RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux denneed08 4.4.0-43-powerpc64-smp #63-Ubuntu SMP Wed Oct 12 14:10:11 UTC 2016 ppc64 Buildd toolchain package versions: launchpad-buildd_140 python-lpbuildd_140 sbuild_0.67.0-2ubuntu7 git_1:2.7.4-0ubuntu1 dpkg-dev_1.18.4ubuntu1.1 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 21 Oct 22:08:26 ntpdate[1158]: adjust time server 10.211.37.1 offset 0.000055 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-11057407', '/home/buildd/filecache-default/f0d95331816c2600b41a871127347d3aa3e00e52'] Unpacking chroot for build PACKAGEBUILD-11057407 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-11057407'] Mounting chroot for build PACKAGEBUILD-11057407 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-11057407', 'deb http://ftpmaster.internal/ubuntu zesty main universe', 'deb http://ftpmaster.internal/ubuntu zesty-security main universe', 'deb http://ftpmaster.internal/ubuntu zesty-updates main universe', 'deb http://ftpmaster.internal/ubuntu zesty-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-11057407 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-11057407', 'powerpc'] Updating debian chroot for build PACKAGEBUILD-11057407 Get:1 http://ftpmaster.internal/ubuntu zesty InRelease [247 kB] Get:2 http://ftpmaster.internal/ubuntu zesty-security InRelease [92.2 kB] Get:3 http://ftpmaster.internal/ubuntu zesty-updates InRelease [92.1 kB] Get:4 http://ftpmaster.internal/ubuntu zesty-proposed InRelease [95.6 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main powerpc Packages [1168 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main Translation-en [583 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/universe powerpc Packages [7464 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/universe Translation-en [4488 kB] Get:9 http://ftpmaster.internal/ubuntu zesty-proposed/main powerpc Packages [39.0 kB] Get:10 http://ftpmaster.internal/ubuntu zesty-proposed/main Translation-en [25.9 kB] Get:11 http://ftpmaster.internal/ubuntu zesty-proposed/universe powerpc Packages [187 kB] Get:12 http://ftpmaster.internal/ubuntu zesty-proposed/universe Translation-en [93.6 kB] Fetched 14.6 MB in 30s (485 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: base-files binutils cpp-6 dmsetup g++-6 gcc-6 gcc-6-base libapparmor1 libasan3 libatomic1 libcc1-0 libdevmapper1.02.1 libgcc-6-dev libgcc1 libgomp1 liblzma5 libstdc++-6-dev libstdc++6 libubsan0 linux-libc-dev tzdata xz-utils 22 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 24.4 MB of archives. After this operation, 314 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu zesty/main powerpc base-files powerpc 9.6ubuntu6 [55.8 kB] Get:2 http://ftpmaster.internal/ubuntu zesty/main powerpc libgomp1 powerpc 6.2.0-8ubuntu1 [69.5 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main powerpc libcc1-0 powerpc 6.2.0-8ubuntu1 [30.2 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/main powerpc libatomic1 powerpc 6.2.0-8ubuntu1 [7418 B] Get:5 http://ftpmaster.internal/ubuntu zesty/main powerpc libasan3 powerpc 6.2.0-8ubuntu1 [261 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main powerpc libubsan0 powerpc 6.2.0-8ubuntu1 [104 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/main powerpc gcc-6-base powerpc 6.2.0-8ubuntu1 [17.5 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/main powerpc libstdc++6 powerpc 6.2.0-8ubuntu1 [410 kB] Get:9 http://ftpmaster.internal/ubuntu zesty/main powerpc g++-6 powerpc 6.2.0-8ubuntu1 [6243 kB] Get:10 http://ftpmaster.internal/ubuntu zesty/main powerpc libstdc++-6-dev powerpc 6.2.0-8ubuntu1 [1392 kB] Get:11 http://ftpmaster.internal/ubuntu zesty/main powerpc libgcc-6-dev powerpc 6.2.0-8ubuntu1 [555 kB] Get:12 http://ftpmaster.internal/ubuntu zesty/main powerpc gcc-6 powerpc 6.2.0-8ubuntu1 [6025 kB] Get:13 http://ftpmaster.internal/ubuntu zesty/main powerpc cpp-6 powerpc 6.2.0-8ubuntu1 [5516 kB] Get:14 http://ftpmaster.internal/ubuntu zesty/main powerpc libgcc1 powerpc 1:6.2.0-8ubuntu1 [26.9 kB] Get:15 http://ftpmaster.internal/ubuntu zesty-proposed/main powerpc binutils powerpc 2.27-9ubuntu1 [2218 kB] Get:16 http://ftpmaster.internal/ubuntu zesty-proposed/main powerpc liblzma5 powerpc 5.2.2-1.2 [91.2 kB] Get:17 http://ftpmaster.internal/ubuntu zesty-proposed/main powerpc tzdata all 2016h-1 [169 kB] Get:18 http://ftpmaster.internal/ubuntu zesty/main powerpc libdevmapper1.02.1 powerpc 2:1.02.133-1ubuntu1 [136 kB] Get:19 http://ftpmaster.internal/ubuntu zesty/main powerpc dmsetup powerpc 2:1.02.133-1ubuntu1 [70.0 kB] Get:20 http://ftpmaster.internal/ubuntu zesty/main powerpc libapparmor1 powerpc 2.10.95-4ubuntu5.1 [29.1 kB] Get:21 http://ftpmaster.internal/ubuntu zesty-proposed/main powerpc xz-utils powerpc 5.2.2-1.2 [83.0 kB] Get:22 http://ftpmaster.internal/ubuntu zesty-proposed/main powerpc linux-libc-dev powerpc 4.8.0-26.28 [842 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 24.4 MB in 41s (587 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12106 files and directories currently installed.) Preparing to unpack .../base-files_9.6ubuntu6_powerpc.deb ... Unpacking base-files (9.6ubuntu6) over (9.6ubuntu5) ... Setting up base-files (9.6ubuntu6) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12104 files and directories currently installed.) Preparing to unpack .../0-binutils_2.27-9ubuntu1_powerpc.deb ... Unpacking binutils (2.27-9ubuntu1) over (2.27-8ubuntu2) ... Preparing to unpack .../1-liblzma5_5.2.2-1.2_powerpc.deb ... Unpacking liblzma5:powerpc (5.2.2-1.2) over (5.1.1alpha+20120614-2.1ubuntu1) ... Setting up liblzma5:powerpc (5.2.2-1.2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12104 files and directories currently installed.) Preparing to unpack .../0-tzdata_2016h-1_all.deb ... Unpacking tzdata (2016h-1) over (2016g-1) ... Preparing to unpack .../1-libdevmapper1.02.1_2%3a1.02.133-1ubuntu1_powerpc.deb ... Unpacking libdevmapper1.02.1:powerpc (2:1.02.133-1ubuntu1) over (2:1.02.130-1ubuntu1) ... Preparing to unpack .../2-dmsetup_2%3a1.02.133-1ubuntu1_powerpc.deb ... Unpacking dmsetup (2:1.02.133-1ubuntu1) over (2:1.02.130-1ubuntu1) ... Preparing to unpack .../3-libapparmor1_2.10.95-4ubuntu5.1_powerpc.deb ... Unpacking libapparmor1:powerpc (2.10.95-4ubuntu5.1) over (2.10.95-4ubuntu5) ... Preparing to unpack .../4-xz-utils_5.2.2-1.2_powerpc.deb ... Unpacking xz-utils (5.2.2-1.2) over (5.1.1alpha+20120614-2.1ubuntu1) ... Preparing to unpack .../5-linux-libc-dev_4.8.0-26.28_powerpc.deb ... Unpacking linux-libc-dev:powerpc (4.8.0-26.28) over (4.8.0-22.24) ... Setting up libgomp1:powerpc (6.2.0-8ubuntu1) ... Setting up libatomic1:powerpc (6.2.0-8ubuntu1) ... Setting up libcc1-0:powerpc (6.2.0-8ubuntu1) ... Setting up libasan3:powerpc (6.2.0-8ubuntu1) ... Setting up tzdata (2016h-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Oct 22 02:09:47 UTC 2016. Universal Time is now: Sat Oct 22 02:09:47 UTC 2016. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libubsan0:powerpc (6.2.0-8ubuntu1) ... Setting up linux-libc-dev:powerpc (4.8.0-26.28) ... Setting up libdevmapper1.02.1:powerpc (2:1.02.133-1ubuntu1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up libapparmor1:powerpc (2.10.95-4ubuntu5.1) ... Setting up xz-utils (5.2.2-1.2) ... Setting up dmsetup (2:1.02.133-1ubuntu1) ... Setting up binutils (2.27-9ubuntu1) ... Setting up cpp-6 (6.2.0-8ubuntu1) ... Setting up libgcc-6-dev:powerpc (6.2.0-8ubuntu1) ... Setting up libstdc++-6-dev:powerpc (6.2.0-8ubuntu1) ... Setting up gcc-6 (6.2.0-8ubuntu1) ... Setting up g++-6 (6.2.0-8ubuntu1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-11057407', 'powerpc', 'zesty-proposed', '-c', 'chroot:autobuild', '--arch=powerpc', '--dist=zesty-proposed', '--purge=never', '--nolog', 'murasaki_1.68.6-6build2.dsc'] Initiating build PACKAGEBUILD-11057407 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-43-powerpc64-smp #63-Ubuntu SMP Wed Oct 12 14:10:11 UTC 2016 ppc sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on denneed08.buildd +==============================================================================+ | murasaki 1.68.6-6build2 (powerpc) 21 Oct 2016 22:09 | +==============================================================================+ Package: murasaki Version: 1.68.6-6build2 Source Version: 1.68.6-6build2 Distribution: zesty-proposed Machine Architecture: powerpc Host Architecture: powerpc Build Architecture: powerpc I: NOTICE: Log filtering will replace 'build/murasaki-GuSxl3/murasaki-1.68.6' with '<>' I: NOTICE: Log filtering will replace 'build/murasaki-GuSxl3' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-11057407/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- murasaki_1.68.6-6build2.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-LW2HXL/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-LW2HXL/apt_archive ./ InRelease Get:2 copy:/<>/resolver-LW2HXL/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-LW2HXL/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-LW2HXL/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-LW2HXL/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (195 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 770 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-LW2HXL/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 770 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12104 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_powerpc.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev Filtered Build-Depends: debhelper (>= 9), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev dpkg-deb: building package 'sbuild-build-depends-murasaki-dummy' in '/<>/resolver-dSmj93/apt_archive/sbuild-build-depends-murasaki-dummy.deb'. Ign:1 copy:/<>/resolver-dSmj93/apt_archive ./ InRelease Get:2 copy:/<>/resolver-dSmj93/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-dSmj93/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-dSmj93/apt_archive ./ Sources [278 B] Get:5 copy:/<>/resolver-dSmj93/apt_archive ./ Packages [598 B] Fetched 2995 B in 0s (235 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install murasaki 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 bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl libboost-filesystem-dev libboost-filesystem1.61-dev libboost-filesystem1.61.0 libboost-iostreams-dev libboost-iostreams1.61-dev libboost-iostreams1.61.0 libboost-regex-dev libboost-regex1.61-dev libboost-regex1.61.0 libboost-system1.61-dev libboost-system1.61.0 libboost1.61-dev libcroco3 libcrypto++-dev libcrypto++6 libfile-stripnondeterminism-perl libglib2.0-0 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu-dev libicu57 libltdl-dev libltdl7 libmagic1 libnl-3-200 libnl-route-3-200 libnuma-dev libnuma1 libopenmpi-dev libopenmpi2 libpciaccess0 libpipeline1 libpstreams-dev libsigsegv2 libterm-readkey-perl libtext-wrapper-perl libtimedate-perl libtool libunistring0 libxml2 m4 man-db ocl-icd-libopencl1 openmpi-common po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost1.61-doc libboost-atomic1.61-dev libboost-chrono1.61-dev libboost-context1.61-dev libboost-coroutine1.61-dev libboost-date-time1.61-dev libboost-exception1.61-dev libboost-graph1.61-dev libboost-graph-parallel1.61-dev libboost-locale1.61-dev libboost-log1.61-dev libboost-math1.61-dev libboost-mpi1.61-dev libboost-mpi-python1.61-dev libboost-program-options1.61-dev libboost-python1.61-dev libboost-random1.61-dev libboost-serialization1.61-dev libboost-signals1.61-dev libboost-test1.61-dev libboost-thread1.61-dev libboost-timer1.61-dev libboost-wave1.61-dev libboost1.61-tools-dev libmpfrc++-dev libntl-dev libhwloc-contrib-plugins icu-doc libtool-doc openmpi-doc pciutils gfortran | fortran95-compiler gcj-jdk less www-browser opencl-icd libmail-box-perl Recommended packages: curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs openmpi-bin xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl libboost-filesystem-dev libboost-filesystem1.61-dev libboost-filesystem1.61.0 libboost-iostreams-dev libboost-iostreams1.61-dev libboost-iostreams1.61.0 libboost-regex-dev libboost-regex1.61-dev libboost-regex1.61.0 libboost-system1.61-dev libboost-system1.61.0 libboost1.61-dev libcroco3 libcrypto++-dev libcrypto++6 libfile-stripnondeterminism-perl libglib2.0-0 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu-dev libicu57 libltdl-dev libltdl7 libmagic1 libnl-3-200 libnl-route-3-200 libnuma-dev libnuma1 libopenmpi-dev libopenmpi2 libpciaccess0 libpipeline1 libpstreams-dev libsigsegv2 libterm-readkey-perl libtext-wrapper-perl libtimedate-perl libtool libunistring0 libxml2 m4 man-db ocl-icd-libopencl1 openmpi-common po-debconf sbuild-build-depends-murasaki-dummy 0 upgraded, 64 newly installed, 0 to remove and 0 not upgraded. Need to get 44.6 MB of archives. After this operation, 299 MB of additional disk space will be used. Get:1 copy:/<>/resolver-dSmj93/apt_archive ./ sbuild-build-depends-murasaki-dummy 0.invalid.0 [844 B] Get:2 http://ftpmaster.internal/ubuntu zesty/main powerpc groff-base powerpc 1.22.3-8 [1194 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main powerpc bsdmainutils powerpc 9.0.6ubuntu3 [172 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/main powerpc libpipeline1 powerpc 1.4.1-2 [24.2 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main powerpc man-db powerpc 2.7.5-1 [835 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main powerpc libunistring0 powerpc 0.9.3-5.2ubuntu1 [254 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/main powerpc libmagic1 powerpc 1:5.28-2ubuntu1 [232 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/main powerpc file powerpc 1:5.28-2ubuntu1 [21.7 kB] Get:9 http://ftpmaster.internal/ubuntu zesty/main powerpc gettext-base powerpc 0.19.8.1-1ubuntu2 [45.5 kB] Get:10 http://ftpmaster.internal/ubuntu zesty/main powerpc libglib2.0-0 powerpc 2.50.0-1 [983 kB] Get:11 http://ftpmaster.internal/ubuntu zesty/main powerpc libicu57 powerpc 57.1-4 [7478 kB] Get:12 http://ftpmaster.internal/ubuntu zesty/main powerpc libnuma1 powerpc 2.0.11-1ubuntu2 [19.3 kB] Get:13 http://ftpmaster.internal/ubuntu zesty/main powerpc libxml2 powerpc 2.9.4+dfsg1-2 [573 kB] Get:14 http://ftpmaster.internal/ubuntu zesty/main powerpc libsigsegv2 powerpc 2.10-5 [13.6 kB] Get:15 http://ftpmaster.internal/ubuntu zesty/main powerpc m4 powerpc 1.4.17-5 [185 kB] Get:16 http://ftpmaster.internal/ubuntu zesty/main powerpc autoconf all 2.69-10 [321 kB] Get:17 http://ftpmaster.internal/ubuntu zesty/main powerpc autotools-dev all 20160430.1 [39.6 kB] Get:18 http://ftpmaster.internal/ubuntu zesty/main powerpc automake all 1:1.15-4ubuntu1 [510 kB] Get:19 http://ftpmaster.internal/ubuntu zesty/main powerpc autopoint all 0.19.8.1-1ubuntu2 [412 kB] Get:20 http://ftpmaster.internal/ubuntu zesty/main powerpc libtool all 2.4.6-1 [194 kB] Get:21 http://ftpmaster.internal/ubuntu zesty/main powerpc dh-autoreconf all 12 [15.8 kB] Get:22 http://ftpmaster.internal/ubuntu zesty/main powerpc libarchive-zip-perl all 1.59-1 [84.0 kB] Get:23 http://ftpmaster.internal/ubuntu zesty/main powerpc libfile-stripnondeterminism-perl all 0.028-1 [12.5 kB] Get:24 http://ftpmaster.internal/ubuntu zesty/main powerpc libtimedate-perl all 2.3000-2 [37.5 kB] Get:25 http://ftpmaster.internal/ubuntu zesty/main powerpc dh-strip-nondeterminism all 0.028-1 [4820 B] Get:26 http://ftpmaster.internal/ubuntu zesty/main powerpc libcroco3 powerpc 0.6.11-1 [69.3 kB] Get:27 http://ftpmaster.internal/ubuntu zesty/main powerpc gettext powerpc 0.19.8.1-1ubuntu2 [1018 kB] Get:28 http://ftpmaster.internal/ubuntu zesty/main powerpc intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:29 http://ftpmaster.internal/ubuntu zesty/main powerpc po-debconf all 1.0.19 [234 kB] Get:30 http://ftpmaster.internal/ubuntu zesty-proposed/main powerpc debhelper all 10.2.2ubuntu1 [742 kB] Get:31 http://ftpmaster.internal/ubuntu zesty/main powerpc icu-devtools powerpc 57.1-4 [156 kB] Get:32 http://ftpmaster.internal/ubuntu zesty-proposed/main powerpc libboost1.61-dev powerpc 1.61.0+dfsg-3 [6821 kB] Get:33 http://ftpmaster.internal/ubuntu zesty-proposed/main powerpc libboost-system1.61.0 powerpc 1.61.0+dfsg-3 [10.5 kB] Get:34 http://ftpmaster.internal/ubuntu zesty-proposed/main powerpc libboost-filesystem1.61.0 powerpc 1.61.0+dfsg-3 [37.4 kB] Get:35 http://ftpmaster.internal/ubuntu zesty-proposed/main powerpc libboost-system1.61-dev powerpc 1.61.0+dfsg-3 [9260 B] Get:36 http://ftpmaster.internal/ubuntu zesty-proposed/universe powerpc libboost-filesystem1.61-dev powerpc 1.61.0+dfsg-3 [45.1 kB] Get:37 http://ftpmaster.internal/ubuntu zesty/universe powerpc libboost-filesystem-dev powerpc 1.61.0.2 [2896 B] Get:38 http://ftpmaster.internal/ubuntu zesty-proposed/main powerpc libboost-regex1.61.0 powerpc 1.61.0+dfsg-3 [238 kB] Get:39 http://ftpmaster.internal/ubuntu zesty/main powerpc libicu-dev powerpc 57.1-4 [15.7 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kB] Get:49 http://ftpmaster.internal/ubuntu zesty/main powerpc libnl-3-200 powerpc 3.2.27-1 [46.7 kB] Get:50 http://ftpmaster.internal/ubuntu zesty/main powerpc libnl-route-3-200 powerpc 3.2.27-1 [104 kB] Get:51 http://ftpmaster.internal/ubuntu zesty/main powerpc libpciaccess0 powerpc 0.13.4-1 [17.1 kB] Get:52 http://ftpmaster.internal/ubuntu zesty/universe powerpc libpstreams-dev all 0.8.0-2 [106 kB] Get:53 http://ftpmaster.internal/ubuntu zesty/universe powerpc libterm-readkey-perl powerpc 2.33-1build1 [26.2 kB] Get:54 http://ftpmaster.internal/ubuntu zesty/universe powerpc libtext-wrapper-perl all 1.05-2 [10.3 kB] Get:55 http://ftpmaster.internal/ubuntu zesty-proposed/universe powerpc openmpi-common all 2.0.1-5ubuntu1 [134 kB] Get:56 http://ftpmaster.internal/ubuntu zesty/universe powerpc libhwloc5 powerpc 1.11.3-2 [86.1 kB] Get:57 http://ftpmaster.internal/ubuntu zesty/main powerpc libnuma-dev powerpc 2.0.11-1ubuntu2 [30.2 kB] Get:58 http://ftpmaster.internal/ubuntu zesty/universe powerpc libhwloc-dev powerpc 1.11.3-2 [144 kB] Get:59 http://ftpmaster.internal/ubuntu zesty/main powerpc ocl-icd-libopencl1 powerpc 2.2.9-2 [29.0 kB] Get:60 http://ftpmaster.internal/ubuntu zesty/universe powerpc libhwloc-plugins powerpc 1.11.3-2 [11.5 kB] Get:61 http://ftpmaster.internal/ubuntu zesty/main powerpc libibverbs1 powerpc 1.2.0-2ubuntu1 [28.2 kB] Get:62 http://ftpmaster.internal/ubuntu zesty/main powerpc libibverbs-dev powerpc 1.2.0-2ubuntu1 [82.3 kB] Get:63 http://ftpmaster.internal/ubuntu zesty-proposed/universe powerpc libopenmpi2 powerpc 2.0.1-5ubuntu1 [1578 kB] Get:64 http://ftpmaster.internal/ubuntu zesty-proposed/universe powerpc libopenmpi-dev powerpc 2.0.1-5ubuntu1 [903 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 44.6 MB in 1min 1s (723 kB/s) Selecting previously unselected package groff-base. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12104 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-8_powerpc.deb ... Unpacking groff-base (1.22.3-8) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_9.0.6ubuntu3_powerpc.deb ... Unpacking bsdmainutils (9.0.6ubuntu3) ... Selecting previously unselected package libpipeline1:powerpc. 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Setting up libxml2:powerpc (2.9.4+dfsg1-2) ... Setting up libterm-readkey-perl (2.33-1build1) ... Setting up libmagic1:powerpc (1:5.28-2ubuntu1) ... Setting up libcroco3:powerpc (0.6.11-1) ... Setting up libboost-filesystem1.61.0:powerpc (1.61.0+dfsg-3) ... Setting up libtext-wrapper-perl (1.05-2) ... Setting up openmpi-common (2.0.1-5ubuntu1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up autotools-dev (20160430.1) ... Setting up libunistring0:powerpc (0.9.3-5.2ubuntu1) ... Setting up libltdl7:powerpc (2.4.6-1) ... Setting up libpciaccess0:powerpc (0.13.4-1) ... Setting up icu-devtools (57.1-4) ... Setting up libnuma-dev:powerpc (2.0.11-1ubuntu2) ... Setting up ocl-icd-libopencl1:powerpc (2.2.9-2) ... Setting up bsdmainutils (9.0.6ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libnl-3-200:powerpc (3.2.27-1) ... Setting up autopoint (0.19.8.1-1ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.028-1) ... Setting up libboost-system1.61-dev:powerpc (1.61.0+dfsg-3) ... Setting up libltdl-dev:powerpc (2.4.6-1) ... Setting up libboost-regex1.61.0:powerpc (1.61.0+dfsg-3) ... Setting up gettext (0.19.8.1-1ubuntu2) ... Setting up libnl-route-3-200:powerpc (3.2.27-1) ... Setting up autoconf (2.69-10) ... Setting up libicu-dev (57.1-4) ... Setting up file (1:5.28-2ubuntu1) ... Setting up libhwloc5:powerpc (1.11.3-2) ... Setting up libhwloc-plugins (1.11.3-2) ... Setting up libboost-filesystem1.61-dev:powerpc (1.61.0+dfsg-3) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libboost-regex1.61-dev:powerpc (1.61.0+dfsg-3) ... Setting up automake (1:1.15-4ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-regex-dev:powerpc (1.61.0.2) ... Setting up libtool (2.4.6-1) ... Setting up libibverbs1 (1.2.0-2ubuntu1) ... Setting up libboost-iostreams1.61-dev:powerpc (1.61.0+dfsg-3) ... Setting up po-debconf (1.0.19) ... Setting up libhwloc-dev:powerpc (1.11.3-2) ... Setting up libboost-filesystem-dev:powerpc (1.61.0.2) ... Setting up libboost-iostreams-dev:powerpc (1.61.0.2) ... Setting up libopenmpi2 (2.0.1-5ubuntu1) ... Setting up libibverbs-dev (1.2.0-2ubuntu1) ... Setting up libopenmpi-dev (2.0.1-5ubuntu1) ... update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode Setting up dh-autoreconf (12) ... Setting up dh-strip-nondeterminism (0.028-1) ... Setting up debhelper (10.2.2ubuntu1) ... Setting up sbuild-build-depends-murasaki-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-43-powerpc64-smp powerpc (ppc) Toolchain package versions: binutils_2.27-9ubuntu1 dpkg-dev_1.18.10ubuntu1 g++-6_6.2.0-8ubuntu1 gcc-6_6.2.0-8ubuntu1 libc6-dev_2.24-3ubuntu1 libstdc++-6-dev_6.2.0-8ubuntu1 libstdc++6_6.2.0-8ubuntu1 linux-libc-dev_4.8.0-26.28 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.3.1 apt-transport-https_1.3.1 autoconf_2.69-10 automake_1:1.15-4ubuntu1 autopoint_0.19.8.1-1ubuntu2 autotools-dev_20160430.1 base-files_9.6ubuntu6 base-passwd_3.5.40 bash_4.3-15ubuntu1 binutils_2.27-9ubuntu1 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.28.2-1ubuntu1 build-essential_12.1ubuntu2 bzip2_1.0.6-8build1 ca-certificates_20160104ubuntu1 coreutils_8.25-2ubuntu2 cpp_4:6.1.1-1ubuntu2 cpp-6_6.2.0-8ubuntu1 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ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 ocl-icd-libopencl1_2.2.9-2 openmpi-common_2.0.1-5ubuntu1 openssl_1.0.2g-1ubuntu9 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu1 patch_2.7.5-1 perl_5.22.2-3 perl-base_5.22.2-3 perl-modules-5.22_5.22.2-3 pinentry-curses_0.9.7-5 pkg-create-dbgsym_0.72 pkgbinarymangler_131 po-debconf_1.0.19 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-murasaki-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 systemd_231-9git1 systemd-sysv_231-9git1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tar_1.29b-1 tzdata_2016h-1 ubuntu-keyring_2016.09.19 util-linux_2.28.2-1ubuntu1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2ubuntu5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Oct 22 01:40:00 2016 UTC gpgv: using RSA key gpgv: issuer "steve.langasek@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./murasaki_1.68.6-6build2.dsc dpkg-source: info: extracting murasaki in murasaki-1.68.6 dpkg-source: info: unpacking murasaki_1.68.6.orig.tar.gz dpkg-source: info: unpacking murasaki_1.68.6-6build2.debian.tar.xz 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 Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<> SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package murasaki dpkg-buildpackage: info: source version 1.68.6-6build2 dpkg-buildpackage: info: source distribution zesty dpkg-source --before-build murasaki-1.68.6 dpkg-buildpackage: info: host architecture powerpc fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean make -j1 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 debian/rules build-arch dh build-arch dh_testdir -a dh_update_autotools_config -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- USE_MPI=YES make -j1 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 In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki.cc:37: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki.cc:37: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki.cc:37: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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] bool revZero=false; ^~~~~~~ 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 /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from dinkymath.cc:27: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from dinkymath.cc:27: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from dinkymath.cc:27: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ dinkymath.cc: In function ‘std::__cxx11::string littleEndianStr(unsigned int, int)’: dinkymath.cc:40:7: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] int last=0; ^~~~ dinkymath.cc: In function ‘std::__cxx11::string littleEndianPat(unsigned int, int)’: dinkymath.cc:53:7: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 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 /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from sequence.cc:28: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from sequence.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from sequence.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ sequence.cc: In destructor ‘Sequence::~Sequence()’: sequence.cc:377:123: warning: throw will always call terminate() [-Wterminate] throw MurasakiException("Couldn't mark System V IPC shared memory region for deletion for sequence "+name+strerror(errno)); ^ sequence.cc:377:123: note: in C++11 destructors default to noexcept sequence.cc: In destructor ‘BitSequence::~BitSequence()’: sequence.cc:1394:133: warning: throw will always call terminate() [-Wterminate] throw MurasakiException("Couldn't detach System V shared memory region for "+(seq ? seq->filename:string("(anon)"))+strerror(errno)); ^ sequence.cc:1394:133: 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] SeqPos shortest=0,shortlen=length(spaces[0]); ^~~~~~~~ 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 /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from msethash.cc:25: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from msethash.cc:25: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from msethash.cc:25: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c options.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from options.h:28, from options.cc:26: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from options.h:28, from options.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from options.h:28, from options.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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 /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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 /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecolist.cc:20: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecolist.cc:20: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecolist.cc:20: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c murasaki_mpi.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki_mpi.cc:33: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki_mpi.cc:33: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki_mpi.cc:33: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ murasaki_mpi.cc: In function ‘void mpi_types_init()’: murasaki_mpi.cc:107:3: warning: ‘int MPI_Address(void*, MPI_Aint*)’ is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.key,disp); ^~~~~~~~~~~ In file included from murasaki_mpi.cc:29:0: /usr/lib/openmpi/include/mpi.h:1200:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:107:28: warning: ‘int MPI_Address(void*, MPI_Aint*)’ is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.key,disp); ^ In file included from murasaki_mpi.cc:29:0: /usr/lib/openmpi/include/mpi.h:1200:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:108:3: warning: ‘int MPI_Address(void*, MPI_Aint*)’ is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.seqno,disp+1); ^~~~~~~~~~~ In file included from murasaki_mpi.cc:29:0: /usr/lib/openmpi/include/mpi.h:1200:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:108:32: warning: ‘int MPI_Address(void*, MPI_Aint*)’ is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.seqno,disp+1); ^ In file included from murasaki_mpi.cc:29:0: /usr/lib/openmpi/include/mpi.h:1200:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:109:3: warning: ‘int MPI_Address(void*, MPI_Aint*)’ is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.pos,disp+1); ^~~~~~~~~~~ In file included from murasaki_mpi.cc:29:0: /usr/lib/openmpi/include/mpi.h:1200:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:109:30: warning: ‘int MPI_Address(void*, MPI_Aint*)’ is deprecated: MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] MPI_Address(&msg.pos,disp+1); ^ In file included from murasaki_mpi.cc:29:0: /usr/lib/openmpi/include/mpi.h:1200:20: note: declared here OMPI_DECLSPEC int MPI_Address(void *location, MPI_Aint *address) ^~~~~~~~~~~ murasaki_mpi.cc:112:3: warning: ‘int MPI_Type_struct(int, int*, MPI_Aint*, ompi_datatype_t**, ompi_datatype_t**)’ is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(3,blocklen,disp,type,&MPI_HashMessage_type); ^~~~~~~~~~~~~~~ In file included from murasaki_mpi.cc:29:0: /usr/lib/openmpi/include/mpi.h:1817:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ murasaki_mpi.cc:112:61: warning: ‘int MPI_Type_struct(int, int*, MPI_Aint*, ompi_datatype_t**, ompi_datatype_t**)’ is deprecated: MPI_Type_struct is superseded by MPI_Type_create_struct in MPI-2.0 [-Wdeprecated-declarations] MPI_Type_struct(3,blocklen,disp,type,&MPI_HashMessage_type); ^ In file included from murasaki_mpi.cc:29:0: /usr/lib/openmpi/include/mpi.h:1817:20: note: declared here OMPI_DECLSPEC int MPI_Type_struct(int count, int array_of_blocklengths[], ^~~~~~~~~~~~~~~ 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] int send_done; ^~~~~~~~~ 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 /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from arrayhash.cc:28: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from arrayhash.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from arrayhash.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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 In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from seqread.cc:28: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from seqread.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from seqread.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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 /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from scoring.cc:27: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from scoring.cc:27: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from scoring.cc:27: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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 /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from openhash.h:29, from openhash.cc:26: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from openhash.h:29, from openhash.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from openhash.h:29, from openhash.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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 In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from binseq.cc:21: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from binseq.cc:21: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from binseq.cc:21: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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,-Bsymbolic-functions -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 -c cgr-image.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-image.cc:33: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-image.cc:33: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-image.cc:33: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr.cc cgr.cc: In member function ‘void Cgr::merge(Cgr&)’: cgr.cc:140:7: warning: variable ‘redist’ set but not used [-Wunused-but-set-variable] int redist=(unsigned long)(rez*rez)<=seedcount; ^~~~~~ cgr.cc: In member function ‘bool Cgr::savePNG(std::__cxx11::string)’: cgr.cc:288:7: warning: variable ‘res’ set but not used [-Wunused-but-set-variable] int res; ^~~ cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::__cxx11::string)’: cgr.cc:435:7: warning: variable ‘wordwidth’ set but not used [-Wunused-but-set-variable] int wordwidth=1; ^~~~~~~~~ cgr.cc: In member function ‘int PgmBuffer::loadBinaryPGM(std::__cxx11::string)’: cgr.cc:546:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] data.push_back(*(gray*)(line)); ^ cgr.cc:557:31: warning: ‘height’ may be used uninitialized in this function [-Wmaybe-uninitialized] if(data.size()<(uint)(height*width)) ~~~~~~~^~~~~~~ cgr.cc:557:31: warning: ‘width’ may be used uninitialized in this function [-Wmaybe-uninitialized] cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::__cxx11::string)’: cgr.cc:485:31: warning: ‘height’ may be used uninitialized in this function [-Wmaybe-uninitialized] if(data.size()<(uint)(height*width)) ~~~~~~~^~~~~~~ cgr.cc:485:31: warning: ‘width’ may be used uninitialized in this function [-Wmaybe-uninitialized] 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,-Bsymbolic-functions -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 -c cgr-compare.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -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 -c cgr-random.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -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 -c cgr-sample.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-sample.cc:35: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-sample.cc:35: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-sample.cc:35: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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] 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 -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -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 -c testeco.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from testeco.cc:20: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from testeco.cc:20: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from testeco.cc:20: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ testeco.cc: In function ‘long int bigrand()’: testeco.cc:29:43: warning: left shift count >= width of type [-Wshift-count-overflow] return (long)(((unsigned long)(rand())<<32) + ((unsigned long)(rand()))); ^~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -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 -c align-compare.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c alignments.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -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 -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 -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -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 -c geneparse.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from geneparse.cc:30: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from geneparse.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from geneparse.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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,-Bsymbolic-functions -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 -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 -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -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 -c align-best.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -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 -c align-coverage.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from align-coverage.cc:35: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from align-coverage.cc:35: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from align-coverage.cc:35: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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] bool seqStats=true; ^~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -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,-Bsymbolic-functions -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 -c getsegments.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from getsegments.cc:30: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from getsegments.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from getsegments.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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,-Bsymbolic-functions -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 -c mbfa.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from mbfa.cc:30: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from mbfa.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from mbfa.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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,-Bsymbolic-functions -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 -j1 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 In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki.cc:37: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki.cc:37: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from murasaki.cc:37: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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] bool revZero=false; ^~~~~~~ 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 /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from dinkymath.cc:27: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from dinkymath.cc:27: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from dinkymath.cc:27: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ dinkymath.cc: In function ‘std::__cxx11::string littleEndianStr(unsigned int, int)’: dinkymath.cc:40:7: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] int last=0; ^~~~ dinkymath.cc: In function ‘std::__cxx11::string littleEndianPat(unsigned int, int)’: dinkymath.cc:53:7: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 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 /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from sequence.cc:28: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from sequence.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from sequence.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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] SeqPos shortest=0,shortlen=length(spaces[0]); ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c msethash.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from msethash.cc:25: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from msethash.cc:25: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from msethash.cc:25: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c options.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from options.h:28, from options.cc:26: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from options.h:28, from options.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from options.h:28, from options.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c ecohash.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecohash.h:29, from ecohash.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c ecolist.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecolist.cc:20: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecolist.cc:20: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from ecolist.cc:20: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c murasaki_mpi.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c arrayhash.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from arrayhash.cc:28: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from arrayhash.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from arrayhash.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c seqread.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from seqread.cc:28: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from seqread.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from seqread.cc:28: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c scoring.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from scoring.cc:27: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from scoring.cc:27: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from murasaki.h:24, from scoring.cc:27: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c openhash.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from openhash.h:29, from openhash.cc:26: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from openhash.h:29, from openhash.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from openhash.h:29, from openhash.cc:26: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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 In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from binseq.cc:21: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from binseq.cc:21: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from binseq.cc:21: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-image.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-image.cc:33: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-image.cc:33: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-image.cc:33: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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] int redist=(unsigned long)(rez*rez)<=seedcount; ^~~~~~ cgr.cc: In member function ‘bool Cgr::savePNG(std::__cxx11::string)’: cgr.cc:288:7: warning: variable ‘res’ set but not used [-Wunused-but-set-variable] int res; ^~~ cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::__cxx11::string)’: cgr.cc:435:7: warning: variable ‘wordwidth’ set but not used [-Wunused-but-set-variable] int wordwidth=1; ^~~~~~~~~ cgr.cc: In member function ‘int PgmBuffer::loadBinaryPGM(std::__cxx11::string)’: cgr.cc:546:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] data.push_back(*(gray*)(line)); ^ cgr.cc:557:31: warning: ‘height’ may be used uninitialized in this function [-Wmaybe-uninitialized] if(data.size()<(uint)(height*width)) ~~~~~~~^~~~~~~ cgr.cc:557:31: warning: ‘width’ may be used uninitialized in this function [-Wmaybe-uninitialized] cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::__cxx11::string)’: cgr.cc:485:31: warning: ‘height’ may be used uninitialized in this function [-Wmaybe-uninitialized] if(data.size()<(uint)(height*width)) ~~~~~~~^~~~~~~ cgr.cc:485:31: warning: ‘width’ may be used uninitialized in this function [-Wmaybe-uninitialized] 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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now 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 -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now 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 -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-sample.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-sample.cc:35: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-sample.cc:35: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from cgr-sample.cc:35: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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] bool repeatmask=false,save=false; ^~~~~~~~~~ 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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c testeco.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from testeco.cc:20: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from testeco.cc:20: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from binseq.hh:31, from sequence.h:32, from ecolist.h:23, from testeco.cc:20: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ testeco.cc: In function ‘long int bigrand()’: testeco.cc:29:43: warning: left shift count >= width of type [-Wshift-count-overflow] return (long)(((unsigned long)(rand())<<32) + ((unsigned long)(rand()))); ^~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now 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 -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now 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 -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c geneparse.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from geneparse.cc:30: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from geneparse.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from geneparse.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now 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 -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now 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 -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now 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 /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from align-coverage.cc:35: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from align-coverage.cc:35: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from align-coverage.cc:35: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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] bool seqStats=true; ^~~~~~~~ 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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c getsegments.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from getsegments.cc:30: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from getsegments.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from getsegments.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c mbfa.cc In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from mbfa.cc:30: /usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated") ^ In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0, from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from mbfa.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0, from /usr/include/boost/iostreams/detail/resolve.hpp:26, from /usr/include/boost/iostreams/detail/push.hpp:24, from /usr/include/boost/iostreams/chain.hpp:29, from /usr/include/boost/iostreams/filtering_streambuf.hpp:17, from seqread.h:34, from mbfa.cc:30: /usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated") ^ 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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test -a fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a 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_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a debian/rules override_dh_link make[1]: Entering directory '/<>' dh_link mkdir -p debian/murasaki-mpi/usr/share/man/man1 for man in debian/murasaki/usr/share/man/man1/* ; do \ ln -s `basename ${man}`.gz debian/murasaki-mpi/usr/share/man/man1/`basename ${man} .1`-mpi.1.gz ; \ done make[1]: Leaving directory '/<>' dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_strip -a dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform powerpc: murasaki murasaki-mpi dh_strip debug symbol extraction: packages to act on: murasaki murasaki-mpi dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol Using buildid for compat level >= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package murasaki-mpi: unused substitution variable ${perl:Depends} /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package murasaki-mpi: unused substitution variable ${perl:Depends} dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform powerpc: murasaki murasaki-mpi dh_gencontrol debug symbol wrapper: packages to act on: murasaki murasaki-mpi dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package murasaki (pkgdir debian/murasaki, ddeb package dir debian/murasaki-dbgsym) dh_gencontrol debug symbol wrapper: building murasaki-dbgsym_1.68.6-6build2_powerpc.ddeb dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-6build2_powerpc.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile murasaki-dbgsym_1.68.6-6build2_powerpc.ddeb science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: processing package murasaki-mpi (pkgdir debian/murasaki-mpi, ddeb package dir debian/murasaki-mpi-dbgsym) dh_gencontrol debug symbol wrapper: building murasaki-mpi-dbgsym_1.68.6-6build2_powerpc.ddeb dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-6build2_powerpc.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile murasaki-mpi-dbgsym_1.68.6-6build2_powerpc.ddeb science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 pkgstriptranslations: processing murasaki (in debian/murasaki); do_strip: , oemstrip: pkgstriptranslations: processing murasaki-mpi (in debian/murasaki-mpi); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/murasaki/DEBIAN/control, package murasaki, directory debian/murasaki pkgstripfiles: Running PNG optimization (using 4 cpus) for package murasaki ... pkgstripfiles: No PNG files. dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-6build2_powerpc.deb'. pkgstripfiles: processing control file: debian/murasaki-mpi/DEBIAN/control, package murasaki-mpi, directory debian/murasaki-mpi pkgstripfiles: Running PNG optimization (using 4 cpus) for package murasaki-mpi ... pkgstripfiles: No PNG files. dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-6build2_powerpc.deb'. dpkg-genchanges --build=any -mLaunchpad Build Daemon >../murasaki_1.68.6-6build2_powerpc.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build murasaki-1.68.6 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20161021-2216 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ murasaki_1.68.6-6build2_powerpc.changes: ---------------------------------------- Format: 1.8 Date: Sat, 22 Oct 2016 01:39:57 +0000 Source: murasaki Binary: murasaki murasaki-mpi murasaki-common Architecture: powerpc Version: 1.68.6-6build2 Distribution: zesty-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steve Langasek 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 (1.68.6-6build2) zesty; urgency=medium . * No-change rebuild against libopenmpi2 Checksums-Sha1: 5b242d8aaf4057c8ef894caae71c3f398b971894 5764376 murasaki-dbgsym_1.68.6-6build2_powerpc.ddeb 0fdc1ac09de2f9207b888795d519d347517171cb 6453942 murasaki-mpi-dbgsym_1.68.6-6build2_powerpc.ddeb 70f1c0f48e3668da1424b236d9c318bb1a5eadeb 502376 murasaki-mpi_1.68.6-6build2_powerpc.deb 7efd5ddb94cabd78c35be572f743e3d704307d40 424420 murasaki_1.68.6-6build2_powerpc.deb Checksums-Sha256: 181bbe2000b1daba1e3551400719dc1d710d4f79b7a4ffe5b240c3ea9be19cdb 5764376 murasaki-dbgsym_1.68.6-6build2_powerpc.ddeb b3c53d45a2eea38b2bd060f68ed9d85b9c327aa911aa14897b6b3d4ee968e1cd 6453942 murasaki-mpi-dbgsym_1.68.6-6build2_powerpc.ddeb 70d607a952137330e12ac9c9652193871dcdee6a15ab18e72db93bc54be78b66 502376 murasaki-mpi_1.68.6-6build2_powerpc.deb 2fdd4299290af6ac6b781677acd948155f3d51e6478c47cd32ca461d2231bef5 424420 murasaki_1.68.6-6build2_powerpc.deb Files: 28268f1a93fa3a8c7379189baff2550b 5764376 science extra murasaki-dbgsym_1.68.6-6build2_powerpc.ddeb 4717ba2e9fae662773f1a739671de51c 6453942 science extra murasaki-mpi-dbgsym_1.68.6-6build2_powerpc.ddeb 134c400fa25492f009ea8549b6209310 502376 science optional murasaki-mpi_1.68.6-6build2_powerpc.deb 5c7194e5c75270b524d8e2e3af3fa273 424420 science optional murasaki_1.68.6-6build2_powerpc.deb Original-Maintainer: Debian Med Packaging Team +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ murasaki-mpi_1.68.6-6build2_powerpc.deb --------------------------------------- new debian package, version 2.0. size 502376 bytes: control archive=1508 bytes. 1449 bytes, 29 lines control 1116 bytes, 17 lines md5sums Package: murasaki-mpi Source: murasaki Version: 1.68.6-6build2 Architecture: powerpc Maintainer: Ubuntu Developers Installed-Size: 4151 Depends: murasaki-common, libboost-filesystem1.61.0, libboost-iostreams1.61.0, libboost-regex1.61.0, libboost-system1.61.0, libc6 (>= 2.4), libgcc1 (>= 1:4.2), libopenmpi2, libstdc++6 (>= 5.2) 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. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2016-10-21 21:39 ./ drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/ drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/bin/ -rwxr-xr-x root/root 264120 2016-10-21 21:39 ./usr/bin/geneparse-mpi -rwxr-xr-x root/root 395204 2016-10-21 21:39 ./usr/bin/mbfa-mpi -rwxr-xr-x root/root 789600 2016-10-21 21:39 ./usr/bin/murasaki-mpi drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/lib/ drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/lib/murasaki/ -rwxr-xr-x root/root 264020 2016-10-21 21:39 ./usr/lib/murasaki/align-and-mpi -rwxr-xr-x root/root 264036 2016-10-21 21:39 ./usr/lib/murasaki/align-best-mpi -rwxr-xr-x root/root 329596 2016-10-21 21:39 ./usr/lib/murasaki/align-compare-mpi -rwxr-xr-x root/root 395220 2016-10-21 21:39 ./usr/lib/murasaki/align-coverage-mpi -rwxr-xr-x root/root 264004 2016-10-21 21:39 ./usr/lib/murasaki/align-or-mpi -rwxr-xr-x root/root 198448 2016-10-21 21:39 ./usr/lib/murasaki/cgr-compare-mpi -rwxr-xr-x root/root 395284 2016-10-21 21:39 ./usr/lib/murasaki/cgr-image-mpi -rwxr-xr-x root/root 7138 2010-08-24 10:18 ./usr/lib/murasaki/cgr-image.pl-mpi -rwxr-xr-x root/root 198484 2016-10-21 21:39 ./usr/lib/murasaki/cgr-random-mpi -rwxr-xr-x root/root 329644 2016-10-21 21:39 ./usr/lib/murasaki/cgr-sample-mpi -rwxr-xr-x root/root 132808 2016-10-21 21:39 ./usr/lib/murasaki/testeco-mpi drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/share/ drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/share/doc/murasaki-mpi/ -rw-r--r-- root/root 249 2016-07-12 03:25 ./usr/share/doc/murasaki-mpi/README.test -rw-r--r-- root/root 840 2016-10-21 21:39 ./usr/share/doc/murasaki-mpi/changelog.Debian.gz -rw-r--r-- root/root 2221 2016-07-12 03:25 ./usr/share/doc/murasaki-mpi/copyright drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/share/man/ drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/share/man/man1/ lrwxrwxrwx root/root 0 2016-10-21 21:39 ./usr/share/man/man1/geneparse-mpi.1.gz -> geneparse.1.gz lrwxrwxrwx root/root 0 2016-10-21 21:39 ./usr/share/man/man1/mbfa-mpi.1.gz -> mbfa.1.gz lrwxrwxrwx root/root 0 2016-10-21 21:39 ./usr/share/man/man1/murasaki-mpi.1.gz -> murasaki.1.gz murasaki_1.68.6-6build2_powerpc.deb ----------------------------------- new debian package, version 2.0. size 424420 bytes: control archive=1436 bytes. 1231 bytes, 24 lines control 1182 bytes, 19 lines md5sums Package: murasaki Version: 1.68.6-6build2 Architecture: powerpc Maintainer: Ubuntu Developers Installed-Size: 3388 Depends: murasaki-common, libboost-filesystem1.61.0, libboost-iostreams1.61.0, libboost-regex1.61.0, libboost-system1.61.0, libc6 (>= 2.4), libgcc1 (>= 1:4.2), libstdc++6 (>= 5.2) 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 Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2016-10-21 21:39 ./ drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/ drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/bin/ -rwxr-xr-x root/root 264120 2016-10-21 21:39 ./usr/bin/geneparse -rwxr-xr-x root/root 329596 2016-10-21 21:39 ./usr/bin/mbfa -rwxr-xr-x root/root 658432 2016-10-21 21:39 ./usr/bin/murasaki drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/lib/ drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/lib/murasaki/ -rwxr-xr-x root/root 198412 2016-10-21 21:39 ./usr/lib/murasaki/align-and -rwxr-xr-x root/root 198428 2016-10-21 21:39 ./usr/lib/murasaki/align-best -rwxr-xr-x root/root 263988 2016-10-21 21:39 ./usr/lib/murasaki/align-compare -rwxr-xr-x root/root 329612 2016-10-21 21:39 ./usr/lib/murasaki/align-coverage -rwxr-xr-x root/root 198396 2016-10-21 21:39 ./usr/lib/murasaki/align-or -rwxr-xr-x root/root 132836 2016-10-21 21:39 ./usr/lib/murasaki/cgr-compare -rwxr-xr-x root/root 329672 2016-10-21 21:39 ./usr/lib/murasaki/cgr-image -rwxr-xr-x root/root 132872 2016-10-21 21:39 ./usr/lib/murasaki/cgr-random -rwxr-xr-x root/root 329644 2016-10-21 21:39 ./usr/lib/murasaki/cgr-sample -rwxr-xr-x root/root 67200 2016-10-21 21:39 ./usr/lib/murasaki/testeco drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/share/ drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/share/doc/murasaki/ -rw-r--r-- root/root 249 2016-07-12 03:25 ./usr/share/doc/murasaki/README.test -rw-r--r-- root/root 840 2016-10-21 21:39 ./usr/share/doc/murasaki/changelog.Debian.gz -rw-r--r-- root/root 2221 2016-07-12 03:25 ./usr/share/doc/murasaki/copyright drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/share/man/ drwxr-xr-x root/root 0 2016-10-21 21:39 ./usr/share/man/man1/ -rw-r--r-- root/root 2518 2016-10-21 21:39 ./usr/share/man/man1/geneparse.1.gz -rw-r--r-- root/root 2721 2016-10-21 21:39 ./usr/share/man/man1/mbfa.1.gz -rw-r--r-- root/root 10888 2016-10-21 21:39 ./usr/share/man/man1/murasaki.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: powerpc Build-Space: 137724 Build-Time: 347 Distribution: zesty-proposed Host Architecture: powerpc Install-Time: 80 Job: murasaki_1.68.6-6build2.dsc Machine Architecture: powerpc Package: murasaki Package-Time: 428 Source-Version: 1.68.6-6build2 Space: 137724 Status: successful Version: 1.68.6-6build2 -------------------------------------------------------------------------------- Finished at 20161021-2216 Build needed 00:07:08, 137724k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-11057407'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-11057407/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-11057407'] Unmounting chroot for build PACKAGEBUILD-11057407... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-11057407'] Removing build PACKAGEBUILD-11057407