sbuild (Debian sbuild) 0.85.9 (29 May 2024) on carme.larted.org.uk +==============================================================================+ | murasaki 1.68.6-13 (amd64) Tue, 04 Jun 2024 17:08:28 +0000 | +==============================================================================+ Package: murasaki Version: 1.68.6-13 Source Version: 1.68.6-13 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-52c29e56-b732-4e55-94fb-651bcb6454d6' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup murasaki_1.68.6-13 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup murasaki_1.68.6-13 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/murasaki-R5PXpj/resolver-3xXYiS' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Get:2 http://localhost:3142/debian unstable InRelease [198 kB] Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Get:3 http://localhost:3142/debian sid InRelease [198 kB] Get:4 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:5 http://localhost:3142/debian unstable/main amd64 Packages T-2024-06-04-1405.10-F-2024-06-03-0205.12.pdiff [81.5 kB] Get:6 file:/srv/reprepro perl-5.40/main amd64 Packages [598 kB] Get:5 http://localhost:3142/debian unstable/main amd64 Packages T-2024-06-04-1405.10-F-2024-06-03-0205.12.pdiff [81.5 kB] Get:7 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2024-06-04-1405.10-F-2024-06-03-0205.12.pdiff [53.9 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2024-06-04-1405.10-F-2024-06-03-0205.12.pdiff [53.9 kB] Fetched 659 kB in 2s (285 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bsdutils libblkid1 libmount1 libsmartcols1 libuuid1 login passwd util-linux 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3414 kB of archives. After this operation, 57.3 kB disk space will be freed. Get:1 http://localhost:3142/debian unstable/main amd64 bsdutils amd64 1:2.40.1-8 [104 kB] Get:2 http://localhost:3142/debian unstable/main amd64 login amd64 1:4.13+dfsg1-5 [590 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libsmartcols1 amd64 2.40.1-8 [137 kB] Get:4 http://localhost:3142/debian unstable/main amd64 libuuid1 amd64 2.40.1-8 [34.7 kB] Get:5 http://localhost:3142/debian unstable/main amd64 libblkid1 amd64 2.40.1-8 [166 kB] Get:6 http://localhost:3142/debian unstable/main amd64 libmount1 amd64 2.40.1-8 [197 kB] Get:7 http://localhost:3142/debian unstable/main amd64 util-linux amd64 2.40.1-8 [1210 kB] Get:8 http://localhost:3142/debian unstable/main amd64 passwd amd64 1:4.13+dfsg1-5 [974 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3414 kB in 0s (103 MB/s) (Reading database ... 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Processing triggers for libc-bin (2.38-12) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/murasaki_1.68.6-13.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/murasaki-R5PXpj/murasaki-1.68.6' with '<>' I: NOTICE: Log filtering will replace 'build/murasaki-R5PXpj' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ 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, libopenmpi-dev, build-essential, fakeroot 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, libopenmpi-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [780 B] Get:5 copy:/<>/apt_archive ./ Packages [812 B] Fetched 2201 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base gfortran-13 gfortran-13-x86-64-linux-gnu groff-base ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libboost-atomic1.83-dev libboost-atomic1.83.0 libboost-filesystem-dev libboost-filesystem1.83-dev libboost-filesystem1.83.0 libboost-iostreams-dev libboost-iostreams1.83-dev libboost-iostreams1.83.0 libboost-regex-dev libboost-regex1.83-dev libboost-regex1.83.0 libboost-system1.83-dev libboost-system1.83.0 libboost1.83-dev libbsd0 libcbor0.10 libcom-err2 libcrypto++-dev libcrypto++8t64 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfakeroot libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu72 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm17t64 libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmunge2 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3t64 libpciaccess0 libpipeline1 libpmix-dev libpmix2t64 libpsm-infinipath1 libpsm2-2 libpstreams-dev librdmacm1t64 libterm-readkey-perl libtext-wrapper-perl libtool libuchardet0 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libz3-4 m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf sensible-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-13-multilib gfortran-13-doc libcoarrays-dev groff libboost1.83-doc libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-graph-parallel1.83-dev libboost-graph1.83-dev libboost-json1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev libboost-numpy1.83-dev libboost-program-options1.83-dev libboost-python1.83-dev libboost-random1.83-dev libboost-serialization1.83-dev libboost-stacktrace1.83-dev libboost-test1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user libhwloc-contrib-plugins icu-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils gcj-jdk m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common krb5-locales libcoarrays-openmpi-dev xauth libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base gfortran-13 gfortran-13-x86-64-linux-gnu groff-base ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libboost-atomic1.83-dev libboost-atomic1.83.0 libboost-filesystem-dev libboost-filesystem1.83-dev libboost-filesystem1.83.0 libboost-iostreams-dev libboost-iostreams1.83-dev libboost-iostreams1.83.0 libboost-regex-dev libboost-regex1.83-dev libboost-regex1.83.0 libboost-system1.83-dev libboost-system1.83.0 libboost1.83-dev libbsd0 libcbor0.10 libcom-err2 libcrypto++-dev libcrypto++8t64 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfakeroot libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu72 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm17t64 libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmunge2 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3t64 libpciaccess0 libpipeline1 libpmix-dev libpmix2t64 libpsm-infinipath1 libpsm2-2 libpstreams-dev librdmacm1t64 libterm-readkey-perl libtext-wrapper-perl libtool libuchardet0 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libz3-4 m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 121 newly installed, 0 to remove and 0 not upgraded. Need to get 131 MB/131 MB of archives. After this operation, 685 MB of additional disk space will be used. 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kB] Get:12 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get:13 http://localhost:3142/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get:14 http://localhost:3142/debian unstable/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB] Get:15 http://localhost:3142/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-1.2 [28.2 kB] Get:16 http://localhost:3142/debian unstable/main amd64 libfido2-1 amd64 1.14.0-1+b2 [77.7 kB] Get:17 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get:18 http://localhost:3142/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:19 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get:20 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:21 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get:22 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get:23 http://localhost:3142/debian unstable/main amd64 openssh-client amd64 1:9.7p1-5 [964 kB] Get:24 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:25 http://localhost:3142/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get:26 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:27 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:28 http://localhost:3142/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get:29 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get:30 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:31 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:32 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:33 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:34 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:35 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get:36 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:37 http://localhost:3142/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:38 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3 [670 kB] Get:39 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get:40 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:41 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:42 http://localhost:3142/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get:43 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.34-1 [28.9 kB] Get:44 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.34-1 [74.0 kB] Get:45 http://localhost:3142/debian unstable/main amd64 libgfortran5 amd64 14.1.0-1 [836 kB] Get:46 http://localhost:3142/debian unstable/main amd64 libgfortran-13-dev amd64 13.2.0-25 [847 kB] Get:47 http://localhost:3142/debian unstable/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-25 [10.6 MB] Get:48 http://localhost:3142/debian unstable/main amd64 gfortran-13 amd64 13.2.0-25 [12.8 kB] Get:49 http://localhost:3142/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get:50 http://localhost:3142/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get:51 http://localhost:3142/debian unstable/main amd64 libibverbs1 amd64 52.0-1 [61.5 kB] Get:52 http://localhost:3142/debian unstable/main amd64 ibverbs-providers amd64 52.0-1 [343 kB] Get:53 http://localhost:3142/debian unstable/main amd64 icu-devtools amd64 72.1-4+b1 [208 kB] Get:54 http://localhost:3142/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get:55 http://localhost:3142/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-12 [23.7 MB] Get:56 http://localhost:3142/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] Get:57 http://localhost:3142/debian unstable/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get:58 http://localhost:3142/debian unstable/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get:59 http://localhost:3142/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get:60 http://localhost:3142/debian unstable/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get:61 http://localhost:3142/debian unstable/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get:62 http://localhost:3142/debian unstable/main amd64 libhsa-runtime64-1 amd64 5.7.1-2 [504 kB] Get:63 http://localhost:3142/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB] Get:64 http://localhost:3142/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-3 [10.6 MB] Get:65 http://localhost:3142/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-3 [233 kB] Get:66 http://localhost:3142/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-3 [235 kB] Get:67 http://localhost:3142/debian unstable/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-3 [280 kB] Get:68 http://localhost:3142/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-3 [230 kB] Get:69 http://localhost:3142/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-3 [231 kB] Get:70 http://localhost:3142/debian unstable/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-3 [295 kB] Get:71 http://localhost:3142/debian unstable/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Get:72 http://localhost:3142/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-3 [324 kB] Get:73 http://localhost:3142/debian unstable/main amd64 libicu-dev amd64 72.1-4+b1 [10.4 MB] Get:74 http://localhost:3142/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-3 [342 kB] Get:75 http://localhost:3142/debian unstable/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-3 [253 kB] Get:76 http://localhost:3142/debian unstable/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-3 [260 kB] Get:77 http://localhost:3142/debian unstable/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get:78 http://localhost:3142/debian unstable/main amd64 libboost-regex-dev amd64 1.83.0.2+b2 [3864 B] Get:79 http://localhost:3142/debian unstable/main amd64 libcrypto++8t64 amd64 8.9.0-1.1 [1159 kB] Get:80 http://localhost:3142/debian unstable/main amd64 libcrypto++-dev amd64 8.9.0-1.1 [1834 kB] Get:81 http://localhost:3142/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [181 kB] Get:82 http://localhost:3142/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10 [131 kB] Get:83 http://localhost:3142/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10 [107 kB] Get:84 http://localhost:3142/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [53.9 kB] Get:85 http://localhost:3142/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10 [60.8 kB] Get:86 http://localhost:3142/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10 [305 kB] Get:87 http://localhost:3142/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get:88 http://localhost:3142/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get:89 http://localhost:3142/debian unstable/main amd64 librdmacm1t64 amd64 52.0-1 [70.1 kB] Get:90 http://localhost:3142/debian unstable/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] Get:91 http://localhost:3142/debian unstable/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB] Get:92 http://localhost:3142/debian unstable/main amd64 libnuma-dev amd64 2.0.18-1 [36.2 kB] Get:93 http://localhost:3142/debian unstable/main amd64 libltdl7 amd64 2.4.7-7+b1 [393 kB] Get:94 http://localhost:3142/debian unstable/main amd64 libltdl-dev amd64 2.4.7-7+b1 [164 kB] Get:95 http://localhost:3142/debian unstable/main amd64 libhwloc-dev amd64 2.10.0-1+b1 [250 kB] Get:96 http://localhost:3142/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get:97 http://localhost:3142/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get:98 http://localhost:3142/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get:99 http://localhost:3142/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get:100 http://localhost:3142/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:101 http://localhost:3142/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get:102 http://localhost:3142/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:103 http://localhost:3142/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] Get:104 http://localhost:3142/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] Get:105 http://localhost:3142/debian unstable/main amd64 libhwloc-plugins amd64 2.10.0-1+b1 [18.0 kB] Get:106 http://localhost:3142/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-0.3 [99.4 kB] Get:107 http://localhost:3142/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-0.3 [199 kB] Get:108 http://localhost:3142/debian unstable/main amd64 libibverbs-dev amd64 52.0-1 [647 kB] Get:109 http://localhost:3142/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:110 http://localhost:3142/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:111 http://localhost:3142/debian unstable/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] Get:112 http://localhost:3142/debian unstable/main amd64 libpmix2t64 amd64 5.0.2-3 [652 kB] Get:113 http://localhost:3142/debian unstable/main amd64 libucx0 amd64 1.16.0+ds-5 [1109 kB] Get:114 http://localhost:3142/debian unstable/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB] Get:115 http://localhost:3142/debian unstable/main amd64 openmpi-common all 4.1.6-13.3 [169 kB] Get:116 http://localhost:3142/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get:117 http://localhost:3142/debian unstable/main amd64 libpmix-dev amd64 5.0.2-3 [3940 kB] Get:118 http://localhost:3142/debian unstable/main amd64 openmpi-bin amd64 4.1.6-13.3 [226 kB] Get:119 http://localhost:3142/debian unstable/main amd64 libopenmpi-dev amd64 4.1.6-13.3 [972 kB] Get:120 http://localhost:3142/debian unstable/main amd64 libpstreams-dev all 1.0.3-1 [134 kB] Get:121 http://localhost:3142/debian unstable/main amd64 libtext-wrapper-perl all 1.05-4 [10.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 131 MB in 6s (22.2 MB/s) Selecting previously unselected package sensible-utils. 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Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up libboost-system1.83-dev:amd64 (1.83.0-3) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libterm-readkey-perl (2.38-2+b4) ... Setting up libfido2-1:amd64 (1.14.0-1+b2) ... Setting up libgfortran-13-dev:amd64 (13.2.0-25) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libicu-dev:amd64 (72.1-4+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libxcb1:amd64 (1.17.0-2) ... 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Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up libnl-3-dev:amd64 (3.7.0-0.3) ... Setting up groff-base (1.23.0-4) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libhwloc-dev:amd64 (2.10.0-1+b1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Setting up libboost-regex-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-filesystem-dev:amd64 (1.83.0.2+b2) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libibverbs1:amd64 (52.0-1) ... Setting up ibverbs-providers:amd64 (52.0-1) ... Setting up libboost-iostreams1.83-dev:amd64 (1.83.0-3) ... Setting up openssh-client (1:9.7p1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libboost-iostreams-dev:amd64 (1.83.0.2+b2) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:amd64 (535.171.04-1) ... 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Setting up openmpi-bin (4.1.6-13.3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (4.1.6-13.3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.38-12) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) amd64 (x86_64) Toolchain package versions: binutils_2.42-4 dpkg-dev_1.22.6 g++-13_13.2.0-25 gcc-13_13.2.0-25 libc6-dev_2.38-12 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 linux-libc-dev_6.8.12-1 Package versions: adduser_3.137 apt_2.9.4 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13.2 base-passwd_3.6.3 bash_5.2.21-2+b1 binutils_2.42-4 binutils-common_2.42-4 binutils-x86-64-linux-gnu_2.42-4 bsdextrautils_2.40.1-8 bsdutils_1:2.40.1-8 build-essential_12.10 bzip2_1.0.8-5.1 coreutils_9.4-3.1 cpp_4:13.2.0-7 cpp-13_13.2.0-25 cpp-13-x86-64-linux-gnu_13.2.0-25 cpp-x86-64-linux-gnu_4:13.2.0-7 dash_0.5.12-8 debconf_1.5.86 debhelper_13.15.3 debian-archive-keyring_2023.4 debianutils_5.17 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-7 dpkg_1.22.6 dpkg-dev_1.22.6 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.34-1 file_1:5.45-3 findutils_4.9.0-6 g++_4:13.2.0-7 g++-13_13.2.0-25 g++-13-x86-64-linux-gnu_13.2.0-25 g++-x86-64-linux-gnu_4:13.2.0-7 gcc_4:13.2.0-7 gcc-13_13.2.0-25 gcc-13-base_13.2.0-25 gcc-13-x86-64-linux-gnu_13.2.0-25 gcc-14-base_14.1.0-1 gcc-x86-64-linux-gnu_4:13.2.0-7 gettext_0.21-14+b1 gettext-base_0.21-14+b1 gfortran-13_13.2.0-25 gfortran-13-x86-64-linux-gnu_13.2.0-25 gnupg_2.2.43-7 gnupg-l10n_2.2.43-7 gnupg-utils_2.2.43-7 gpg_2.2.43-7 gpg-agent_2.2.43-7 gpg-wks-client_2.2.43-7 gpgconf_2.2.43-7 gpgsm_2.2.43-7 gpgv_2.2.43-7 grep_3.11-4 groff-base_1.23.0-4 gzip_1.12-1.1 hostname_3.23+nmu2 ibverbs-providers_52.0-1 icu-devtools_72.1-4+b1 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b1 libamdhip64-5_5.7.1-3 libapt-pkg6.0t64_2.9.4 libarchive-zip-perl_1.68-1 libasan8_14.1.0-1 libassuan0_2.5.6-1+b1 libatomic1_14.1.0-1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libbinutils_2.42-4 libblkid1_2.40.1-8 libboost-atomic1.83-dev_1.83.0-3 libboost-atomic1.83.0_1.83.0-3 libboost-filesystem-dev_1.83.0.2+b2 libboost-filesystem1.83-dev_1.83.0-3 libboost-filesystem1.83.0_1.83.0-3 libboost-iostreams-dev_1.83.0.2+b2 libboost-iostreams1.83-dev_1.83.0-3 libboost-iostreams1.83.0_1.83.0-3 libboost-regex-dev_1.83.0.2+b2 libboost-regex1.83-dev_1.83.0-3 libboost-regex1.83.0_1.83.0-3 libboost-system1.83-dev_1.83.0-3 libboost-system1.83.0_1.83.0-3 libboost1.83-dev_1.83.0-3 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-5.1 libc-bin_2.38-12 libc-dev-bin_2.38-12 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sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 sysvinit-utils_3.09-1 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.1-8 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg+really1.3.1-1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: murasaki Binary: murasaki, murasaki-mpi, murasaki-common Architecture: any all Version: 1.68.6-13 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Nilesh Patra Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/murasaki Vcs-Git: https://salsa.debian.org/med-team/murasaki.git Testsuite: autopkgtest Testsuite-Triggers: libboost-filesystem-dev, libboost-iostreams-dev, libboost-regex-dev, libcrypto++-dev, libopenmpi-dev, libpstreams-dev, libterm-readkey-perl, libtext-wrapper-perl Build-Depends: debhelper-compat (= 13), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev Package-List: murasaki deb science optional arch=any murasaki-common deb science optional arch=all murasaki-mpi deb science optional arch=any Checksums-Sha1: 039363a4ee16888adc629ebbf658ccf2805370bd 3944341 murasaki_1.68.6.orig-debian-tests-data.tar.gz 398a53fe76476ec3c756754d13541dd25d98a58a 307745 murasaki_1.68.6.orig.tar.gz 9faf611f7851b6599d6242b8e05b0896988887fc 11204 murasaki_1.68.6-13.debian.tar.xz Checksums-Sha256: bb3fee13bdf2ee9184667c9a3535dcd54525d9d98782e67c8c8713393cbb7862 3944341 murasaki_1.68.6.orig-debian-tests-data.tar.gz ebb3f3df2c0b3dc9f43977685f6c5e37ea483fb4189f7d965acc634bd10aaefe 307745 murasaki_1.68.6.orig.tar.gz 3a960dbbbda6e51d8a4b98c9889c8135b85a465a29c3c33a643d0528a7492128 11204 murasaki_1.68.6-13.debian.tar.xz Files: f7c0e6bdc9dea8bc893e806db571d228 3944341 murasaki_1.68.6.orig-debian-tests-data.tar.gz 25477c77aa21246d4a639527836e6c77 307745 murasaki_1.68.6.orig.tar.gz 445de24812178cef498ad9bd02b86b7c 11204 murasaki_1.68.6-13.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmEZYE8UHG5wYXRyYTk3 NEBnbWFpbC5jb20ACgkQALrnSzQzafEBZA/+JiiuRMk72tNtXdqXsruZn2As0AzG 1OUQVAlofluJXJg3BMVuDzVZT3/F1Jh1lpCR1NbSDlHzxN7f+8SEHzteeaYiTEge +V4b7MksGcRynuQqkJ7J6c1+5z2CQ5Bc9WqbZkwHVzLYDYTlWAnkyKncavS3wHvG NP+t8p73ylFTp7bRAipv/UlTBq1uouuDwxJnGyQHnQwvOgP9lJtBZnc0RrnzSxc3 CDn5PQaoXu4Efsrpvoq8bW8RtSsLMyMdy7Xk2G+DOh65GvIywBMjLc3KXPle/yeF 3cJ2KTG+aSvZy1CmuxQtCuPPSDW1kX/g6FlazuIrZP/Jya1k9nlxCOtsTu2jFe98 59YTRWyLS7iQCgesTQkAoULfzHH9Ujse+CICiJ3OBkLXSmxzNCM4xNY0iZA5m3We QWF0S5r9qxeU7V4OfFFZC4YSD0RvTpkSk13CFM8v3eMgbt9AzJCb/Sc9HIOmHvsJ nsL3Qbs5cyV/rPbWN4SI1EGqEdE2XeBKJu7cDlAaHp1fJ0zYCqPDD4FofOIUJpLA YxpC5HBvFv4hqKKCeUDQvpo4ZwYHIfhmrCboFAX1SR9HDVBL82JLXaw/+xXc9FjR OsuR8ZFLuHLilSjHLrHFzy1y+ssIzWyZ3HJHEpz1tJgf6p0iG6TBRjzL0B0NgcBm NGHCKTq6/ELzWCM= =c/ZJ -----END PGP SIGNATURE----- gpgv: Signature made Sun Aug 15 18:43:27 2021 UTC gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./murasaki_1.68.6-13.dsc: no acceptable signature found dpkg-source: info: extracting murasaki in /<> dpkg-source: info: unpacking murasaki_1.68.6.orig.tar.gz dpkg-source: info: unpacking murasaki_1.68.6.orig-debian-tests-data.tar.gz dpkg-source: info: unpacking murasaki_1.68.6-13.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc11.patch dpkg-source: info: applying use_proper_libboost_names.patch dpkg-source: info: applying include_libpstream.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying man_syntax.patch dpkg-source: info: applying freebsd.patch dpkg-source: info: applying gcc-6.patch dpkg-source: info: applying fix_mpi.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network murasaki_1.68.6-13 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network murasaki_1.68.6-13 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-52c29e56-b732-4e55-94fb-651bcb6454d6 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package murasaki dpkg-buildpackage: info: source version 1.68.6-13 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j2 clean make[1]: Entering directory '/<>' rm -rf *.o *~ .*~ core make -C src clean make[2]: Entering directory '/<>/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 '/<>/src' make[1]: Leaving directory '/<>' 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_1.68.6-13.debian.tar.xz dpkg-source: info: building murasaki in murasaki_1.68.6-13.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 '/<>' dh_auto_build -- USE_MPI=YES make -j2 "INSTALL=install --strip-program=true" USE_MPI=YES make[2]: Entering directory '/<>' make -C src all make[3]: Entering directory '/<>/src' mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c murasaki.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c timing.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c dinkymath.cc In file included from murasaki.h:24, from murasaki.cc:37: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from murasaki.cc:29: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ murasaki.cc: In function ‘void procLocs(LocList&, std::__cxx11::list&, int, int)’: murasaki.cc:1008:8: warning: variable ‘revZero’ set but not used [-Wunused-but-set-variable] 1008 | bool revZero=false; | ^~~~~~~ murasaki.cc: In function ‘bool convertPattern(std::string&)’: murasaki.cc:1287:17: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 1287 | random_shuffle(randomStr.begin(),randomStr.end()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from /usr/include/boost/regex/v5/regex_workaround.hpp:23, from /usr/include/boost/regex/v5/regex.hpp:29, from /usr/include/boost/regex.hpp:34, from seqread.h:33, from binseq.hh:31, from sequence.h:32: /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here 4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ In file included from murasaki.h:24, from dinkymath.cc:27: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from dinkymath.h:24, from dinkymath.cc:26: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ dinkymath.cc: In function ‘std::string littleEndianStr(unsigned int, int)’: dinkymath.cc:40:7: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 40 | int last=0; | ^~~~ dinkymath.cc: In function ‘std::string littleEndianPat(unsigned int, int)’: dinkymath.cc:53:7: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 53 | int last=0; | ^~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c sequence.cc In file included from murasaki.h:24, from sequence.cc:28: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ sequence.cc: In destructor ‘Sequence::~Sequence()’: sequence.cc:377:9: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 377 | throw MurasakiException("Couldn't mark System V IPC shared memory region for deletion for sequence "+name+strerror(errno)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence.cc:377:9: note: in C++11 destructors default to ‘noexcept’ sequence.cc: In member function ‘void BitSequence::loadBinary(const SequenceBinary&)’: sequence.cc:1113:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘ShmVector >::val_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1113 | memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/bits/stl_tree.h:63: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘ShmVector >::val_type’ {aka ‘struct std::pair’} declared here 187 | struct pair | ^~~~ sequence.cc:1114:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘ShmVector >::val_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1114 | memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘ShmVector >::val_type’ {aka ‘struct std::pair’} declared here 187 | struct pair | ^~~~ sequence.cc: In destructor ‘BitSequence::~BitSequence()’: sequence.cc:1394:9: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 1394 | throw MurasakiException("Couldn't detach System V shared memory region for "+(seq ? seq->filename:string("(anon)"))+strerror(errno)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence.cc:1394:9: note: in C++11 destructors default to ‘noexcept’ sequence.cc: In member function ‘std::pair IntervalSet::entropy() const’: sequence.cc:3332:10: warning: variable ‘shortest’ set but not used [-Wunused-but-set-variable] 3332 | SeqPos shortest=0,shortlen=length(spaces[0]); | ^~~~~~~~ In file included from sequence.cc:41: hashing.h: In instantiation of ‘SBox::SBox(int) [with T = short unsigned int]’: sequence.cc:162:29: required from here hashing.h:56:21: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = short unsigned int*]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 56 | random_shuffle(boxes[b],boxes[b]+boxsize); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from /usr/include/boost/regex/v5/regex_workaround.hpp:23, from /usr/include/boost/regex/v5/regex.hpp:29, from /usr/include/boost/regex.hpp:34, from seqread.h:33, from binseq.hh:31, from sequence.h:32: /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here 4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ 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]’ sequence.cc:1110:17: required from here shmvector.hh:225:13: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 225 | memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c msethash.cc In file included from msethash.cc:25: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c options.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecohash.cc In file included from options.h:28, from options.cc:26: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecolist.cc In file included from ecolist.h:23, from ecolist.cc:20: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ecolist.cc:467:26: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 467 | struct less_map : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c murasaki_mpi.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c arrayhash.cc In file included from murasaki.h:24, from murasaki_mpi.cc:33: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/map:62, from /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:42, from /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:2911, from murasaki_mpi.cc:29: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ murasaki_mpi.cc:89:29: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 89 | struct lt_mpi_worldMemory : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ murasaki_mpi.cc:95:29: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 95 | struct gt_mpi_worldMemory : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ murasaki_mpi.cc: In function ‘void mpi_hasher_client_mode(BitSequence*)’: murasaki_mpi.cc:561:9: warning: variable ‘send_done’ set but not used [-Wunused-but-set-variable] 561 | int send_done; | ^~~~~~~~~ In file included from murasaki.h:24, from arrayhash.cc:28: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c seqread.cc murasaki_mpi.cc: In function ‘void mpi_types_init()’: murasaki_mpi.cc:107:18: warning: ‘msg’ may be used uninitialized [-Wmaybe-uninitialized] 107 | MPI_Get_address(&msg.key,disp); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:1589:20: note: by argument 1 of type ‘const void*’ to ‘int MPI_Get_address(const void*, MPI_Aint*)’ declared here 1589 | OMPI_DECLSPEC int MPI_Get_address(const void *location, MPI_Aint *address); | ^~~~~~~~~~~~~~~ murasaki_mpi.cc:102:19: note: ‘msg’ declared here 102 | MPI_HashMessage msg; | ^~~ seqread.cc: In member function ‘void SequenceByteReader::addRedirect(boost::cmatch)’: seqread.cc:264:38: warning: ‘boost::filesystem::path boost::filesystem::path::branch_path() const’ is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 264 | stitchPath=stitchfile.branch_path(); | ~~~~~~~~~~~~~~~~~~~~~~^~ In file included from seqread.cc:35: /usr/include/boost/filesystem/path.hpp:1129:10: note: declared here 1129 | path branch_path() const { return parent_path(); } | ^~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c scoring.cc In file included from murasaki.h:24, from scoring.cc:27: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c 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++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c genopts.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c binseq.cc binseq.cc: In member function ‘bool SequenceBinary::save(std::string)’: binseq.cc:70:28: warning: catching polymorphic type ‘class std::ios_base::failure’ by value [-Wcatch-value=] 70 | }catch(ofstream::failure e){ | ^ binseq.cc: In member function ‘void SequenceBinary::fillCopyVectors()’: binseq.cc:158:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 158 | memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 187 | struct pair | ^~~~ binseq.cc:160:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 160 | memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 187 | struct pair | ^~~~ binseq.cc:162:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 162 | memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 187 | struct pair | ^~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-image.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-compare.cc cgr.cc: In member function ‘void Cgr::merge(Cgr&)’: cgr.cc:140:7: warning: variable ‘redist’ set but not used [-Wunused-but-set-variable] 140 | int redist=(unsigned long)(rez*rez)<=seedcount; | ^~~~~~ cgr.cc: In member function ‘bool Cgr::savePNG(std::string)’: cgr.cc:288:7: warning: variable ‘res’ set but not used [-Wunused-but-set-variable] 288 | int res; | ^~~ cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::string)’: cgr.cc:435:7: warning: variable ‘wordwidth’ set but not used [-Wunused-but-set-variable] 435 | int wordwidth=1; | ^~~~~~~~~ cgr.cc: In member function ‘std::pair Cgr::sampleHighLow(double, double)’: cgr.cc:339:10: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 339 | delete alt; | ^~~ cgr.cc:330:24: note: returned from ‘void* operator new [](std::size_t)’ 330 | pix *alt=new pix[size]; | ^ cgr.cc: In member function ‘std::pair Cgr::sampleHighLow(int, int)’: cgr.cc:354:10: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 354 | delete alt; | ^~~ cgr.cc:345:24: note: returned from ‘void* operator new [](std::size_t)’ 345 | pix *alt=new pix[size]; | ^ cgr.cc: In member function ‘std::pair Cgr::findNiceRange()’: cgr.cc:395:10: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 395 | delete alt; | ^~~ cgr.cc:376:24: note: returned from ‘void* operator new [](std::size_t)’ 376 | pix *alt=new pix[size]; | ^ cgr.cc: In member function ‘int PgmBuffer::loadBinaryPGM(std::string)’: cgr.cc:547:7: warning: ‘maxval’ may be used uninitialized [-Wmaybe-uninitialized] 547 | switch(maxval){ | ^~~~~~ cgr.cc:494:8: note: ‘maxval’ was declared here 494 | gray maxval; | ^~~~~~ cgr.cc:557:31: warning: ‘width’ may be used uninitialized [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:493:7: note: ‘width’ was declared here 493 | int width,height; | ^~~~~ cgr.cc:557:31: warning: ‘height’ may be used uninitialized [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:493:13: note: ‘height’ was declared here 493 | int width,height; | ^~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-random.cc cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::string)’: cgr.cc:485:31: warning: ‘width’ may be used uninitialized [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:426:7: note: ‘width’ was declared here 426 | int width,height; | ^~~~~ cgr.cc:485:31: warning: ‘height’ may be used uninitialized [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:426:13: note: ‘height’ was declared here 426 | int width,height; | ^~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-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; | ^~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c testeco.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-compare.cc In file included from ecolist.h:23, from testeco.cc:20: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c alignments.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-or.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c geneparse.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-and.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-best.cc In file included from align-best.cc:33: In function ‘std::ostream& Itree::operator<<(std::ostream&, const Interval<_IntType>&) [with _IntType = long int]’, inlined from ‘int main(int, char**)’ at align-best.cc:173:35: itree.h:79:27: warning: array subscript -1 is outside array bounds of ‘Itree::Interval [576460752303423487]’ [-Warray-bounds=] 79 | return os << "[" << i.start << "~" << i.stop << "]"; | ~~^~~~~ itree.h:79:45: warning: array subscript -1 is outside array bounds of ‘Itree::Interval [576460752303423487]’ [-Warray-bounds=] 79 | return os << "[" << i.start << "~" << i.stop << "]"; | ~~^~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-coverage.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c getsegments.cc align-coverage.cc: In function ‘int main(int, char**)’: align-coverage.cc:148:10: warning: variable ‘seqStats’ set but not used [-Wunused-but-set-variable] 148 | bool seqStats=true; | ^~~~~~~~ getsegments.cc: In function ‘size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::string)’: getsegments.cc:153:29: warning: catching polymorphic type ‘class boost::bad_lexical_cast’ by value [-Wcatch-value=] 153 | }catch(bad_lexical_cast e){ | ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c mbfa.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' for bin in geneparse mbfa murasaki cgr-* testeco align-* ; do \ mv ${bin} ${bin}-mpi ; \ done make clean make[2]: Entering directory '/<>' rm -rf *.o *~ .*~ core make -C src clean make[3]: Entering directory '/<>/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 '/<>/src' make[2]: Leaving directory '/<>' dh_auto_build -- USE_MPI=NO make -j2 "INSTALL=install --strip-program=true" USE_MPI=NO make[2]: Entering directory '/<>' make -C src all make[3]: Entering directory '/<>/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c murasaki.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c timing.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c dinkymath.cc In file included from murasaki.h:24, from murasaki.cc:37: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from murasaki.cc:29: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ murasaki.cc: In function ‘void procLocs(LocList&, std::__cxx11::list&, int, int)’: murasaki.cc:1008:8: warning: variable ‘revZero’ set but not used [-Wunused-but-set-variable] 1008 | bool revZero=false; | ^~~~~~~ murasaki.cc: In function ‘bool convertPattern(std::string&)’: murasaki.cc:1287:17: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 1287 | random_shuffle(randomStr.begin(),randomStr.end()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from /usr/include/boost/regex/v5/regex_workaround.hpp:23, from /usr/include/boost/regex/v5/regex.hpp:29, from /usr/include/boost/regex.hpp:34, from seqread.h:33, from binseq.hh:31, from sequence.h:32: /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here 4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ In file included from murasaki.h:24, from dinkymath.cc:27: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from dinkymath.h:24, from dinkymath.cc:26: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ dinkymath.cc: In function ‘std::string littleEndianStr(unsigned int, int)’: dinkymath.cc:40:7: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 40 | int last=0; | ^~~~ dinkymath.cc: In function ‘std::string littleEndianPat(unsigned int, int)’: dinkymath.cc:53:7: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 53 | int last=0; | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c sequence.cc In file included from murasaki.h:24, from sequence.cc:28: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ sequence.cc: In member function ‘void BitSequence::loadBinary(const SequenceBinary&)’: sequence.cc:1113:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘ShmVector >::val_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1113 | memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/bits/stl_tree.h:63: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘ShmVector >::val_type’ {aka ‘struct std::pair’} declared here 187 | struct pair | ^~~~ sequence.cc:1114:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘ShmVector >::val_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1114 | memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘ShmVector >::val_type’ {aka ‘struct std::pair’} declared here 187 | struct pair | ^~~~ sequence.cc: In member function ‘std::pair IntervalSet::entropy() const’: sequence.cc:3332:10: warning: variable ‘shortest’ set but not used [-Wunused-but-set-variable] 3332 | SeqPos shortest=0,shortlen=length(spaces[0]); | ^~~~~~~~ In file included from sequence.cc:41: hashing.h: In instantiation of ‘SBox::SBox(int) [with T = short unsigned int]’: sequence.cc:162:29: required from here hashing.h:56:21: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = short unsigned int*]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 56 | random_shuffle(boxes[b],boxes[b]+boxsize); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from /usr/include/boost/regex/v5/regex_workaround.hpp:23, from /usr/include/boost/regex/v5/regex.hpp:29, from /usr/include/boost/regex.hpp:34, from seqread.h:33, from binseq.hh:31, from sequence.h:32: /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here 4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ 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]’ sequence.cc:1110:17: required from here shmvector.hh:225:13: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 225 | memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘struct std::pair’ declared here 187 | struct pair | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c msethash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c options.cc In file included from msethash.cc:25: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -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++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c 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++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ecolist.cc:467:26: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 467 | struct less_map : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c murasaki_mpi.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c arrayhash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c seqread.cc In file included from murasaki.h:24, from arrayhash.cc:28: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ seqread.cc: In member function ‘void SequenceByteReader::addRedirect(boost::cmatch)’: seqread.cc:264:38: warning: ‘boost::filesystem::path boost::filesystem::path::branch_path() const’ is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 264 | stitchPath=stitchfile.branch_path(); | ~~~~~~~~~~~~~~~~~~~~~~^~ In file included from seqread.cc:35: /usr/include/boost/filesystem/path.hpp:1129:10: note: declared here 1129 | path branch_path() const { return parent_path(); } | ^~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c scoring.cc In file included from murasaki.h:24, from scoring.cc:27: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c openhash.cc In file included from ecolist.h:23, from openhash.h:29, from openhash.cc:26: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c genopts.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c binseq.cc binseq.cc: In member function ‘bool SequenceBinary::save(std::string)’: binseq.cc:70:28: warning: catching polymorphic type ‘class std::ios_base::failure’ by value [-Wcatch-value=] 70 | }catch(ofstream::failure e){ | ^ binseq.cc: In member function ‘void SequenceBinary::fillCopyVectors()’: binseq.cc:158:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 158 | memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 187 | struct pair | ^~~~ binseq.cc:160:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 160 | memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 187 | struct pair | ^~~~ binseq.cc:162:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 162 | memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_pair.h:187:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 187 | struct pair | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-image.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr.cc cgr.cc: In member function ‘void Cgr::merge(Cgr&)’: cgr.cc:140:7: warning: variable ‘redist’ set but not used [-Wunused-but-set-variable] 140 | int redist=(unsigned long)(rez*rez)<=seedcount; | ^~~~~~ cgr.cc: In member function ‘bool Cgr::savePNG(std::string)’: cgr.cc:288:7: warning: variable ‘res’ set but not used [-Wunused-but-set-variable] 288 | int res; | ^~~ cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::string)’: cgr.cc:435:7: warning: variable ‘wordwidth’ set but not used [-Wunused-but-set-variable] 435 | int wordwidth=1; | ^~~~~~~~~ cgr.cc: In member function ‘std::pair Cgr::sampleHighLow(double, double)’: cgr.cc:339:10: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 339 | delete alt; | ^~~ cgr.cc:330:24: note: returned from ‘void* operator new [](std::size_t)’ 330 | pix *alt=new pix[size]; | ^ cgr.cc: In member function ‘std::pair Cgr::sampleHighLow(int, int)’: cgr.cc:354:10: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 354 | delete alt; | ^~~ cgr.cc:345:24: note: returned from ‘void* operator new [](std::size_t)’ 345 | pix *alt=new pix[size]; | ^ cgr.cc: In member function ‘std::pair Cgr::findNiceRange()’: cgr.cc:395:10: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 395 | delete alt; | ^~~ cgr.cc:376:24: note: returned from ‘void* operator new [](std::size_t)’ 376 | pix *alt=new pix[size]; | ^ cgr.cc: In member function ‘int PgmBuffer::loadBinaryPGM(std::string)’: cgr.cc:547:7: warning: ‘maxval’ may be used uninitialized [-Wmaybe-uninitialized] 547 | switch(maxval){ | ^~~~~~ cgr.cc:494:8: note: ‘maxval’ was declared here 494 | gray maxval; | ^~~~~~ cgr.cc:557:31: warning: ‘width’ may be used uninitialized [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:493:7: note: ‘width’ was declared here 493 | int width,height; | ^~~~~ cgr.cc:557:31: warning: ‘height’ may be used uninitialized [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:493:13: note: ‘height’ was declared here 493 | int width,height; | ^~~~~~ cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::string)’: cgr.cc:485:31: warning: ‘width’ may be used uninitialized [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:426:7: note: ‘width’ was declared here 426 | int width,height; | ^~~~~ cgr.cc:485:31: warning: ‘height’ may be used uninitialized [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:426:13: note: ‘height’ was declared here 426 | int width,height; | ^~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-compare.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-random.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-sample.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c testeco.cc In file included from ecolist.h:23, from testeco.cc:20: sequence.h:444:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from cmultiset.h:33, from sequence.h:30: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ cgr-sample.cc: In function ‘int main(int, char**)’: cgr-sample.cc:54:8: warning: variable ‘repeatmask’ set but not used [-Wunused-but-set-variable] 54 | bool repeatmask=false,save=false; | ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-compare.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c alignments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-or.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c geneparse.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-and.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-best.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-coverage.cc In file included from align-best.cc:33: In function ‘std::ostream& Itree::operator<<(std::ostream&, const Interval<_IntType>&) [with _IntType = long int]’, inlined from ‘int main(int, char**)’ at align-best.cc:173:35: itree.h:79:27: warning: array subscript -1 is outside array bounds of ‘Itree::Interval [576460752303423487]’ [-Warray-bounds=] 79 | return os << "[" << i.start << "~" << i.stop << "]"; | ~~^~~~~ itree.h:79:45: warning: array subscript -1 is outside array bounds of ‘Itree::Interval [576460752303423487]’ [-Warray-bounds=] 79 | return os << "[" << i.start << "~" << i.stop << "]"; | ~~^~~~ align-coverage.cc: In function ‘int main(int, char**)’: align-coverage.cc:148:10: warning: variable ‘seqStats’ set but not used [-Wunused-but-set-variable] 148 | bool seqStats=true; | ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c getsegments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c mbfa.cc getsegments.cc: In function ‘size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::string)’: getsegments.cc:153:29: warning: catching polymorphic type ‘class boost::bad_lexical_cast’ by value [-Wcatch-value=] 153 | }catch(bad_lexical_cast e){ | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install-arch make[1]: Entering directory '/<>' 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 '/<>' dh_install -Nmurasaki -Nmurasaki-mpi dh_installdocs dh_installchangelogs debian/rules override_dh_installman-arch make[1]: Entering directory '/<>' 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 '/<>' debian/rules override_dh_installman-indep make[1]: Entering directory '/<>' dh_installman -i # create manpages for PL files mkdir -p debian/murasaki-common/usr/share/man/man1 for pscript in debian/murasaki-common/usr/lib/debian-med/bin/* ; do \ pod2man ${pscript} > debian/murasaki-common/usr/share/man/man1/`basename ${pscript}`.1 ; \ done pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/anchors2maf.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/anchors2osfinder.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/antisense.pl debian/murasaki-common/usr/lib/debian-med/bin/chromostitch.pl around line 134: '=item' outside of any '=over' debian/murasaki-common/usr/lib/debian-med/bin/chromostitch.pl around line 141: You forgot a '=back' before '=head1' POD document had syntax errors at /usr/bin/pod2man line 69. pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/dna2binary.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/dnashuffle.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/geneparse.pl debian/murasaki-common/usr/lib/debian-med/bin/getcds.pl around line 646: '=item' outside of any '=over' debian/murasaki-common/usr/lib/debian-med/bin/getcds.pl around line 646: =over without closing =back POD document had syntax errors at /usr/bin/pod2man line 69. pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/humantime.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/osfinder2anchors.pl pod2man: unable to format debian/murasaki-common/usr/lib/debian-med/bin/randpat.pl find debian/murasaki-common/usr/share/man/man1 -empty -delete make[1]: Leaving directory '/<>' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms-indep make[1]: Entering directory '/<>' dh_fixperms -i chmod a+x debian/murasaki-common/usr/share/perl5/murasaki/config.pl make[1]: Leaving directory '/<>' 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_1.68.6-13_amd64.deb'. dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-13_amd64.deb'. dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-13_amd64.deb'. dpkg-deb: building package 'murasaki-common' in '../murasaki-common_1.68.6-13_all.deb'. dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-13_amd64.deb'. dpkg-genbuildinfo -O../murasaki_1.68.6-13_amd64.buildinfo dpkg-genchanges -O../murasaki_1.68.6-13_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 2024-06-04T17:11:28Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ murasaki_1.68.6-13_amd64.changes: --------------------------------- Format: 1.8 Date: Mon, 16 Aug 2021 00:06:48 +0530 Source: murasaki Binary: murasaki murasaki-common murasaki-dbgsym murasaki-mpi murasaki-mpi-dbgsym Architecture: source all amd64 Version: 1.68.6-13 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: murasaki - homology detection tool across multiple large genomes murasaki-common - homology detection tool across multiple large genomes (common fil murasaki-mpi - homology detection tool across multiple large genomes (MPI-versio Changes: murasaki (1.68.6-13) unstable; urgency=medium . * d/p/gcc11.patch: Fix gcc-11 FTBFS * Add myself to uploaders Checksums-Sha1: 6988a5425d0e690e62a208d517c6226480a1a084 1880 murasaki_1.68.6-13.dsc 5066f61fba06f88a3e86929eff0155fa6d427ecd 11212 murasaki_1.68.6-13.debian.tar.xz 0eb1ef214870fddb9b47995af9a458fe624053b9 116792 murasaki-common_1.68.6-13_all.deb 375bb601f2a828d7c33ae863a89c906422c9ef87 14562040 murasaki-dbgsym_1.68.6-13_amd64.deb 1980466ff314a1e2277a2e2d4df2be7b20bce457 16001504 murasaki-mpi-dbgsym_1.68.6-13_amd64.deb e860bc536ace946a8bacec2afd37400f7e24dae6 742176 murasaki-mpi_1.68.6-13_amd64.deb 55830b58c008975262116c4f966c0fd4d33a7a4d 9135 murasaki_1.68.6-13_amd64.buildinfo 5f7d4b4fb5a2eb94d9f1c3e1a024937d4852e1af 625224 murasaki_1.68.6-13_amd64.deb Checksums-Sha256: 0bad52274e1391d84092006d879dccc511237033520a29ec212159970d0ae3f9 1880 murasaki_1.68.6-13.dsc 71a84cbc41600faf3cc9b82de39e3e34f6a706c045220f1e496317316b70da05 11212 murasaki_1.68.6-13.debian.tar.xz 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d225d36fb9a1034f2784b1523e358dd9 16001504 debug optional murasaki-mpi-dbgsym_1.68.6-13_amd64.deb 12c25cd07a1763e8e23e0f190bad599e 742176 science optional murasaki-mpi_1.68.6-13_amd64.deb db2f11917ebcc15f6c81b6f3df6baa66 9135 science optional murasaki_1.68.6-13_amd64.buildinfo e11f6a95122239bd09b4d57ec64ea309 625224 science optional murasaki_1.68.6-13_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: murasaki Binary: murasaki murasaki-common murasaki-dbgsym murasaki-mpi murasaki-mpi-dbgsym Architecture: all amd64 source Version: 1.68.6-13 Checksums-Md5: 650a199f8e42f64afc836977b40d88a5 1880 murasaki_1.68.6-13.dsc 5882ef103ad8f6ad030b6bb82fb5b6dc 116792 murasaki-common_1.68.6-13_all.deb 660a2b9964d59e22d9d52bd72d053e0a 14562040 murasaki-dbgsym_1.68.6-13_amd64.deb d225d36fb9a1034f2784b1523e358dd9 16001504 murasaki-mpi-dbgsym_1.68.6-13_amd64.deb 12c25cd07a1763e8e23e0f190bad599e 742176 murasaki-mpi_1.68.6-13_amd64.deb e11f6a95122239bd09b4d57ec64ea309 625224 murasaki_1.68.6-13_amd64.deb Checksums-Sha1: 6988a5425d0e690e62a208d517c6226480a1a084 1880 murasaki_1.68.6-13.dsc 0eb1ef214870fddb9b47995af9a458fe624053b9 116792 murasaki-common_1.68.6-13_all.deb 375bb601f2a828d7c33ae863a89c906422c9ef87 14562040 murasaki-dbgsym_1.68.6-13_amd64.deb 1980466ff314a1e2277a2e2d4df2be7b20bce457 16001504 murasaki-mpi-dbgsym_1.68.6-13_amd64.deb e860bc536ace946a8bacec2afd37400f7e24dae6 742176 murasaki-mpi_1.68.6-13_amd64.deb 5f7d4b4fb5a2eb94d9f1c3e1a024937d4852e1af 625224 murasaki_1.68.6-13_amd64.deb Checksums-Sha256: 0bad52274e1391d84092006d879dccc511237033520a29ec212159970d0ae3f9 1880 murasaki_1.68.6-13.dsc 70950f90e58c34e869c488e95da415a3144216f501aa56ff75521ee7be29e519 116792 murasaki-common_1.68.6-13_all.deb fb2a25b9027b952155b268a7ea62cb0b6791d35ca20a59f4d19e8361c6607224 14562040 murasaki-dbgsym_1.68.6-13_amd64.deb f43e2d4c19b897fdfb5d7cfdf67bcd6352d8780d86d73cc4a4b01fc8b661d89d 16001504 murasaki-mpi-dbgsym_1.68.6-13_amd64.deb 01a7ceabcb3bd6cd1391175589cd1393b41b448c80412abfe3930ceb8158533f 742176 murasaki-mpi_1.68.6-13_amd64.deb dc9eece4276b47f5081fe2370d12fcda0db05a467d88b2cb0d3662bf4435dab3 625224 murasaki_1.68.6-13_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 04 Jun 2024 17:11:27 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: adduser (= 3.137), autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-14), autotools-dev (= 20220109.1), base-files (= 13.2), base-passwd (= 3.6.3), bash (= 5.2.21-2+b1), binutils (= 2.42-4), binutils-common (= 2.42-4), binutils-x86-64-linux-gnu (= 2.42-4), bsdextrautils (= 2.40.1-8), bsdutils (= 1:2.40.1-8), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3.1), cpp (= 4:13.2.0-7), cpp-13 (= 13.2.0-25), cpp-13-x86-64-linux-gnu (= 13.2.0-25), cpp-x86-64-linux-gnu (= 4:13.2.0-7), dash (= 0.5.12-8), debconf (= 1.5.86), debhelper (= 13.15.3), debianutils (= 5.17), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.6), dpkg-dev (= 1.22.6), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.9.0-6), g++ (= 4:13.2.0-7), g++-13 (= 13.2.0-25), g++-13-x86-64-linux-gnu (= 13.2.0-25), g++-x86-64-linux-gnu (= 4:13.2.0-7), gcc (= 4:13.2.0-7), gcc-13 (= 13.2.0-25), gcc-13-base (= 13.2.0-25), gcc-13-x86-64-linux-gnu (= 13.2.0-25), gcc-14-base (= 14.1.0-1), gcc-x86-64-linux-gnu (= 4:13.2.0-7), gettext (= 0.21-14+b1), gettext-base (= 0.21-14+b1), gfortran-13 (= 13.2.0-25), gfortran-13-x86-64-linux-gnu (= 13.2.0-25), grep (= 3.11-4), groff-base (= 1.23.0-4), gzip (= 1.12-1.1), hostname (= 3.23+nmu2), ibverbs-providers (= 52.0-1), icu-devtools (= 72.1-4+b1), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libamd-comgr2 (= 6.0+git20231212.4510c28+dfsg-3+b1), libamdhip64-5 (= 5.7.1-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.1.0-1), libatomic1 (= 14.1.0-1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1), libaudit1 (= 1:3.1.2-2.1), libbinutils (= 2.42-4), libblkid1 (= 2.40.1-8), libboost-atomic1.83-dev (= 1.83.0-3), libboost-atomic1.83.0 (= 1.83.0-3), libboost-filesystem-dev (= 1.83.0.2+b2), libboost-filesystem1.83-dev (= 1.83.0-3), libboost-filesystem1.83.0 (= 1.83.0-3), libboost-iostreams-dev (= 1.83.0.2+b2), libboost-iostreams1.83-dev (= 1.83.0-3), libboost-iostreams1.83.0 (= 1.83.0-3), libboost-regex-dev (= 1.83.0.2+b2), libboost-regex1.83-dev (= 1.83.0-3), libboost-regex1.83.0 (= 1.83.0-3), libboost-system1.83-dev (= 1.83.0-3), libboost-system1.83.0 (= 1.83.0-3), libboost1.83-dev (= 1.83.0-3), libbsd0 (= 0.12.2-1), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.38-12), libc-dev-bin (= 2.38-12), libc6 (= 2.38-12), libc6-dev (= 2.38-12), libcap-ng0 (= 0.8.5-1), libcap2 (= 1:2.66-5), libcbor0.10 (= 0.10.2-1.2), libcc1-0 (= 14.1.0-1), libcom-err2 (= 1.47.1-1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libcrypto++-dev (= 8.9.0-1.1), libcrypto++8t64 (= 8.9.0-1.1), libctf-nobfd0 (= 2.42-4), libctf0 (= 2.42-4), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.15.3), libdpkg-perl (= 1.22.6), libdrm-amdgpu1 (= 2.4.120-2), libdrm-common (= 2.4.120-2), libdrm2 (= 2.4.120-2), libedit2 (= 3.1-20240517-1), libelf1t64 (= 0.191-1+b1), libevent-2.1-7t64 (= 2.1.12-stable-10), libevent-core-2.1-7t64 (= 2.1.12-stable-10), libevent-dev (= 2.1.12-stable-10), libevent-extra-2.1-7t64 (= 2.1.12-stable-10), libevent-openssl-2.1-7t64 (= 2.1.12-stable-10), libevent-pthreads-2.1-7t64 (= 2.1.12-stable-10), libfabric1 (= 1.17.0-3+b1), libffi8 (= 3.4.6-1), libfido2-1 (= 1.14.0-1+b2), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.2.0-25), libgcc-s1 (= 14.1.0-1), libgdbm-compat4t64 (= 1.23-5.1+b1), libgdbm6t64 (= 1.23-5.1+b1), libgfortran-13-dev (= 13.2.0-25), libgfortran5 (= 14.1.0-1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgomp1 (= 14.1.0-1), libgprofng0 (= 2.42-4), libgssapi-krb5-2 (= 1.20.1-6+b1), libhsa-runtime64-1 (= 5.7.1-2), libhsakmt1 (= 5.7.0-1), libhwasan0 (= 14.1.0-1), libhwloc-dev (= 2.10.0-1+b1), libhwloc-plugins (= 2.10.0-1+b1), libhwloc15 (= 2.10.0-1+b1), libibverbs-dev (= 52.0-1), libibverbs1 (= 52.0-1), libicu-dev (= 72.1-4+b1), libicu72 (= 72.1-4+b1), libisl23 (= 0.26-3+b2), libitm1 (= 14.1.0-1), libjansson4 (= 2.14-2+b2), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libk5crypto3 (= 1.20.1-6+b1), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.20.1-6+b1), libkrb5support0 (= 1.20.1-6+b1), libllvm17t64 (= 1:17.0.6-12), liblsan0 (= 14.1.0-1), libltdl-dev (= 2.4.7-7+b1), libltdl7 (= 2.4.7-7+b1), liblzma5 (= 5.6.1+really5.4.5-1), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.1-8), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libmunge2 (= 0.5.15-4), libnl-3-200 (= 3.7.0-0.3), libnl-3-dev (= 3.7.0-0.3), libnl-route-3-200 (= 3.7.0-0.3), libnl-route-3-dev (= 3.7.0-0.3), libnuma-dev (= 2.0.18-1), libnuma1 (= 2.0.18-1), libopenmpi-dev (= 4.1.6-13.3), libopenmpi3t64 (= 4.1.6-13.3), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpciaccess0 (= 0.17-3+b1), libpcre2-8-0 (= 10.42-4+b1), libperl5.40 (= 5.40.0~rc1-1), libpipeline1 (= 1.5.7-2), libpmix-dev (= 5.0.2-3), libpmix2t64 (= 5.0.2-3), libpsm-infinipath1 (= 3.3+20.604758e7-6.3), libpsm2-2 (= 11.2.185-2), libpstreams-dev (= 1.0.3-1), libquadmath0 (= 14.1.0-1), librdmacm1t64 (= 52.0-1), libseccomp2 (= 2.5.5-1), libselinux1 (= 3.5-2+b2), libsemanage-common (= 3.5-1), libsemanage2 (= 3.5-1+b3), libsepol2 (= 3.5-2+b1), libsframe1 (= 2.42-4), libsmartcols1 (= 2.40.1-8), libssl3t64 (= 3.2.1-3), libstdc++-13-dev (= 13.2.0-25), libstdc++6 (= 14.1.0-1), libsystemd0 (= 256~rc3-7), libterm-readkey-perl (= 2.38-2+b4), libtext-wrapper-perl (= 1.05-4), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.1.0-1), libubsan1 (= 14.1.0-1), libuchardet0 (= 0.0.8-1+b1), libucx0 (= 1.16.0+ds-5), libudev1 (= 256~rc3-7), libunistring5 (= 1.2-1), libuuid1 (= 2.40.1-8), libx11-6 (= 2:1.8.7-1+b1), libx11-data (= 2:1.8.7-1), libxau6 (= 1:1.0.9-1+b1), libxcb1 (= 1.17.0-2), libxdmcp6 (= 1:1.1.2-3+b1), libxext6 (= 2:1.3.4-1+b1), libxml2 (= 2.12.7+dfsg-3), libxnvctrl0 (= 535.171.04-1), libz3-4 (= 4.8.12-3.1+b2), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.12-1), login (= 1:4.13+dfsg1-5), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-1), mawk (= 1.3.4.20240123-1), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), ocl-icd-libopencl1 (= 2.3.2-1+b1), openmpi-bin (= 4.1.6-13.3), openmpi-common (= 4.1.6-13.3), openssh-client (= 1:9.7p1-5), passwd (= 1:4.13+dfsg1-5), patch (= 2.7.6-7), perl (= 5.40.0~rc1-1), perl-base (= 5.40.0~rc1-1), perl-modules-5.40 (= 5.40.0~rc1-1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.22), sysvinit-utils (= 3.09-1), tar (= 1.35+dfsg-3), usr-is-merged (= 39), util-linux (= 2.40.1-8), xz-utils (= 5.6.1+really5.4.5-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1629052608" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ murasaki-common_1.68.6-13_all.deb --------------------------------- new Debian package, version 2.0. size 116792 bytes: control archive=3232 bytes. 1282 bytes, 28 lines control 6185 bytes, 85 lines md5sums Package: murasaki-common Source: murasaki Version: 1.68.6-13 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 407 Depends: gnuplot | gnuplot5, libbio-perl-perl, r-cran-rocr, imagemagick Recommends: libterm-readkey-perl, libtext-wrapi18n-perl | libtext-wrapper-perl Section: science Priority: optional Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Description: homology detection tool across multiple large genomes (common files) Murasaki is a scalable and fast, language theory-based homology detection tool across multiple large genomes. It enable whole-genome scale multiple genome global alignments. Supports unlimited length gapped-seed patterns and unique TF-IDF based filtering. . Murasaki is an anchor alignment software, which is * exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 52 wall minutes)) * scalable (Arbitrarily parallelizable across multiple nodes using MPI. Even a single node with 16GB of ram can handle over 1Gbp of sequence.) * unlimited pattern length * repeat tolerant * intelligent noise reduction . This package contains all files that are common to the single core murasaki package and the multi core murasaki-mpi package. drwxr-xr-x root/root 0 2021-08-15 18:36 ./ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/debian-med/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./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 2021-08-15 18:36 ./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 2021-08-15 18:36 ./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 2021-08-15 18:36 ./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 2021-08-15 18:36 ./usr/lib/debian-med/bin/substitch.pl drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/doc/murasaki-common/ -rw-r--r-- root/root 238 2021-03-19 18:45 ./usr/share/doc/murasaki-common/README.Debian -rw-r--r-- root/root 800 2021-08-15 18:36 ./usr/share/doc/murasaki-common/changelog.Debian.gz -rw-r--r-- root/root 2225 2021-03-19 18:45 ./usr/share/doc/murasaki-common/copyright drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/lintian/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 70 2021-03-19 18:45 ./usr/share/lintian/overrides/murasaki-common drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/man/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/man/man1/ -rw-r--r-- root/root 1013 2021-08-15 18:36 ./usr/share/man/man1/align2kog.pl.1.gz -rw-r--r-- root/root 995 2021-08-15 18:36 ./usr/share/man/man1/analyze-pat.pl.1.gz -rw-r--r-- root/root 1231 2021-08-15 18:36 ./usr/share/man/man1/chromostitch.pl.1.gz -rw-r--r-- root/root 1073 2021-08-15 18:36 ./usr/share/man/man1/faformat.pl.1.gz -rw-r--r-- root/root 3073 2021-08-15 18:36 ./usr/share/man/man1/filter.pl.1.gz -rw-r--r-- 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size 742176 bytes: control archive=1596 bytes. 1358 bytes, 28 lines control 1326 bytes, 20 lines md5sums Package: murasaki-mpi Source: murasaki Version: 1.68.6-13 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 5094 Depends: murasaki-common, libboost-filesystem1.83.0 (>= 1.83.0), libboost-iostreams1.83.0 (>= 1.83.0), libc6 (>= 2.38), libgcc-s1 (>= 3.0), libopenmpi3t64 (>= 4.1.6), libstdc++6 (>= 13.1) 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 2021-08-15 18:36 ./ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/bin/ -rwxr-xr-x root/root 352760 2021-08-15 18:36 ./usr/bin/geneparse-mpi -rwxr-xr-x root/root 463224 2021-08-15 18:36 ./usr/bin/mbfa-mpi -rwxr-xr-x root/root 961672 2021-08-15 18:36 ./usr/bin/murasaki-mpi drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/murasaki/ -rwxr-xr-x root/root 368936 2021-08-15 18:36 ./usr/lib/murasaki/align-and-mpi -rwxr-xr-x root/root 373064 2021-08-15 18:36 ./usr/lib/murasaki/align-best-mpi -rwxr-xr-x root/root 418656 2021-08-15 18:36 ./usr/lib/murasaki/align-compare-mpi -rwxr-xr-x root/root 516968 2021-08-15 18:36 ./usr/lib/murasaki/align-coverage-mpi -rwxr-xr-x root/root 364808 2021-08-15 18:36 ./usr/lib/murasaki/align-or-mpi -rwxr-xr-x root/root 166456 2021-08-15 18:36 ./usr/lib/murasaki/cgr-compare-mpi -rwxr-xr-x root/root 475608 2021-08-15 18:36 ./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 174688 2021-08-15 18:36 ./usr/lib/murasaki/cgr-random-mpi -rwxr-xr-x root/root 397736 2021-08-15 18:36 ./usr/lib/murasaki/cgr-sample-mpi -rwxr-xr-x root/root 133536 2021-08-15 18:36 ./usr/lib/murasaki/testeco-mpi drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/doc/murasaki-mpi/ -rw-r--r-- root/root 249 2021-03-19 18:45 ./usr/share/doc/murasaki-mpi/README.test -rw-r--r-- root/root 798 2021-08-15 18:36 ./usr/share/doc/murasaki-mpi/changelog.Debian.gz -rw-r--r-- root/root 2225 2021-03-19 18:45 ./usr/share/doc/murasaki-mpi/copyright drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/man/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/man/man1/ -rw-r--r-- root/root 2518 2021-08-15 18:36 ./usr/share/man/man1/geneparse-mpi.1.gz -rw-r--r-- root/root 2721 2021-08-15 18:36 ./usr/share/man/man1/mbfa-mpi.1.gz -rw-r--r-- root/root 10888 2021-08-15 18:36 ./usr/share/man/man1/murasaki-mpi.1.gz murasaki_1.68.6-13_amd64.deb ---------------------------- new Debian package, version 2.0. size 625224 bytes: control archive=1440 bytes. 1126 bytes, 23 lines control 1182 bytes, 19 lines md5sums Package: murasaki Version: 1.68.6-13 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 4247 Depends: murasaki-common, libboost-filesystem1.83.0 (>= 1.83.0), libboost-iostreams1.83.0 (>= 1.83.0), libc6 (>= 2.38), libgcc-s1 (>= 3.0), libstdc++6 (>= 13.1) Section: science Priority: optional Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Description: homology detection tool across multiple large genomes Murasaki is a scalable and fast, language theory-based homology detection tool across multiple large genomes. It enable whole-genome scale multiple genome global alignments. Supports unlimited length gapped-seed patterns and unique TF-IDF based filtering. . Murasaki is an anchor alignment software, which is * exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 52 wall minutes)) * scalable (Arbitrarily parallelizable across multiple nodes using MPI. Even a single node with 16GB of ram can handle over 1Gbp of sequence.) * unlimited pattern length * repeat tolerant * intelligent noise reduction drwxr-xr-x root/root 0 2021-08-15 18:36 ./ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/bin/ -rwxr-xr-x root/root 352760 2021-08-15 18:36 ./usr/bin/geneparse -rwxr-xr-x root/root 397688 2021-08-15 18:36 ./usr/bin/mbfa -rwxr-xr-x root/root 781416 2021-08-15 18:36 ./usr/bin/murasaki drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/lib/murasaki/ -rwxr-xr-x root/root 299296 2021-08-15 18:36 ./usr/lib/murasaki/align-and -rwxr-xr-x root/root 307520 2021-08-15 18:36 ./usr/lib/murasaki/align-best -rwxr-xr-x root/root 349016 2021-08-15 18:36 ./usr/lib/murasaki/align-compare -rwxr-xr-x root/root 451432 2021-08-15 18:36 ./usr/lib/murasaki/align-coverage -rwxr-xr-x root/root 295168 2021-08-15 18:36 ./usr/lib/murasaki/align-or -rwxr-xr-x root/root 96816 2021-08-15 18:36 ./usr/lib/murasaki/cgr-compare -rwxr-xr-x root/root 405976 2021-08-15 18:36 ./usr/lib/murasaki/cgr-image -rwxr-xr-x root/root 105048 2021-08-15 18:36 ./usr/lib/murasaki/cgr-random -rwxr-xr-x root/root 397736 2021-08-15 18:36 ./usr/lib/murasaki/cgr-sample -rwxr-xr-x root/root 67992 2021-08-15 18:36 ./usr/lib/murasaki/testeco drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/doc/murasaki/ -rw-r--r-- root/root 249 2021-03-19 18:45 ./usr/share/doc/murasaki/README.test -rw-r--r-- root/root 796 2021-08-15 18:36 ./usr/share/doc/murasaki/changelog.Debian.gz -rw-r--r-- root/root 2225 2021-03-19 18:45 ./usr/share/doc/murasaki/copyright drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/man/ drwxr-xr-x root/root 0 2021-08-15 18:36 ./usr/share/man/man1/ -rw-r--r-- root/root 2518 2021-08-15 18:36 ./usr/share/man/man1/geneparse.1.gz -rw-r--r-- root/root 2721 2021-08-15 18:36 ./usr/share/man/man1/mbfa.1.gz -rw-r--r-- root/root 10888 2021-08-15 18:36 ./usr/share/man/man1/murasaki.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 290056 Build-Time: 153 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 20 Job: /srv/debomatic/incoming/murasaki_1.68.6-13.dsc Machine Architecture: amd64 Package: murasaki Package-Time: 180 Source-Version: 1.68.6-13 Space: 290056 Status: successful Version: 1.68.6-13 -------------------------------------------------------------------------------- Finished at 2024-06-04T17:11:28Z Build needed 00:03:00, 290056k disk space