54e 118396 murasaki-common_1.68.6-17_all.deb b82ecf91300f9ddb9244b29d91c54207f4d2bd53 15647292 murasaki-dbgsym_1.68.6-17_amd64.deb b048cf252087e7e1c74352891bf8b7bfce40a717 16277308 murasaki-mpi-dbgsym_1.68.6-17_amd64.deb 16ebcd316b9fc040ada0b44f8b3b58676a6d3d8d 674080 murasaki-mpi_1.68.6-17_amd64.deb d274daf17ee0b41c8f80e62dd92d727150644f60 9562 murasaki_1.68.6-17_amd64.buildinfo c6e03f0a3c9824f5f69d9d6d0ae8801cb9ad8a9f 626724 murasaki_1.68.6-17_amd64.deb 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murasaki_1.68.6-17.debian.tar.xz cdd840d99628d226e31d665303211c5c 118396 science optional murasaki-common_1.68.6-17_all.deb 9e20d8ab814c46da8c5fe0992b014c42 15647292 debug optional murasaki-dbgsym_1.68.6-17_amd64.deb d23e78176f54f3b2b7e1fe936b1a33a9 16277308 debug optional murasaki-mpi-dbgsym_1.68.6-17_amd64.deb 148f19e43b87d55df9cb8a9d5d813860 674080 science optional murasaki-mpi_1.68.6-17_amd64.deb d7dd8911d62053362ec75ef99fa5f0c2 9562 science optional murasaki_1.68.6-17_amd64.buildinfo 292035ae23c6b5d7bcb7660edb1828f1 626724 science optional murasaki_1.68.6-17_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Mon, 29 Jun 2026 09:43:12 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: murasaki Binary: murasaki murasaki-common murasaki-dbgsym murasaki-mpi murasaki-mpi-dbgsym Architecture: all amd64 source Version: 1.68.6-17 Checksums-Md5: 50721804b28d51e6df871c4fd82bd877 1848 murasaki_1.68.6-17.dsc cdd840d99628d226e31d665303211c5c 118396 murasaki-common_1.68.6-17_all.deb 9e20d8ab814c46da8c5fe0992b014c42 15647292 murasaki-dbgsym_1.68.6-17_amd64.deb d23e78176f54f3b2b7e1fe936b1a33a9 16277308 murasaki-mpi-dbgsym_1.68.6-17_amd64.deb 148f19e43b87d55df9cb8a9d5d813860 674080 murasaki-mpi_1.68.6-17_amd64.deb 292035ae23c6b5d7bcb7660edb1828f1 626724 murasaki_1.68.6-17_amd64.deb Checksums-Sha1: baf63ad8c78d38ea5d7b4385af853b823a3e9482 1848 murasaki_1.68.6-17.dsc 200f21a167599acfd70fac1159f90f6e4e09c54e 118396 murasaki-common_1.68.6-17_all.deb b82ecf91300f9ddb9244b29d91c54207f4d2bd53 15647292 murasaki-dbgsym_1.68.6-17_amd64.deb b048cf252087e7e1c74352891bf8b7bfce40a717 16277308 murasaki-mpi-dbgsym_1.68.6-17_amd64.deb 16ebcd316b9fc040ada0b44f8b3b58676a6d3d8d 674080 murasaki-mpi_1.68.6-17_amd64.deb c6e03f0a3c9824f5f69d9d6d0ae8801cb9ad8a9f 626724 murasaki_1.68.6-17_amd64.deb Checksums-Sha256: 7aa6217202903d2b6552a92b0ad839c2d69ffbb8c29f8e9e4d43fc7f11e2f4ce 1848 murasaki_1.68.6-17.dsc 1b34991a0f3a6c36cfd2a538ccb91a0a3477ee3d1ccf7e02443ada4107e7d5f9 118396 murasaki-common_1.68.6-17_all.deb 80ff76138fbc0809ec696aeeb03ebb9ab320686297a04342fc199c3fdad0292d 15647292 murasaki-dbgsym_1.68.6-17_amd64.deb 70cde5529bdd0b85fabb2ab9a48dae9711fd38c1ee28212b689a0ed2a4dc1976 16277308 murasaki-mpi-dbgsym_1.68.6-17_amd64.deb e01e9e624c3e8c10014d7eb5703d6148bb7d6d91e915dfc47d7a6ca9d9eb98e7 674080 murasaki-mpi_1.68.6-17_amd64.deb 2b4bf68440a77171e4f6e0d485919f6f1398b5ade820b31d2b28f27c5af86fe0 626724 murasaki_1.68.6-17_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 29 Jun 2026 09:43:11 +0000 Build-Path: /build/murasaki-rAzmfo/murasaki-1.68.6 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.18.1-4), autopoint (= 1.0-1), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-3), binutils (= 2.46.50.20260617-1), binutils-common (= 2.46.50.20260617-1), binutils-x86-64-linux-gnu (= 2.46.50.20260617-1), bsdextrautils (= 2.42.2-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-15 (= 15.3.0-1), cpp-15-x86-64-linux-gnu (= 15.3.0-1), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.2), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.47-4), findutils (= 4.10.0-4), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.3.0-1), g++-15-x86-64-linux-gnu (= 15.3.0-1), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-15 (= 15.3.0-1), gcc-15-base (= 15.3.0-1), gcc-15-x86-64-linux-gnu (= 15.3.0-1), gcc-16-base (= 16.1.0-2), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gettext (= 1.0-1), gettext-base (= 1.0-1), gfortran-15 (= 15.3.0-1), gfortran-15-x86-64-linux-gnu (= 15.3.0-1), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.13-1), hostname (= 3.25), ibverbs-providers (= 63.0-1.1+b3), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-3), libamd-comgr3 (= 7.0.2+dfsg-3), libamdhip64-6 (= 6.4.3-5), libarchive-zip-perl (= 1.68-1), libasan8 (= 16.1.0-2), libatomic1 (= 16.1.0-2), libattr1 (= 1:2.5.2-4), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46.50.20260617-1), libblkid1 (= 2.42.2-1), libboost-atomic1.90-dev (= 1.90.0-6), libboost-atomic1.90.0 (= 1.90.0-6), libboost-filesystem-dev (= 1.90.0.2), libboost-filesystem1.90-dev (= 1.90.0-6), libboost-filesystem1.90.0 (= 1.90.0-6), libboost-iostreams-dev (= 1.90.0.2), libboost-iostreams1.90-dev (= 1.90.0-6), libboost-iostreams1.90.0 (= 1.90.0-6), libboost-random1.90-dev (= 1.90.0-6), libboost-random1.90.0 (= 1.90.0-6), libboost-regex-dev (= 1.90.0.2), libboost-regex1.90-dev (= 1.90.0-6), libboost-regex1.90.0 (= 1.90.0-6), libboost1.90-dev (= 1.90.0-6), libbsd0 (= 0.12.2-3), libbz2-1.0 (= 1.0.8-6+b2), libc-bin (= 2.42-17), libc-dev-bin (= 2.42-17), libc-gconv-modules-extra (= 2.42-17), libc6 (= 2.42-17), libc6-dev (= 2.42-17), libcap-ng0 (= 0.9.3-1), libcbor0.10 (= 0.10.2-2.1+b1), libcc1-0 (= 16.1.0-2), libclang-common-21-dev (= 1:21.1.8-7+b4), libcom-err2 (= 1.47.4-1), libcrypt1 (= 1:4.5.1-1+b1), libcrypto++-dev (= 8.9.0-2+b2), libcrypto++8t64 (= 8.9.0-2+b2), libctf-nobfd0 (= 2.46.50.20260617-1), libctf0 (= 2.46.50.20260617-1), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.2), libdpkg-perl (= 1.23.7), libdrm-amdgpu1 (= 2.4.134-2), libdrm-common (= 2.4.134-2), libdrm2 (= 2.4.134-2), libedit2 (= 3.1-20260512-1), libelf1t64 (= 0.195-1), libevent-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-core-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-dev (= 2.1.12-stable-10+b2), libevent-extra-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-openssl-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-pthreads-2.1-7t64 (= 2.1.12-stable-10+b2), libfabric1 (= 2.1.0-1.1+b2), libffi8 (= 3.5.2-4), libfido2-1 (= 1.17.0-1), libfile-stripnondeterminism-perl (= 1.15.1-1), libfuse3-4 (= 3.18.2-2), libgcc-15-dev (= 15.3.0-1), libgcc-s1 (= 16.1.0-2), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgfortran-15-dev (= 15.3.0-1), libgfortran5 (= 16.1.0-2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgomp1 (= 16.1.0-2), libgprofng0 (= 2.46.50.20260617-1), libgssapi-krb5-2 (= 1.22.1-3), libhsa-runtime64-1 (= 6.4.3+dfsg-5), libhwasan0 (= 16.1.0-2), libhwloc-dev (= 2.14.0-2), libhwloc-plugins (= 2.14.0-2), libhwloc15 (= 2.14.0-2), libibmad5 (= 63.0-1.1+b3), libibumad3 (= 63.0-1.1+b3), libibverbs-dev (= 63.0-1.1+b3), libibverbs1 (= 63.0-1.1+b3), libisl23 (= 0.27-2), libitm1 (= 16.1.0-2), libjansson4 (= 2.15.0-1), libjs-jquery (= 3.7.1+dfsg+~3.5.33-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libk5crypto3 (= 1.22.1-3), libkeyutils1 (= 1.6.3-6+b2), libkrb5-3 (= 1.22.1-3), libkrb5support0 (= 1.22.1-3), libllvm21 (= 1:21.1.8-7+b4), liblsan0 (= 16.1.0-2), libltdl-dev (= 2.5.4-11), libltdl7 (= 2.5.4-11), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libmount1 (= 2.42.2-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libmunge2 (= 0.5.18-1), libnl-3-200 (= 3.12.0-2+b1), libnl-3-dev (= 3.12.0-2+b1), libnl-route-3-200 (= 3.12.0-2+b1), libnl-route-3-dev (= 3.12.0-2+b1), libnuma-dev (= 2.0.19-1+b2), libnuma1 (= 2.0.19-1+b2), libopenmpi-dev (= 5.0.10-1), libopenmpi40 (= 5.0.10-1), libpam-modules (= 1.7.0-6), libpam-modules-bin (= 1.7.0-6), libpam-runtime (= 1.7.0-6), libpam0g (= 1.7.0-6), libpciaccess0 (= 0.17-3+b4), libpcre2-8-0 (= 10.46-1+b2), libperl5.44 (= 5.44.0~rc1-1), libpipeline1 (= 1.5.8-3), libpmix2t64 (= 6.0.0+really5.0.9-3+b2), libprrte-bin (= 3.0.13-3), libprrte-dev (= 3.0.13-3), libprrte3 (= 3.0.13-3), libpsm2-2 (= 11.2.185-2.1), libpstreams-dev (= 1.0.4-2), libquadmath0 (= 16.1.0-2), librdmacm1t64 (= 63.0-1.1+b3), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.10-1), libsframe3 (= 2.46.50.20260617-1), libsmartcols1 (= 2.42.2-1), libssl3t64 (= 3.6.3-1), libstdc++-15-dev (= 15.3.0-1), libstdc++6 (= 16.1.0-2), libsystemd-shared (= 261.1-2), libsystemd0 (= 261.1-2), libterm-readkey-perl (= 2.38-2+b5), libtext-wrapper-perl (= 1.05-4), libtinfo6 (= 6.6+20251231-1+b1), libtool (= 2.5.4-11), libtsan2 (= 16.1.0-2), libtss2-esys-3.0.2-0t64 (= 4.1.3-6), libtss2-mu-4.0.1-0t64 (= 4.1.3-6), libtss2-rc0t64 (= 4.1.3-6), libtss2-sys1t64 (= 4.1.3-6), libtss2-tcti-cmd0t64 (= 4.1.3-6), libtss2-tcti-device0t64 (= 4.1.3-6), libtss2-tcti-mssim0t64 (= 4.1.3-6), libtss2-tcti-swtpm0t64 (= 4.1.3-6), libubsan1 (= 16.1.0-2), libucc1 (= 1.8.0-2), libuchardet0 (= 0.0.8-2+b2), libucx0 (= 1.21.0-1), libudev1 (= 261.1-2), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.2-1), libx11-6 (= 2:1.8.13-1), libx11-data (= 2:1.8.13-1), libxau6 (= 1:1.0.11-1+b2), libxcb1 (= 1.17.0-2+b2), libxdmcp6 (= 1:1.1.5-2+b1), libxext6 (= 2:1.3.4-1+b4), libxml2-16 (= 2.15.3+dfsg-1), libxnvctrl0 (= 535.171.04-1+b3), libz3-4 (= 4.13.3-1.1), libze1 (= 1.28.2-2), libzstd1 (= 1.5.7+dfsg-3+b2), linux-libc-dev (= 7.0.13-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), mount (= 2.42.2-1), mpi-default-dev (= 1.20), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1+b1), ocl-icd-libopencl1 (= 2.3.4-1+b1), openmpi-bin (= 5.0.10-1), openmpi-common (= 5.0.10-1), openssh-client (= 1:10.3p1-5), openssl-provider-legacy (= 3.6.3-1), patch (= 2.8-2), perl (= 5.44.0~rc1-1), perl-base (= 5.44.0~rc1-1), perl-modules-5.44 (= 5.44.0~rc1-1), po-debconf (= 1.0.22), rpcsvc-proto (= 1.4.4-1), sed (= 4.9-3), sensible-utils (= 0.0.26), systemd (= 261.1-2), systemd-tpm (= 261.1-2), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), tpm-udev (= 4.1.3-6), util-linux (= 2.42.2-1), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1771696122" +------------------------------------------------------------------------------+ | Package contents Mon, 29 Jun 2026 09:43:13 +0000 | +------------------------------------------------------------------------------+ murasaki-common_1.68.6-17_all.deb --------------------------------- new Debian package, version 2.0. size 118396 bytes: control archive=3232 bytes. 1285 bytes, 28 lines control 6185 bytes, 85 lines md5sums Package: murasaki-common Source: murasaki Version: 1.68.6-17 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 412 Depends: gnuplot-nox | gnuplot, 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 2026-02-21 17:48 ./ drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/ drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/lib/ drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/lib/debian-med/ drwxr-xr-x root/root 0 2026-02-21 17:48 ./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 2026-02-21 17:48 ./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 2026-02-21 17:48 ./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 2026-02-21 17:48 ./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 2026-02-21 17:48 ./usr/lib/debian-med/bin/substitch.pl drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/share/ drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/share/doc/murasaki-common/ -rw-r--r-- root/root 238 2026-02-21 17:48 ./usr/share/doc/murasaki-common/README.Debian -rw-r--r-- root/root 909 2026-02-21 17:48 ./usr/share/doc/murasaki-common/changelog.Debian.gz -rw-r--r-- root/root 2421 2026-02-21 17:48 ./usr/share/doc/murasaki-common/copyright drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/share/lintian/ drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 70 2026-02-21 17:48 ./usr/share/lintian/overrides/murasaki-common drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/share/man/ drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/share/man/man1/ -rw-r--r-- root/root 1047 2026-02-21 17:48 ./usr/share/man/man1/align2kog.pl.1.gz -rw-r--r-- root/root 1029 2026-02-21 17:48 ./usr/share/man/man1/analyze-pat.pl.1.gz -rw-r--r-- root/root 1268 2026-02-21 17:48 ./usr/share/man/man1/chromostitch.pl.1.gz -rw-r--r-- root/root 1108 2026-02-21 17:48 ./usr/share/man/man1/faformat.pl.1.gz -rw-r--r-- root/root 3109 2026-02-21 17:48 ./usr/share/man/man1/filter.pl.1.gz -rw-r--r-- root/root 1100 2026-02-21 17:48 ./usr/share/man/man1/gatherstats.pl.1.gz -rw-r--r-- root/root 1808 2026-02-21 17:48 ./usr/share/man/man1/getcds.pl.1.gz -rw-r--r-- root/root 1040 2026-02-21 17:48 ./usr/share/man/man1/getgene.pl.1.gz -rw-r--r-- root/root 1100 2026-02-21 17:48 ./usr/share/man/man1/histocomp.pl.1.gz -rw-r--r-- root/root 1480 2026-02-21 17:48 ./usr/share/man/man1/histoplot.pl.1.gz -rw-r--r-- root/root 1096 2026-02-21 17:48 ./usr/share/man/man1/homology-score.pl.1.gz -rw-r--r-- root/root 1063 2026-02-21 17:48 ./usr/share/man/man1/interpolate.pl.1.gz -rw-r--r-- root/root 1026 2026-02-21 17:48 ./usr/share/man/man1/kogalign.pl.1.gz -rw-r--r-- root/root 1208 2026-02-21 17:48 ./usr/share/man/man1/lav2murasaki.pl.1.gz -rw-r--r-- root/root 1357 2026-02-21 17:48 ./usr/share/man/man1/maf2anchors.pl.1.gz -rw-r--r-- root/root 998 2026-02-21 17:48 ./usr/share/man/man1/mauve2anchors.pl.1.gz -rw-r--r-- root/root 1112 2026-02-21 17:48 ./usr/share/man/man1/mauveAlignment2anchors.pl.1.gz -rw-r--r-- root/root 1019 2026-02-21 17:48 ./usr/share/man/man1/mbgd-to-kog.pl.1.gz -rw-r--r-- root/root 951 2026-02-21 17:48 ./usr/share/man/man1/mfasplit.pl.1.gz -rw-r--r-- root/root 1134 2026-02-21 17:48 ./usr/share/man/man1/names2kog.pl.1.gz -rw-r--r-- root/root 1228 2026-02-21 17:48 ./usr/share/man/man1/overlay.pl.1.gz -rw-r--r-- root/root 997 2026-02-21 17:48 ./usr/share/man/man1/phAlignment2anchors.pl.1.gz -rw-r--r-- root/root 1408 2026-02-21 17:48 ./usr/share/man/man1/qlob.pl.1.gz -rw-r--r-- root/root 1031 2026-02-21 17:48 ./usr/share/man/man1/rearrange.pl.1.gz -rw-r--r-- root/root 974 2026-02-21 17:48 ./usr/share/man/man1/repeats2anchors.pl.1.gz -rw-r--r-- root/root 1596 2026-02-21 17:48 ./usr/share/man/man1/repeatviz.pl.1.gz -rw-r--r-- root/root 1478 2026-02-21 17:48 ./usr/share/man/man1/roc-at-cutoff.pl.1.gz -rw-r--r-- root/root 1152 2026-02-21 17:48 ./usr/share/man/man1/simpal.pl.1.gz -rw-r--r-- root/root 1427 2026-02-21 17:48 ./usr/share/man/man1/simplegraph.pl.1.gz -rw-r--r-- root/root 1373 2026-02-21 17:48 ./usr/share/man/man1/stat-histo.pl.1.gz -rw-r--r-- root/root 1465 2026-02-21 17:48 ./usr/share/man/man1/stat-vs-stat.pl.1.gz -rw-r--r-- root/root 1510 2026-02-21 17:48 ./usr/share/man/man1/substitch.pl.1.gz drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/share/perl5/ drwxr-xr-x root/root 0 2026-02-21 17:48 ./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 2026-02-21 17:48 ./usr/share/perl5/murasaki/config.pl murasaki-dbgsym_1.68.6-17_amd64.deb ----------------------------------- new Debian package, version 2.0. size 15647292 bytes: control archive=1192 bytes. 872 bytes, 12 lines control 1463 bytes, 14 lines md5sums Package: murasaki-dbgsym Source: murasaki Version: 1.68.6-17 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 17280 Depends: murasaki (= 1.68.6-17) Section: debug Priority: optional Description: debug symbols for murasaki Build-Ids: 16553c337249caa462e8a6303a98b1ed8ec931bb 1827bc60fa3e3e8fc2cef6a3ddac4730a9f439c1 24f5076e903109f2f9e989642f9cfdb63f83ec5c 2b5d6decccdcbc420723171a297a1294378b0644 444b066ff8ac57bb7a25803a857d6882250d05a3 58537e0cab216efea766ffd65c38578d51b325d3 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./usr/lib/debug/.build-id/c6/8f5a53a54db15d8f322a360f9bd8df464497d7.debug drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/lib/debug/.build-id/d8/ -rw-r--r-- root/root 1256784 2026-02-21 17:48 ./usr/lib/debug/.build-id/d8/da50cfc2f4331ce5f018827a6fae4bb187a4d6.debug drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/lib/debug/.build-id/f2/ -rw-r--r-- root/root 192496 2026-02-21 17:48 ./usr/lib/debug/.build-id/f2/96faba8c1d02efcb030a7a46ff83bc9c8bf81f.debug drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 860760 2026-02-21 17:48 ./usr/lib/debug/.dwz/x86_64-linux-gnu/murasaki-mpi.debug drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/share/ drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-02-21 17:48 ./usr/share/doc/murasaki-mpi-dbgsym -> murasaki-mpi murasaki-mpi_1.68.6-17_amd64.deb -------------------------------- new Debian package, version 2.0. size 674080 bytes: control archive=1592 bytes. 1355 bytes, 28 lines control 1326 bytes, 20 lines md5sums Package: murasaki-mpi Source: murasaki Version: 1.68.6-17 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 4370 Depends: murasaki-common, libboost-filesystem1.90.0 (>= 1.90.0), libboost-iostreams1.90.0 (>= 1.90.0), libc6 (>= 2.38), libgcc-s1 (>= 3.0), libopenmpi40 (>= 5.0.10), 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 2026-02-21 17:48 ./ drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/ drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/bin/ -rwxr-xr-x root/root 360952 2026-02-21 17:48 ./usr/bin/geneparse-mpi -rwxr-xr-x root/root 401784 2026-02-21 17:48 ./usr/bin/mbfa-mpi -rwxr-xr-x root/root 892040 2026-02-21 17:48 ./usr/bin/murasaki-mpi drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/lib/ drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/lib/murasaki/ -rwxr-xr-x root/root 299304 2026-02-21 17:48 ./usr/lib/murasaki/align-and-mpi -rwxr-xr-x root/root 307528 2026-02-21 17:48 ./usr/lib/murasaki/align-best-mpi -rwxr-xr-x root/root 344928 2026-02-21 17:48 ./usr/lib/murasaki/align-compare-mpi -rwxr-xr-x root/root 451432 2026-02-21 17:48 ./usr/lib/murasaki/align-coverage-mpi -rwxr-xr-x root/root 295176 2026-02-21 17:48 ./usr/lib/murasaki/align-or-mpi -rwxr-xr-x root/root 92728 2026-02-21 17:48 ./usr/lib/murasaki/cgr-compare-mpi -rwxr-xr-x root/root 414168 2026-02-21 17:48 ./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 2026-02-21 17:48 ./usr/lib/murasaki/cgr-random-mpi -rwxr-xr-x root/root 401832 2026-02-21 17:48 ./usr/lib/murasaki/cgr-sample-mpi -rwxr-xr-x root/root 59808 2026-02-21 17:48 ./usr/lib/murasaki/testeco-mpi drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/share/ drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/share/doc/murasaki-mpi/ -rw-r--r-- root/root 249 2026-02-21 17:48 ./usr/share/doc/murasaki-mpi/README.test -rw-r--r-- root/root 908 2026-02-21 17:48 ./usr/share/doc/murasaki-mpi/changelog.Debian.gz -rw-r--r-- root/root 2421 2026-02-21 17:48 ./usr/share/doc/murasaki-mpi/copyright drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/share/man/ drwxr-xr-x root/root 0 2026-02-21 17:48 ./usr/share/man/man1/ -rw-r--r-- root/root 2518 2026-02-21 17:48 ./usr/share/man/man1/geneparse-mpi.1.gz -rw-r--r-- root/root 2721 2026-02-21 17:48 ./usr/share/man/man1/mbfa-mpi.1.gz -rw-r--r-- root/root 10888 2026-02-21 17:48 ./usr/share/man/man1/murasaki-mpi.1.gz murasaki_1.68.6-17_amd64.deb ---------------------------- new Debian package, version 2.0. size 626724 bytes: control archive=1440 bytes. 1124 bytes, 23 lines control 1182 bytes, 19 lines md5sums Package: murasaki Version: 1.68.6-17 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 4247 Depends: murasaki-common, libboost-filesystem1.90.0 (>= 1.90.0), libboost-iostreams1.90.0 (>= 1.90.0), 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. 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