https://launchpad.net/ubuntu/+source/blasr/5.3.2+dfsg-1.1/+build/16358884 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-ppc64el-008 4.4.0-142-generic #168-Ubuntu SMP Wed Jan 16 20:59:29 UTC 2019 ppc64le Buildd toolchain package versions: launchpad-buildd_166 python-lpbuildd_166 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 6 Feb 17:10:04 ntpdate[1778]: adjust time server 10.211.37.1 offset -0.032561 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=ppc64el PACKAGEBUILD-16358884 /home/buildd/filecache-default/8ecade3ba39252410f2285d8b2f76e6336361d85 Creating target for build PACKAGEBUILD-16358884 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=ppc64el PACKAGEBUILD-16358884 Starting target for build PACKAGEBUILD-16358884 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=ppc64el PACKAGEBUILD-16358884 'deb http://ftpmaster.internal/ubuntu disco main universe' 'deb http://ftpmaster.internal/ubuntu disco-security main universe' 'deb http://ftpmaster.internal/ubuntu disco-updates main universe' 'deb http://ftpmaster.internal/ubuntu disco-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-16358884 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=ppc64el PACKAGEBUILD-16358884 Updating target for build PACKAGEBUILD-16358884 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [243 kB] Get:2 http://ftpmaster.internal/ubuntu disco-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed InRelease [93.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main ppc64el Packages [951 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [508 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe ppc64el Packages [8789 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5255 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el Packages [35.4 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [20.9 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe ppc64el Packages [158 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [95.8 kB] Fetched 16.3 MB in 6s (2625 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libreadline7 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: gcc-9-base libreadline8 The following packages will be upgraded: adduser apt bash binutils binutils-common binutils-powerpc64le-linux-gnu bsdutils ca-certificates coreutils cpp-8 dash debconf debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk findutils g++-8 gcc-8 gcc-8-base gpg gpg-agent gpgconf gpgv grep gzip init init-system-helpers libapt-pkg5.0 libargon2-1 libasan5 libassuan0 libatomic1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcom-err2 libcomerr2 libcryptsetup12 libdb5.3 libdebconfclient0 libdpkg-perl libext2fs2 libfdisk1 libgcc-8-dev libgcc1 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libhogweed4 libip4tc0 libitm1 libjson-c3 liblsan0 liblz4-1 liblzma5 libmount1 libmpfr6 libnettle6 libperl5.28 libpng16-16 libquadmath0 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libss2 libstdc++-8-dev libstdc++6 libsystemd0 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login lsb-base mount passwd perl perl-base perl-modules-5.28 pkgbinarymangler readline-common sed systemd systemd-sysv tar tzdata util-linux xz-utils zlib1g 98 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 68.9 MB of archives. After this operation, 9183 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main ppc64el debianutils ppc64el 4.8.6.1 [86.4 kB] Get:2 http://ftpmaster.internal/ubuntu disco/main ppc64el bash ppc64el 5.0-2ubuntu1 [730 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main ppc64el bsdutils ppc64el 1:2.33.1-0.1ubuntu1 [69.5 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main ppc64el coreutils ppc64el 8.30-1ubuntu1 [1313 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main ppc64el tar ppc64el 1.30+dfsg-5 [288 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main ppc64el dpkg ppc64el 1.19.2ubuntu2 [1138 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main ppc64el libperl5.28 ppc64el 5.28.1-4 [3814 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main ppc64el perl ppc64el 5.28.1-4 [204 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main ppc64el perl-base ppc64el 5.28.1-4 [1513 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main ppc64el perl-modules-5.28 all 5.28.1-4 [2811 kB] Get:11 http://ftpmaster.internal/ubuntu disco/main ppc64el libdb5.3 ppc64el 5.3.28+dfsg1-0.3 [724 kB] Get:12 http://ftpmaster.internal/ubuntu disco/main ppc64el libgdbm6 ppc64el 1.18.1-2build1 [32.1 kB] Get:13 http://ftpmaster.internal/ubuntu disco/main ppc64el libgdbm-compat4 ppc64el 1.18.1-2build1 [6680 B] Get:14 http://ftpmaster.internal/ubuntu disco/main ppc64el zlib1g ppc64el 1:1.2.11.dfsg-1ubuntu2 [57.9 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main ppc64el debconf all 1.5.70 [122 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main ppc64el dash ppc64el 0.5.10.2-4ubuntu1 [101 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main ppc64el findutils ppc64el 4.6.0+git+20190105-2 [367 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main ppc64el grep ppc64el 3.3-1 [157 kB] Get:19 http://ftpmaster.internal/ubuntu disco/main ppc64el gzip ppc64el 1.9-3 [107 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main ppc64el libsmartcols1 ppc64el 2.33.1-0.1ubuntu1 [108 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main ppc64el libuuid1 ppc64el 2.33.1-0.1ubuntu1 [22.6 kB] Get:22 http://ftpmaster.internal/ubuntu disco/main ppc64el libblkid1 ppc64el 2.33.1-0.1ubuntu1 [159 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main ppc64el libfdisk1 ppc64el 2.33.1-0.1ubuntu1 [196 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main ppc64el libmount1 ppc64el 2.33.1-0.1ubuntu1 [173 kB] Get:25 http://ftpmaster.internal/ubuntu disco/main ppc64el fdisk ppc64el 2.33.1-0.1ubuntu1 [130 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main ppc64el login ppc64el 1:4.5-1.1ubuntu1 [269 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main ppc64el util-linux ppc64el 2.33.1-0.1ubuntu1 [1056 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main ppc64el sed ppc64el 4.7-1 [203 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main ppc64el init-system-helpers all 1.56+nmu1 [38.2 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main ppc64el libnettle6 ppc64el 3.4.1-1 [145 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main ppc64el libhogweed4 ppc64el 3.4.1-1 [145 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main ppc64el libgnutls30 ppc64el 3.6.5-2ubuntu1 [758 kB] Get:33 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el gcc-9-base ppc64el 9-20190202-1ubuntu1 [17.1 kB] Get:34 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el libgcc1 ppc64el 1:9-20190202-1ubuntu1 [29.9 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main ppc64el liblz4-1 ppc64el 1.8.3-1ubuntu1 [74.0 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main ppc64el liblzma5 ppc64el 5.2.4-1 [110 kB] Get:37 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el libstdc++6 ppc64el 9-20190202-1ubuntu1 [545 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main ppc64el libudev1 ppc64el 240-5ubuntu3 [82.4 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main ppc64el libzstd1 ppc64el 1.3.8+dfsg-3 [291 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main ppc64el libapt-pkg5.0 ppc64el 1.8.0~rc2 [902 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main ppc64el libsemanage-common all 2.8-2 [7016 B] Get:42 http://ftpmaster.internal/ubuntu disco/main ppc64el libsemanage1 ppc64el 2.8-2 [97.5 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main ppc64el passwd ppc64el 1:4.5-1.1ubuntu1 [829 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main ppc64el adduser all 3.118ubuntu1 [163 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main ppc64el libgpg-error0 ppc64el 1.35-1 [70.7 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main ppc64el gpgv ppc64el 2.2.12-1ubuntu3 [237 kB] Get:47 http://ftpmaster.internal/ubuntu disco/main ppc64el apt ppc64el 1.8.0~rc2 [1209 kB] Get:48 http://ftpmaster.internal/ubuntu disco/main ppc64el systemd-sysv ppc64el 240-5ubuntu3 [9384 B] Get:49 http://ftpmaster.internal/ubuntu disco/main ppc64el libargon2-1 ppc64el 0~20171227-0.2 [21.9 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main ppc64el libjson-c3 ppc64el 0.12.1+ds-2 [24.8 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main ppc64el libcryptsetup12 ppc64el 2:2.0.6-1ubuntu1 [171 kB] Get:52 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el libip4tc0 ppc64el 1.8.2-3ubuntu1 [24.6 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main ppc64el mount ppc64el 2.33.1-0.1ubuntu1 [122 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main ppc64el systemd ppc64el 240-5ubuntu3 [4031 kB] Get:55 http://ftpmaster.internal/ubuntu disco/main ppc64el libsystemd0 ppc64el 240-5ubuntu3 [303 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main ppc64el libext2fs2 ppc64el 1.44.5-1 [191 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main ppc64el e2fsprogs ppc64el 1.44.5-1 [554 kB] Get:58 http://ftpmaster.internal/ubuntu disco/main ppc64el init ppc64el 1.56+nmu1 [6080 B] Get:59 http://ftpmaster.internal/ubuntu disco/main ppc64el libcap-ng0 ppc64el 0.7.9-2 [12.4 kB] Get:60 http://ftpmaster.internal/ubuntu disco/main ppc64el libdebconfclient0 ppc64el 0.246ubuntu1 [6420 B] Get:61 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el libgomp1 ppc64el 9-20190202-1ubuntu1 [91.7 kB] Get:62 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el libitm1 ppc64el 9-20190202-1ubuntu1 [29.9 kB] Get:63 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el libatomic1 ppc64el 9-20190202-1ubuntu1 [9992 B] Get:64 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el libasan5 ppc64el 9-20190202-1ubuntu1 [412 kB] Get:65 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el liblsan0 ppc64el 9-20190202-1ubuntu1 [150 kB] Get:66 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el libtsan0 ppc64el 9-20190202-1ubuntu1 [309 kB] Get:67 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el libubsan1 ppc64el 9-20190202-1ubuntu1 [142 kB] Get:68 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el libquadmath0 ppc64el 9-20190202-1ubuntu1 [148 kB] Get:69 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el g++-8 ppc64el 8.2.0-17ubuntu6 [10.7 MB] Get:70 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el gcc-8 ppc64el 8.2.0-17ubuntu6 [10.2 MB] Get:71 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el libstdc++-8-dev ppc64el 8.2.0-17ubuntu6 [1573 kB] Get:72 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el libgcc-8-dev ppc64el 8.2.0-17ubuntu6 [1209 kB] Get:73 http://ftpmaster.internal/ubuntu disco/main ppc64el libmpfr6 ppc64el 4.0.2-1 [263 kB] Get:74 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el libcc1-0 ppc64el 9-20190202-1ubuntu1 [52.9 kB] Get:75 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.32-1ubuntu1 [2056 kB] Get:76 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el libbinutils ppc64el 2.32-1ubuntu1 [513 kB] Get:77 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el binutils ppc64el 2.32-1ubuntu1 [3384 B] Get:78 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el binutils-common ppc64el 2.32-1ubuntu1 [200 kB] Get:79 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el cpp-8 ppc64el 8.2.0-17ubuntu6 [9355 kB] Get:80 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el gcc-8-base ppc64el 8.2.0-17ubuntu6 [19.0 kB] Get:81 http://ftpmaster.internal/ubuntu disco/main ppc64el libcom-err2 ppc64el 1.44.5-1 [9956 B] Get:82 http://ftpmaster.internal/ubuntu disco/main ppc64el libss2 ppc64el 1.44.5-1 [12.6 kB] Get:83 http://ftpmaster.internal/ubuntu disco/main ppc64el lsb-base all 10.2018112800ubuntu1 [12.6 kB] Get:84 http://ftpmaster.internal/ubuntu disco/main ppc64el ca-certificates all 20190110 [146 kB] Get:85 http://ftpmaster.internal/ubuntu disco/main ppc64el readline-common all 8.0-1 [53.4 kB] Get:86 http://ftpmaster.internal/ubuntu disco/main ppc64el libreadline8 ppc64el 8.0-1 [144 kB] Get:87 http://ftpmaster.internal/ubuntu disco/main ppc64el libsqlite3-0 ppc64el 3.26.0+fossilbc891ac6b-2 [564 kB] Get:88 http://ftpmaster.internal/ubuntu disco/main ppc64el tzdata all 2018i-1 [189 kB] Get:89 http://ftpmaster.internal/ubuntu disco/main ppc64el xz-utils ppc64el 5.2.4-1 [87.9 kB] Get:90 http://ftpmaster.internal/ubuntu disco/main ppc64el libpng16-16 ppc64el 1.6.36-5 [209 kB] Get:91 http://ftpmaster.internal/ubuntu disco/main ppc64el dpkg-dev all 1.19.2ubuntu2 [549 kB] Get:92 http://ftpmaster.internal/ubuntu disco/main ppc64el libdpkg-perl all 1.19.2ubuntu2 [227 kB] Get:93 http://ftpmaster.internal/ubuntu disco/main ppc64el e2fslibs ppc64el 1.44.5-1 [2704 B] Get:94 http://ftpmaster.internal/ubuntu disco/main ppc64el libassuan0 ppc64el 2.5.2-1 [38.7 kB] Get:95 http://ftpmaster.internal/ubuntu disco/main ppc64el gpg ppc64el 2.2.12-1ubuntu3 [540 kB] Get:96 http://ftpmaster.internal/ubuntu disco/main ppc64el gpgconf ppc64el 2.2.12-1ubuntu3 [147 kB] Get:97 http://ftpmaster.internal/ubuntu disco/main ppc64el gpg-agent ppc64el 2.2.12-1ubuntu3 [268 kB] Get:98 http://ftpmaster.internal/ubuntu disco/main ppc64el libcomerr2 ppc64el 1.44.5-1 [2700 B] Get:99 http://ftpmaster.internal/ubuntu disco/main ppc64el linux-libc-dev ppc64el 4.19.0-12.13 [1064 kB] Get:100 http://ftpmaster.internal/ubuntu disco/main ppc64el pkgbinarymangler all 144 [55.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 68.9 MB in 14s (4785 kB/s) (Reading database ... 12596 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.6.1_ppc64el.deb ... Unpacking debianutils (4.8.6.1) over (4.8.6) ... Setting up debianutils (4.8.6.1) ... (Reading database ... 12596 files and directories currently installed.) Preparing to unpack .../bash_5.0-2ubuntu1_ppc64el.deb ... Unpacking bash (5.0-2ubuntu1) over (4.4.18-2ubuntu3) ... Setting up bash (5.0-2ubuntu1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 12596 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.33.1-0.1ubuntu1_ppc64el.deb ... Unpacking bsdutils (1:2.33.1-0.1ubuntu1) over (1:2.32-0.1ubuntu2) ... Setting up bsdutils (1:2.33.1-0.1ubuntu1) ... (Reading database ... 12596 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-1ubuntu1_ppc64el.deb ... Unpacking coreutils (8.30-1ubuntu1) over (8.28-1ubuntu2) ... 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-16358884 ppc64el disco-proposed -c chroot:build-PACKAGEBUILD-16358884 --arch=ppc64el --dist=disco-proposed --nolog blasr_5.3.2+dfsg-1.1.dsc Initiating build PACKAGEBUILD-16358884 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-142-generic #168-Ubuntu SMP Wed Jan 16 20:59:29 UTC 2019 ppc64le sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-ppc64el-008.buildd +==============================================================================+ | blasr 5.3.2+dfsg-1.1 (ppc64el) 06 Feb 2019 17:10 | +==============================================================================+ Package: blasr Version: 5.3.2+dfsg-1.1 Source Version: 5.3.2+dfsg-1.1 Distribution: disco-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el I: NOTICE: Log filtering will replace 'build/blasr-vZBu0p/blasr-5.3.2+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/blasr-vZBu0p' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-16358884/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- blasr_5.3.2+dfsg-1.1.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-BKxiDZ/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-BKxiDZ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-BKxiDZ/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-BKxiDZ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-BKxiDZ/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-BKxiDZ/apt_archive ./ Packages [528 B] Fetched 2861 B in 0s (250 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 package was automatically installed and is no longer required: libreadline7 Use 'apt autoremove' to remove it. 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 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-BKxiDZ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12632 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 12~), python, meson, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev (>= 0~20160912), libpbbam-dev (>= 0.18.0~), libpbdata-dev, libgtest-dev, libblasr-dev (>= 5.3.1+dfsg-2) Filtered Build-Depends: debhelper (>= 12~), python, meson, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev (>= 0~20160912), libpbbam-dev (>= 0.18.0~), libpbdata-dev, libgtest-dev, libblasr-dev (>= 5.3.1+dfsg-2) dpkg-deb: building package 'sbuild-build-depends-blasr-dummy' in '/<>/resolver-PMJSf5/apt_archive/sbuild-build-depends-blasr-dummy.deb'. Ign:1 copy:/<>/resolver-PMJSf5/apt_archive ./ InRelease Get:2 copy:/<>/resolver-PMJSf5/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-PMJSf5/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-PMJSf5/apt_archive ./ Sources [304 B] Get:5 copy:/<>/resolver-PMJSf5/apt_archive ./ Packages [622 B] Fetched 3045 B in 0s (245 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install blasr build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libreadline7 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libasn1-8-heimdal libblasr libblasr-dev libboost-dev libboost1.67-dev libbsd0 libcroco3 libcurl3-gnutls libdeflate0 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libgtest-dev libhcrypto4-heimdal libhdf5-103 libhdf5-cpp-103 libhdf5-dev libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu63 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpbbam-dev libpbbam0.19.0 libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpbseq-dev libpipeline1 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsz2 libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db meson mime-support ninja-build pkg-config po-debconf python python-minimal python2 python2-minimal python2.7 python2.7-minimal python3 python3-minimal python3-pkg-resources python3.7 python3.7-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc libboost1.67-doc libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev libboost-coroutine1.67-dev libboost-date-time1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev libboost-filesystem1.67-dev libboost-graph1.67-dev libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev libboost-program-options1.67-dev libboost-python1.67-dev libboost-random1.67-dev libboost-regex1.67-dev libboost-serialization1.67-dev libboost-signals1.67-dev libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user libhdf5-doc liblzma-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk python2-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3-setuptools python3.7-venv python3.7-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libasn1-8-heimdal libblasr libblasr-dev libboost-dev libboost1.67-dev libbsd0 libcroco3 libcurl3-gnutls libdeflate0 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libgtest-dev libhcrypto4-heimdal libhdf5-103 libhdf5-cpp-103 libhdf5-dev libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu63 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpbbam-dev libpbbam0.19.0 libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpbseq-dev libpipeline1 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsz2 libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db meson mime-support ninja-build pkg-config po-debconf python python-minimal python2 python2-minimal python2.7 python2.7-minimal python3 python3-minimal python3-pkg-resources python3.7 python3.7-minimal sbuild-build-depends-blasr-dummy zlib1g-dev 0 upgraded, 111 newly installed, 0 to remove and 0 not upgraded. Need to get 54.9 MB of archives. After this operation, 336 MB of additional disk space will be used. Get:1 copy:/<>/resolver-PMJSf5/apt_archive ./ sbuild-build-depends-blasr-dummy 0.invalid.0 [948 B] Get:2 http://ftpmaster.internal/ubuntu disco/main ppc64el libpython3.7-minimal ppc64el 3.7.2-2 [549 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main ppc64el libexpat1 ppc64el 2.2.6-1 [87.0 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main ppc64el python3.7-minimal ppc64el 3.7.2-2 [1974 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main ppc64el python3-minimal ppc64el 3.7.2-1 [23.5 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main ppc64el mime-support all 3.60ubuntu1 [30.1 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main ppc64el libmpdec2 ppc64el 2.4.2-2 [86.8 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main ppc64el libpython3.7-stdlib ppc64el 3.7.2-2 [1793 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main ppc64el python3.7 ppc64el 3.7.2-2 [278 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main ppc64el libpython3-stdlib ppc64el 3.7.2-1 [7028 B] Get:11 http://ftpmaster.internal/ubuntu disco/main ppc64el python3 ppc64el 3.7.2-1 [47.2 kB] Get:12 http://ftpmaster.internal/ubuntu disco/main ppc64el libbsd0 ppc64el 0.9.1-1 [53.6 kB] Get:13 http://ftpmaster.internal/ubuntu disco/main ppc64el bsdmainutils ppc64el 11.1.2ubuntu2 [185 kB] Get:14 http://ftpmaster.internal/ubuntu disco/main ppc64el libuchardet0 ppc64el 0.0.6-3 [67.7 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main ppc64el groff-base ppc64el 1.22.4-2 [935 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main ppc64el libpipeline1 ppc64el 1.5.1-1 [27.8 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main ppc64el man-db ppc64el 2.8.5-1 [1140 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main ppc64el libpython2.7-minimal ppc64el 2.7.15-8 [335 kB] Get:19 http://ftpmaster.internal/ubuntu disco/main ppc64el python2.7-minimal ppc64el 2.7.15-8 [1469 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main ppc64el python2-minimal ppc64el 2.7.15-4 [28.0 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main ppc64el python-minimal ppc64el 2.7.15-4 [5980 B] Get:22 http://ftpmaster.internal/ubuntu disco/main ppc64el libpython2.7-stdlib ppc64el 2.7.15-8 [2002 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main ppc64el python2.7 ppc64el 2.7.15-8 [239 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main ppc64el libpython2-stdlib ppc64el 2.7.15-4 [7596 B] Get:25 http://ftpmaster.internal/ubuntu disco/main ppc64el libpython-stdlib ppc64el 2.7.15-4 [5824 B] Get:26 http://ftpmaster.internal/ubuntu disco/main ppc64el python2 ppc64el 2.7.15-4 [26.5 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main ppc64el python ppc64el 2.7.15-4 [7832 B] Get:28 http://ftpmaster.internal/ubuntu disco/main ppc64el libmagic-mgc ppc64el 1:5.35-2 [200 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main ppc64el libmagic1 ppc64el 1:5.35-2 [90.9 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main ppc64el file ppc64el 1:5.35-2 [24.2 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main ppc64el libelf1 ppc64el 0.175-2 [52.3 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main ppc64el libglib2.0-0 ppc64el 2.58.2-4 [1333 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main ppc64el libicu63 ppc64el 63.1-6 [8520 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main ppc64el libxml2 ppc64el 2.9.4+dfsg1-7ubuntu3 [666 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main ppc64el gettext-base ppc64el 0.19.8.1-9 [52.8 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main ppc64el libkrb5support0 ppc64el 1.17-1 [37.7 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main ppc64el libk5crypto3 ppc64el 1.17-1 [111 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main ppc64el libkeyutils1 ppc64el 1.5.9-9.3 [10.8 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main ppc64el libkrb5-3 ppc64el 1.17-1 [383 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main ppc64el libgssapi-krb5-2 ppc64el 1.17-1 [137 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main ppc64el libpsl5 ppc64el 0.20.2-2 [52.2 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main ppc64el libsigsegv2 ppc64el 2.12-2 [13.9 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main ppc64el m4 ppc64el 1.4.18-2 [203 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main ppc64el autoconf all 2.69-11 [322 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main ppc64el autotools-dev all 20180224.1 [39.6 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main ppc64el automake all 1:1.16.1-4ubuntu3 [522 kB] Get:47 http://ftpmaster.internal/ubuntu disco/main ppc64el autopoint all 0.19.8.1-9 [412 kB] Get:48 http://ftpmaster.internal/ubuntu disco/main ppc64el libtool all 2.4.6-9 [194 kB] Get:49 http://ftpmaster.internal/ubuntu disco/main ppc64el dh-autoreconf all 19 [16.1 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main ppc64el libarchive-zip-perl all 1.64-1 [84.9 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main ppc64el libfile-stripnondeterminism-perl all 1.1.0-1 [13.6 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main ppc64el dh-strip-nondeterminism all 1.1.0-1 [5100 B] Get:53 http://ftpmaster.internal/ubuntu disco/main ppc64el dwz ppc64el 0.12-3 [87.4 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main ppc64el libcroco3 ppc64el 0.6.12-3 [92.5 kB] Get:55 http://ftpmaster.internal/ubuntu disco/main ppc64el gettext ppc64el 0.19.8.1-9 [978 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main ppc64el intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main ppc64el po-debconf all 1.0.21 [233 kB] Get:58 http://ftpmaster.internal/ubuntu disco/main ppc64el debhelper all 12ubuntu1 [887 kB] Get:59 http://ftpmaster.internal/ubuntu disco-proposed/universe ppc64el googletest ppc64el 1.8.1-3 [901 kB] Get:60 http://ftpmaster.internal/ubuntu disco/universe ppc64el hdf5-helpers ppc64el 1.10.4+repack-10 [13.9 kB] Get:61 http://ftpmaster.internal/ubuntu disco/universe ppc64el libaec0 ppc64el 1.0.2-1 [23.1 kB] Get:62 http://ftpmaster.internal/ubuntu disco/main ppc64el libroken18-heimdal ppc64el 7.5.0+dfsg-2.1 [47.3 kB] Get:63 http://ftpmaster.internal/ubuntu disco/main ppc64el libasn1-8-heimdal ppc64el 7.5.0+dfsg-2.1 [178 kB] Get:64 http://ftpmaster.internal/ubuntu disco/main ppc64el libheimbase1-heimdal ppc64el 7.5.0+dfsg-2.1 [34.4 kB] Get:65 http://ftpmaster.internal/ubuntu disco/main ppc64el libhcrypto4-heimdal ppc64el 7.5.0+dfsg-2.1 [107 kB] Get:66 http://ftpmaster.internal/ubuntu disco/main ppc64el libwind0-heimdal ppc64el 7.5.0+dfsg-2.1 [48.8 kB] Get:67 http://ftpmaster.internal/ubuntu disco/main ppc64el libhx509-5-heimdal ppc64el 7.5.0+dfsg-2.1 [123 kB] Get:68 http://ftpmaster.internal/ubuntu disco/main ppc64el libkrb5-26-heimdal ppc64el 7.5.0+dfsg-2.1 [241 kB] Get:69 http://ftpmaster.internal/ubuntu disco/main ppc64el libheimntlm0-heimdal ppc64el 7.5.0+dfsg-2.1 [17.1 kB] Get:70 http://ftpmaster.internal/ubuntu disco/main ppc64el libgssapi3-heimdal ppc64el 7.5.0+dfsg-2.1 [107 kB] Get:71 http://ftpmaster.internal/ubuntu disco/main ppc64el libsasl2-modules-db ppc64el 2.1.27+dfsg-1 [17.0 kB] Get:72 http://ftpmaster.internal/ubuntu disco/main ppc64el libsasl2-2 ppc64el 2.1.27+dfsg-1 [62.0 kB] Get:73 http://ftpmaster.internal/ubuntu disco/main ppc64el libldap-common all 2.4.47+dfsg-2ubuntu1 [16.2 kB] Get:74 http://ftpmaster.internal/ubuntu disco/main ppc64el libldap-2.4-2 ppc64el 2.4.47+dfsg-2ubuntu1 [178 kB] Get:75 http://ftpmaster.internal/ubuntu disco/main ppc64el libnghttp2-14 ppc64el 1.36.0-2 [92.6 kB] Get:76 http://ftpmaster.internal/ubuntu disco/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2 [54.5 kB] Get:77 http://ftpmaster.internal/ubuntu disco/main ppc64el libssh-4 ppc64el 0.8.6-2 [220 kB] Get:78 http://ftpmaster.internal/ubuntu disco/main ppc64el libcurl3-gnutls ppc64el 7.63.0-1ubuntu1 [259 kB] Get:79 http://ftpmaster.internal/ubuntu disco/universe ppc64el libdeflate0 ppc64el 1.2-1 [61.6 kB] Get:80 http://ftpmaster.internal/ubuntu disco-proposed/universe ppc64el libhts2 ppc64el 1.9-10 [342 kB] Get:81 http://ftpmaster.internal/ubuntu disco-proposed/universe ppc64el libpbbam0.19.0 ppc64el 0.19.0+dfsg-3.1 [609 kB] Get:82 http://ftpmaster.internal/ubuntu disco/universe ppc64el libpbdata ppc64el 5.3.1+dfsg-2.1 [129 kB] Get:83 http://ftpmaster.internal/ubuntu disco-proposed/main ppc64el libgfortran5 ppc64el 9-20190202-1ubuntu1 [398 kB] Get:84 http://ftpmaster.internal/ubuntu disco/universe ppc64el libsz2 ppc64el 1.0.2-1 [5284 B] Get:85 http://ftpmaster.internal/ubuntu disco/universe ppc64el libhdf5-103 ppc64el 1.10.4+repack-10 [1266 kB] Get:86 http://ftpmaster.internal/ubuntu disco/universe ppc64el libhdf5-cpp-103 ppc64el 1.10.4+repack-10 [115 kB] Get:87 http://ftpmaster.internal/ubuntu disco/universe ppc64el libpbihdf ppc64el 5.3.1+dfsg-2.1 [161 kB] Get:88 http://ftpmaster.internal/ubuntu disco/universe ppc64el libblasr ppc64el 5.3.1+dfsg-2.1 [876 kB] Get:89 http://ftpmaster.internal/ubuntu disco/universe ppc64el libpbdata-dev ppc64el 5.3.1+dfsg-2.1 [206 kB] Get:90 http://ftpmaster.internal/ubuntu disco/universe ppc64el libblasr-dev ppc64el 5.3.1+dfsg-2.1 [1709 kB] Get:91 http://ftpmaster.internal/ubuntu disco/main ppc64el libboost1.67-dev ppc64el 1.67.0-13 [8362 kB] Get:92 http://ftpmaster.internal/ubuntu disco/main ppc64el libboost-dev ppc64el 1.67.0.1 [3232 B] Get:93 http://ftpmaster.internal/ubuntu disco-proposed/universe ppc64el libgtest-dev ppc64el 1.8.1-3 [224 kB] Get:94 http://ftpmaster.internal/ubuntu disco/main ppc64el zlib1g-dev ppc64el 1:1.2.11.dfsg-1ubuntu2 [176 kB] Get:95 http://ftpmaster.internal/ubuntu disco/main ppc64el libjpeg-turbo8 ppc64el 2.0.1-0ubuntu1 [157 kB] Get:96 http://ftpmaster.internal/ubuntu disco/main ppc64el libjpeg-turbo8-dev ppc64el 2.0.1-0ubuntu1 [279 kB] Get:97 http://ftpmaster.internal/ubuntu disco/main ppc64el libjpeg8 ppc64el 8c-2ubuntu8 [2146 B] Get:98 http://ftpmaster.internal/ubuntu disco/main ppc64el libjpeg8-dev ppc64el 8c-2ubuntu8 [1606 B] Get:99 http://ftpmaster.internal/ubuntu disco/main ppc64el libjpeg-dev ppc64el 8c-2ubuntu8 [1602 B] Get:100 http://ftpmaster.internal/ubuntu disco/universe ppc64el libaec-dev ppc64el 1.0.2-1 [22.0 kB] Get:101 http://ftpmaster.internal/ubuntu disco/universe ppc64el libhdf5-dev ppc64el 1.10.4+repack-10 [2822 kB] Get:102 http://ftpmaster.internal/ubuntu disco/main ppc64el liblzma-dev ppc64el 5.2.4-1 [166 kB] Get:103 http://ftpmaster.internal/ubuntu disco-proposed/universe ppc64el libhts-dev ppc64el 1.9-10 [4326 kB] Get:104 http://ftpmaster.internal/ubuntu disco/main ppc64el libssl-dev ppc64el 1.1.1a-1ubuntu2 [1603 kB] Get:105 http://ftpmaster.internal/ubuntu disco-proposed/universe ppc64el libpbbam-dev ppc64el 0.19.0+dfsg-3.1 [84.0 kB] Get:106 http://ftpmaster.internal/ubuntu disco/universe ppc64el libpbihdf-dev ppc64el 5.3.1+dfsg-2.1 [264 kB] Get:107 http://ftpmaster.internal/ubuntu disco/universe ppc64el libpbseq-dev all 5.3.1+dfsg-2.1 [3220 B] Get:108 http://ftpmaster.internal/ubuntu disco/universe ppc64el ninja-build ppc64el 1.8.2-1 [111 kB] Get:109 http://ftpmaster.internal/ubuntu disco/main ppc64el python3-pkg-resources all 40.7.1-1 [99.6 kB] Get:110 http://ftpmaster.internal/ubuntu disco/universe ppc64el meson all 0.49.0-2ubuntu1 [278 kB] Get:111 http://ftpmaster.internal/ubuntu disco/main ppc64el pkg-config ppc64el 0.29.1-0ubuntu2 [44.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 54.9 MB in 3s (18.2 MB/s) Selecting previously unselected package libpython3.7-minimal:ppc64el. (Reading database ... 12632 files and directories currently installed.) Preparing to unpack .../libpython3.7-minimal_3.7.2-2_ppc64el.deb ... Unpacking libpython3.7-minimal:ppc64el (3.7.2-2) ... Selecting previously unselected package libexpat1:ppc64el. Preparing to unpack .../libexpat1_2.2.6-1_ppc64el.deb ... Unpacking libexpat1:ppc64el (2.2.6-1) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../python3.7-minimal_3.7.2-2_ppc64el.deb ... Unpacking python3.7-minimal (3.7.2-2) ... Setting up libpython3.7-minimal:ppc64el (3.7.2-2) ... Setting up libexpat1:ppc64el (2.2.6-1) ... Setting up python3.7-minimal (3.7.2-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 12881 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.7.2-1_ppc64el.deb ... Unpacking python3-minimal (3.7.2-1) ... Selecting previously unselected package mime-support. 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Unpacking meson (0.49.0-2ubuntu1) ... Selecting previously unselected package pkg-config. Preparing to unpack .../84-pkg-config_0.29.1-0ubuntu2_ppc64el.deb ... Unpacking pkg-config (0.29.1-0ubuntu2) ... Selecting previously unselected package sbuild-build-depends-blasr-dummy. Preparing to unpack .../85-sbuild-build-depends-blasr-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-blasr-dummy (0.invalid.0) ... Setting up libaec0:ppc64el (1.0.2-1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libnghttp2-14:ppc64el (1.36.0-2) ... Setting up mime-support (3.60ubuntu1) ... Setting up libicu63:ppc64el (63.1-6) ... Setting up libsigsegv2:ppc64el (2.12-2) ... Setting up libldap-common (2.4.47+dfsg-2ubuntu1) ... Setting up libdeflate0:ppc64el (1.2-1) ... Setting up libpsl5:ppc64el (0.20.2-2) ... Setting up libelf1:ppc64el (0.175-2) ... Setting up libssl-dev:ppc64el (1.1.1a-1ubuntu2) ... Setting up libglib2.0-0:ppc64el (2.58.2-4) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:ppc64el (2.1.27+dfsg-1) ... Setting up libsasl2-2:ppc64el (2.1.27+dfsg-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libjpeg-turbo8:ppc64el (2.0.1-0ubuntu1) ... Setting up libpipeline1:ppc64el (1.5.1-1) ... Setting up libroken18-heimdal:ppc64el (7.5.0+dfsg-2.1) ... Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2) ... Setting up m4 (1.4.18-2) ... Setting up libbsd0:ppc64el (0.9.1-1) ... Setting up libkrb5support0:ppc64el (1.17-1) ... Setting up libxml2:ppc64el (2.9.4+dfsg1-7ubuntu3) ... Setting up libuchardet0:ppc64el (0.0.6-3) ... Setting up libmagic-mgc (1:5.35-2) ... Setting up libmagic1:ppc64el (1:5.35-2) ... Setting up libcroco3:ppc64el (0.6.12-3) ... Setting up pkg-config (0.29.1-0ubuntu2) ... Setting up libjpeg-turbo8-dev:ppc64el (2.0.1-0ubuntu1) ... Setting up googletest:ppc64el (1.8.1-3) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up dwz (0.12-3) ... Setting up autotools-dev (20180224.1) ... Setting up libboost1.67-dev:ppc64el (1.67.0-13) ... Setting up libheimbase1-heimdal:ppc64el (7.5.0+dfsg-2.1) ... Setting up libgtest-dev:ppc64el (1.8.1-3) ... Setting up libboost-dev:ppc64el (1.67.0.1) ... Setting up liblzma-dev:ppc64el (5.2.4-1) ... Setting up libkeyutils1:ppc64el (1.5.9-9.3) ... Setting up bsdmainutils (11.1.2ubuntu2) ... 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 ninja-build (1.8.2-1) ... Setting up libgfortran5:ppc64el (9-20190202-1ubuntu1) ... Setting up hdf5-helpers (1.10.4+repack-10) ... Setting up libpython2.7-stdlib:ppc64el (2.7.15-8) ... Setting up autopoint (0.19.8.1-9) ... Setting up libmpdec2:ppc64el (2.4.2-2) ... Setting up libsz2:ppc64el (1.0.2-1) ... Setting up zlib1g-dev:ppc64el (1:1.2.11.dfsg-1ubuntu2) ... Setting up libfile-stripnondeterminism-perl (1.1.0-1) ... Setting up libjpeg8:ppc64el (8c-2ubuntu8) ... Setting up libk5crypto3:ppc64el (1.17-1) ... Setting up libpython3.7-stdlib:ppc64el (3.7.2-2) ... Setting up libwind0-heimdal:ppc64el (7.5.0+dfsg-2.1) ... Setting up gettext (0.19.8.1-9) ... Setting up libasn1-8-heimdal:ppc64el (7.5.0+dfsg-2.1) ... Setting up groff-base (1.22.4-2) ... Setting up libhcrypto4-heimdal:ppc64el (7.5.0+dfsg-2.1) ... Setting up libaec-dev:ppc64el (1.0.2-1) ... Setting up python2.7 (2.7.15-8) ... Setting up python3.7 (3.7.2-2) ... Setting up autoconf (2.69-11) ... Setting up libhdf5-103:ppc64el (1.10.4+repack-10) ... Setting up file (1:5.35-2) ... Setting up libhx509-5-heimdal:ppc64el (7.5.0+dfsg-2.1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libjpeg8-dev:ppc64el (8c-2ubuntu8) ... Setting up libjpeg-dev:ppc64el (8c-2ubuntu8) ... Setting up automake (1:1.16.1-4ubuntu3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.5-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libpython2-stdlib:ppc64el (2.7.15-4) ... Setting up libkrb5-3:ppc64el (1.17-1) ... Setting up libkrb5-26-heimdal:ppc64el (7.5.0+dfsg-2.1) ... Setting up libheimntlm0-heimdal:ppc64el (7.5.0+dfsg-2.1) ... Setting up libtool (2.4.6-9) ... Setting up libpython3-stdlib:ppc64el (3.7.2-1) ... Setting up po-debconf (1.0.21) ... Setting up python3 (3.7.2-1) ... Setting up libhdf5-cpp-103:ppc64el (1.10.4+repack-10) ... Setting up libhdf5-dev (1.10.4+repack-10) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/powerpc64le-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up python3-pkg-resources (40.7.1-1) ... Setting up python2 (2.7.15-4) ... Setting up libgssapi-krb5-2:ppc64el (1.17-1) ... Setting up libpython-stdlib:ppc64el (2.7.15-4) ... Setting up libssh-4:ppc64el (0.8.6-2) ... Setting up meson (0.49.0-2ubuntu1) ... Setting up libgssapi3-heimdal:ppc64el (7.5.0+dfsg-2.1) ... Setting up python (2.7.15-4) ... Setting up libldap-2.4-2:ppc64el (2.4.47+dfsg-2ubuntu1) ... Setting up libcurl3-gnutls:ppc64el (7.63.0-1ubuntu1) ... Setting up libhts2:ppc64el (1.9-10) ... Setting up libhts-dev:ppc64el (1.9-10) ... Setting up libpbbam0.19.0:ppc64el (0.19.0+dfsg-3.1) ... Setting up libpbdata:ppc64el (5.3.1+dfsg-2.1) ... Setting up libpbihdf:ppc64el (5.3.1+dfsg-2.1) ... Setting up libblasr:ppc64el (5.3.1+dfsg-2.1) ... Setting up libpbbam-dev (0.19.0+dfsg-3.1) ... Setting up libpbihdf-dev:ppc64el (5.3.1+dfsg-2.1) ... Setting up libpbdata-dev:ppc64el (5.3.1+dfsg-2.1) ... Setting up libblasr-dev:ppc64el (5.3.1+dfsg-2.1) ... Setting up libpbseq-dev (5.3.1+dfsg-2.1) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12ubuntu1) ... Setting up sbuild-build-depends-blasr-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (1.1.0-1) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-142-generic ppc64el (ppc64le) Toolchain package versions: binutils_2.32-1ubuntu1 dpkg-dev_1.19.2ubuntu2 g++-8_8.2.0-17ubuntu6 gcc-8_8.2.0-17ubuntu6 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-17ubuntu6 libstdc++6_9-20190202-1ubuntu1 linux-libc-dev_4.19.0-12.13 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-1 apt_1.8.0~rc2 autoconf_2.69-11 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_5.0-2ubuntu1 binutils_2.32-1ubuntu1 binutils-common_2.32-1ubuntu1 binutils-powerpc64le-linux-gnu_2.32-1ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.33.1-0.1ubuntu1 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20190110 coreutils_8.30-1ubuntu1 cpp_4:8.2.0-2ubuntu2 cpp-8_8.2.0-17ubuntu6 dash_0.5.10.2-4ubuntu1 debconf_1.5.70 debhelper_12ubuntu1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.0-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu4 dpkg_1.19.2ubuntu2 dpkg-dev_1.19.2ubuntu2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1ubuntu1 file_1:5.35-2 findutils_4.6.0+git+20190105-2 g++_4:8.2.0-2ubuntu2 g++-8_8.2.0-17ubuntu6 gcc_4:8.2.0-2ubuntu2 gcc-8_8.2.0-17ubuntu6 gcc-8-base_8.2.0-17ubuntu6 gcc-9-base_9-20190202-1ubuntu1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 googletest_1.8.1-3 gpg_2.2.12-1ubuntu3 gpg-agent_2.2.12-1ubuntu3 gpgconf_2.2.12-1ubuntu3 gpgv_2.2.12-1ubuntu3 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hdf5-helpers_1.10.4+repack-10 hostname_3.21 init_1.56+nmu1 init-system-helpers_1.56+nmu1 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.5 libacl1_2.2.52-3build1 libaec-dev_1.0.2-1 libaec0_1.0.2-1 libapparmor1_2.12-4ubuntu10 libapt-pkg5.0_1.8.0~rc2 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.2 libasan5_9-20190202-1ubuntu1 libasn1-8-heimdal_7.5.0+dfsg-2.1 libassuan0_2.5.2-1 libatomic1_9-20190202-1ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu3 libaudit1_1:2.8.3-1ubuntu3 libbinutils_2.32-1ubuntu1 libblasr_5.3.1+dfsg-2.1 libblasr-dev_5.3.1+dfsg-2.1 libblkid1_2.33.1-0.1ubuntu1 libboost-dev_1.67.0.1 libboost1.67-dev_1.67.0-13 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-0ubuntu1 libc-dev-bin_2.28-0ubuntu1 libc6_2.28-0ubuntu1 libc6-dev_2.28-0ubuntu1 libcap-ng0_0.7.9-2 libcap2_1:2.25-1.2 libcc1-0_9-20190202-1ubuntu1 libcom-err2_1.44.5-1 libcomerr2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.0.6-1ubuntu1 libcurl3-gnutls_7.63.0-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.3 libdebconfclient0_0.246ubuntu1 libdeflate0_1.2-1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu4 libdpkg-perl_1.19.2ubuntu2 libelf1_0.175-2 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1ubuntu1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.0-1 libgcc-8-dev_8.2.0-17ubuntu6 libgcc1_1:9-20190202-1ubuntu1 libgcrypt20_1.8.4-3ubuntu1 libgdbm-compat4_1.18.1-2build1 libgdbm6_1.18.1-2build1 libgfortran5_9-20190202-1ubuntu1 libglib2.0-0_2.58.2-4 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2ubuntu1 libgomp1_9-20190202-1ubuntu1 libgpg-error0_1.35-1 libgssapi-krb5-2_1.17-1 libgssapi3-heimdal_7.5.0+dfsg-2.1 libgtest-dev_1.8.1-3 libhcrypto4-heimdal_7.5.0+dfsg-2.1 libhdf5-103_1.10.4+repack-10 libhdf5-cpp-103_1.10.4+repack-10 libhdf5-dev_1.10.4+repack-10 libheimbase1-heimdal_7.5.0+dfsg-2.1 libheimntlm0-heimdal_7.5.0+dfsg-2.1 libhogweed4_3.4.1-1 libhts-dev_1.9-10 libhts2_1.9-10 libhx509-5-heimdal_7.5.0+dfsg-2.1 libicu63_63.1-6 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3ubuntu1 libisl19_0.20-2 libitm1_9-20190202-1ubuntu1 libjpeg-dev_8c-2ubuntu8 libjpeg-turbo8_2.0.1-0ubuntu1 libjpeg-turbo8-dev_2.0.1-0ubuntu1 libjpeg8_8c-2ubuntu8 libjpeg8-dev_8c-2ubuntu8 libjson-c3_0.12.1+ds-2 libk5crypto3_1.17-1 libkeyutils1_1.5.9-9.3 libkmod2_25-1ubuntu2 libkrb5-26-heimdal_7.5.0+dfsg-2.1 libkrb5-3_1.17-1 libkrb5support0_1.17-1 libldap-2.4-2_2.4.47+dfsg-2ubuntu1 libldap-common_2.4.47+dfsg-2ubuntu1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblsan0_9-20190202-1ubuntu1 liblz4-1_1.8.3-1ubuntu1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-2 libmagic1_1:5.35-2 libmount1_2.33.1-0.1ubuntu1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4.1-1 libnghttp2-14_1.36.0-2 libnpth0_1.6-1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpbbam-dev_0.19.0+dfsg-3.1 libpbbam0.19.0_0.19.0+dfsg-3.1 libpbdata_5.3.1+dfsg-2.1 libpbdata-dev_5.3.1+dfsg-2.1 libpbihdf_5.3.1+dfsg-2.1 libpbihdf-dev_5.3.1+dfsg-2.1 libpbseq-dev_5.3.1+dfsg-2.1 libpcre3_2:8.39-11 libperl5.28_5.28.1-4 libpipeline1_1.5.1-1 libpng16-16_1.6.36-5 libprocps7_2:3.3.15-2ubuntu1 libpsl5_0.20.2-2 libpython-stdlib_2.7.15-4 libpython2-stdlib_2.7.15-4 libpython2.7-minimal_2.7.15-8 libpython2.7-stdlib_2.7.15-8 libpython3-stdlib_3.7.2-1 libpython3.7-minimal_3.7.2-2 libpython3.7-stdlib_3.7.2-2 libquadmath0_9-20190202-1ubuntu1 libreadline7_7.0-5 libreadline8_8.0-1 libroken18-heimdal_7.5.0+dfsg-2.1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-3ubuntu2 libselinux1_2.8-1build2 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.33.1-0.1ubuntu1 libsqlite3-0_3.26.0+fossilbc891ac6b-2 libss2_1.44.5-1 libssh-4_0.8.6-2 libssl-dev_1.1.1a-1ubuntu2 libssl1.1_1.1.1a-1ubuntu2 libstdc++-8-dev_8.2.0-17ubuntu6 libstdc++6_9-20190202-1ubuntu1 libsystemd0_240-5ubuntu3 libsz2_1.0.2-1 libtasn1-6_4.13-3 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-9 libtsan0_9-20190202-1ubuntu1 libubsan1_9-20190202-1ubuntu1 libuchardet0_0.0.6-3 libudev1_240-5ubuntu3 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libustr-1.0-1_1.0.4-6 libuuid1_2.33.1-0.1ubuntu1 libwind0-heimdal_7.5.0+dfsg-2.1 libxml2_2.9.4+dfsg1-7ubuntu3 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.0-12.13 lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu1 lsb-base_10.2018112800ubuntu1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-1 mawk_1.3.3-17ubuntu3 meson_0.49.0-2ubuntu1 mime-support_3.60ubuntu1 mount_2.33.1-0.1ubuntu1 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 ninja-build_1.8.2-1 openssl_1.1.1a-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1.1ubuntu1 patch_2.7.6-3 perl_5.28.1-4 perl-base_5.28.1-4 perl-modules-5.28_5.28.1-4 pinentry-curses_1.1.0-1build2 pkg-config_0.29.1-0ubuntu2 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 python_2.7.15-4 python-minimal_2.7.15-4 python2_2.7.15-4 python2-minimal_2.7.15-4 python2.7_2.7.15-8 python2.7-minimal_2.7.15-8 python3_3.7.2-1 python3-minimal_3.7.2-1 python3-pkg-resources_40.7.1-1 python3.7_3.7.2-2 python3.7-minimal_3.7.2-2 readline-common_8.0-1 sbuild-build-depends-blasr-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-5ubuntu3 systemd-sysv_240-5ubuntu3 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tar_1.30+dfsg-5 tzdata_2018i-1 ubuntu-keyring_2018.09.18.1 util-linux_2.33.1-0.1ubuntu1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu2 zlib1g-dev_1:1.2.11.dfsg-1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Wed Feb 6 07:27:30 2019 UTC gpgv: using RSA key 3AFA757FAC6EA11D2FF45DF088D24287A2D898B1 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./blasr_5.3.2+dfsg-1.1.dsc dpkg-source: info: extracting blasr in blasr-5.3.2+dfsg dpkg-source: info: unpacking blasr_5.3.2+dfsg.orig.tar.xz dpkg-source: info: unpacking blasr_5.3.2+dfsg-1.1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_pblibs.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-16358884 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-16358884 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-16358884 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package blasr dpkg-buildpackage: info: source version 5.3.2+dfsg-1.1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture ppc64el fakeroot debian/rules clean dh clean --buildsystem=meson dh_auto_clean -O--buildsystem=meson dh_autoreconf_clean -O--buildsystem=meson dh_clean -O--buildsystem=meson debian/rules build-arch dh build-arch --buildsystem=meson dh_update_autotools_config -a -O--buildsystem=meson dh_autoreconf -a -O--buildsystem=meson debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/blasr-5.3.2+dfsg' LDFLAGS="-L/usr/lib/powerpc64le-linux-gnu -L/usr/lib/powerpc64le-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5" CPPFLAGS="-isystem /usr/include/hdf5/serial" meson -Dtests=false -Dprefix=/usr build . The Meson build system Version: 0.49.0 Source dir: /<>/blasr-5.3.2+dfsg Build dir: /<>/blasr-5.3.2+dfsg/build Build type: native build Project name: blasr Project version: 5.3.2 Appending CXXFLAGS from environment: '-Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1' Appending LDFLAGS from environment: '-L/usr/lib/powerpc64le-linux-gnu -L/usr/lib/powerpc64le-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5' Appending CPPFLAGS from environment: '-isystem /usr/include/hdf5/serial' Native C++ compiler: c++ (gcc 8.2.1 "c++ (Ubuntu 8.2.0-17ubuntu6) 8.2.1 20190204") Build machine cpu family: ppc64 Build machine cpu: ppc64le Compiler for C++ supports arguments -Wno-delete-non-virtual-dtor -Wdelete-non-virtual-dtor: YES Compiler for C++ supports arguments -Wno-non-virtual-dtor -Wnon-virtual-dtor: YES Compiler for C++ supports arguments -Wno-unused-but-set-variable -Wunused-but-set-variable: YES Compiler for C++ supports arguments -Wno-unused-variable -Wunused-variable: YES Dependency threads found: YES Dependency Boost found: YES 1.67 Found pkg-config: /usr/bin/pkg-config (0.29.1) Dependency pbbam found: YES 0.19.0 Dependency libblasr found: YES 5.3.1 Dependency zlib found: YES 1.2.11 Library pbdata found: YES Library pbihdf found: YES Configuring BlasrVersion.h using configuration Build targets in project: 5 Found ninja-1.8.2 at /usr/bin/ninja make[1]: Leaving directory '/<>/blasr-5.3.2+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/<>/blasr-5.3.2+dfsg' ln -s build obj-powerpc64le-linux-gnu dh_auto_build cd obj-powerpc64le-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v [1/25] /usr/bin/meson --internal vcstagger ../BlasrGitHash.h.in BlasrGitHash.h '' /<>/blasr-5.3.2+dfsg @BLASR_GIT_SHA1@ '(.*)' /<>/blasr-5.3.2+dfsg/git describe --always '--dirty=*' [2/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' -MF 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o.d' -o 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' -c ../extrautils/SuffixArrayToBWT.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/alignment/bwt/Occ.hpp:8, from /usr/include/pbseq/alignment/bwt/BWT.hpp:7, from ../extrautils/SuffixArrayToBWT.cpp:4: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition In file included from ../extrautils/SuffixArrayToBWT.cpp:4: /usr/include/pbseq/alignment/bwt/BWT.hpp: In member function ‘void Bwt::InitializeDNACharacterCount() [with T_BWT_Sequence = PackedDNASequence; T_DNASequence = FASTASequence]’: /usr/include/pbseq/alignment/bwt/BWT.hpp:192:21: warning: this statement may fall through [-Wimplicit-fallthrough=] charCount[0]++; ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:193:17: note: here case 0: //A ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:194:21: warning: this statement may fall through [-Wimplicit-fallthrough=] charCount[1]++; ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:195:17: note: here case 1: //C ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:196:21: warning: this statement may fall through [-Wimplicit-fallthrough=] charCount[2]++; ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:197:17: note: here case 2: //G ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:198:21: warning: this statement may fall through [-Wimplicit-fallthrough=] charCount[3]++; ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:199:17: note: here case 3: //T ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:200:21: warning: this statement may fall through [-Wimplicit-fallthrough=] charCount[4]++; ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:201:17: note: here case 4: //N ^~~~ [3/25] c++ -Isawriter@exe -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -DCMAKE_BUILD=1 -MD -MQ 'sawriter@exe/utils_SAWriter.cpp.o' -MF 'sawriter@exe/utils_SAWriter.cpp.o.d' -o 'sawriter@exe/utils_SAWriter.cpp.o' -c ../utils/SAWriter.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/alignment/algorithms/sorting/Karkkainen.hpp:4, from ../utils/SAWriter.cpp:5: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition [4/25] c++ -ItoAfg@exe -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -DCMAKE_BUILD=1 -MD -MQ 'toAfg@exe/utils_ToAfg.cpp.o' -MF 'toAfg@exe/utils_ToAfg.cpp.o.d' -o 'toAfg@exe/utils_ToAfg.cpp.o' -c ../utils/ToAfg.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:19, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:13, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../utils/ToAfg.cpp:6: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition In file included from ../utils/ToAfg.cpp:9: /usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’: /usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] } catch (DataSetIException e) { ^ [5/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' -MF 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o.d' -o 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' -c ../extrautils/BwtToSuffixArray.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/alignment/bwt/Occ.hpp:8, from /usr/include/pbseq/alignment/bwt/BWT.hpp:7, from ../extrautils/BwtToSuffixArray.cpp:5: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition [6/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SAModify.cpp.o' -MF 'blasr_impl@sta/extrautils_SAModify.cpp.o.d' -o 'blasr_impl@sta/extrautils_SAModify.cpp.o' -c ../extrautils/SAModify.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/pbdata/FASTASequence.hpp:13, from /usr/include/pbseq/alignment/algorithms/sorting/MultikeyQuicksort.hpp:21, from /usr/include/pbseq/alignment/algorithms/sorting/LightweightSuffixArray.hpp:8, from /usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:13, from ../extrautils/SAModify.cpp:5: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition [7/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' -MF 'blasr_impl@sta/extrautils_SWMatcher.cpp.o.d' -o 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' -c ../extrautils/SWMatcher.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13, from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6, from ../extrautils/SWMatcher.cpp:6: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition [8/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' -MF 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o.d' -o 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' -c ../extrautils/ExciseRepeats.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/pbdata/FASTASequence.hpp:13, from /usr/include/pbseq/pbdata/FASTAReader.hpp:7, from ../extrautils/ExciseRepeats.cpp:3: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition [9/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SALS.cpp.o' -MF 'blasr_impl@sta/extrautils_SALS.cpp.o.d' -o 'blasr_impl@sta/extrautils_SALS.cpp.o' -c ../extrautils/SALS.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/pbdata/FASTASequence.hpp:13, from /usr/include/pbseq/alignment/algorithms/sorting/MultikeyQuicksort.hpp:21, from /usr/include/pbseq/alignment/algorithms/sorting/LightweightSuffixArray.hpp:8, from /usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:13, from ../extrautils/SALS.cpp:4: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition [10/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' -MF 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o.d' -o 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' -c ../extrautils/SimpleShredder.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/pbdata/FASTASequence.hpp:13, from /usr/include/pbseq/pbdata/FASTAReader.hpp:7, from ../extrautils/SimpleShredder.cpp:6: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition [11/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o' -MF 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o.d' -o 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o' -c ../extrautils/StoreQualityByContextFromCmpH5.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:19, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:13, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:2: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:13, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:2: /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = std::__cxx11::basic_string; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:9: required from ‘void HDFArray::Write(const T*, int) [with T = std::__cxx11::basic_string]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:36:43: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:9: required from ‘void HDFArray::Write(const T*, int) [with T = unsigned int]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:44:29: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = float; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = float; UInt = unsigned int]’ /usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp:81:60: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] [12/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_Evolve.cpp.o' -MF 'blasr_impl@sta/extrautils_Evolve.cpp.o.d' -o 'blasr_impl@sta/extrautils_Evolve.cpp.o' -c ../extrautils/Evolve.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/pbdata/FASTASequence.hpp:13, from /usr/include/pbseq/pbdata/FASTAReader.hpp:7, from ../extrautils/Evolve.cpp:6: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition [13/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' -MF 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o.d' -o 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' -c ../extrautils/BuildSequenceDB.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/pbdata/FASTASequence.hpp:13, from /usr/include/pbseq/pbdata/FASTAReader.hpp:7, from ../extrautils/BuildSequenceDB.cpp:5: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition [14/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' -MF 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o.d' -o 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' -c ../extrautils/PrintTupleCountTable.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/alignment/tuples/DNATuple.hpp:15, from /usr/include/pbseq/alignment/tuples/CompressedDNATuple.hpp:4, from ../extrautils/PrintTupleCountTable.cpp:6: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition [15/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SamToM4.cpp.o' -MF 'blasr_impl@sta/utils_SamToM4.cpp.o.d' -o 'blasr_impl@sta/utils_SamToM4.cpp.o' -c ../utils/SamToM4.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13, from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6, from ../utils/SamToM4.cpp:21: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition [16/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' -MF 'blasr_impl@sta/utils_SamToCmpH5.cpp.o.d' -o 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' -c ../utils/SamToCmpH5.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:9, from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, from ../utils/SamToCmpH5.cpp:3: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFAlnGroupGroup.hpp:6, from /usr/include/pbseq/hdf/HDFCmpFile.hpp:12, from /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:7, from ../utils/SamToCmpH5.cpp:5: /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = std::__cxx11::basic_string; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:9: required from ‘void HDFArray::Write(const T*, int) [with T = std::__cxx11::basic_string]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:36:43: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:9: required from ‘void HDFArray::Write(const T*, int) [with T = unsigned int]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:44:29: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = float; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = float; UInt = unsigned int]’ /usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp:81:60: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] [17/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SDPMatcher.cpp.o' -MF 'blasr_impl@sta/utils_SDPMatcher.cpp.o.d' -o 'blasr_impl@sta/utils_SDPMatcher.cpp.o' -c ../utils/SDPMatcher.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13, from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6, from ../utils/SDPMatcher.cpp:8: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition [18/25] c++ -Iblasr@exe -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -DCMAKE_BUILD=1 -MD -MQ 'blasr@exe/Blasr.cpp.o' -MF 'blasr@exe/Blasr.cpp.o.d' -o 'blasr@exe/Blasr.cpp.o' -c ../Blasr.cpp In file included from ../iblasr/BlasrHeaders.h:22, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition In file included from ../iblasr/BlasrUtils.hpp:138, from ../iblasr/BlasrAlignImpl.hpp:4, from ../iblasr/BlasrAlign.hpp:67, from ../Blasr.cpp:3: ../iblasr/BlasrUtilsImpl.hpp: In function ‘void PrintAlignment(T_AlignmentCandidate&, SMRTSequence&, MappingParameters&, AlignmentContext&, std::ostream&, SMRTSequence&, PacBio::BAM::IRecordWriter*)’: ../iblasr/BlasrUtilsImpl.hpp:976:36: warning: catching polymorphic type ‘class std::ios_base::failure’ by value [-Wcatch-value=] } catch (std::ostream::failure f) { ^ ../Blasr.cpp: In function ‘int main(int, char**)’: ../Blasr.cpp:1411:51: warning: cast between incompatible function types from ‘void (*)(MappingData >, FASTASequence, DNATuple>*)’ to ‘void* (*)(void*)’ [-Wcast-function-type] (void *(*)(void *))MapReads, &mapdb[procIndex]); ^~~~~~~~ ../Blasr.cpp:1466:37: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] } catch (std::exception e) { ^ In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29, from ../iblasr/BlasrHeaders.h:60, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In instantiation of ‘void AlignmentToBamRecord(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:167:25: required from ‘void BAMOutput::PrintAlignment(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::IRecordWriter&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrUtilsImpl.hpp:953:65: required from here /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:27:45: warning: the compiler can assume that the address of ‘read’ will never be NULL [-Waddress] if (dynamic_cast(&read) == NULL) { ^ /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In function ‘void AlignmentToBamRecord(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence]’: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:27:5: warning: nonnull argument ‘read’ compared to NULL [-Wnonnull-compare] if (dynamic_cast(&read) == NULL) { ^~ [19/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_PulseToFasta.cpp.o' -MF 'blasr_impl@sta/utils_PulseToFasta.cpp.o.d' -o 'blasr_impl@sta/utils_PulseToFasta.cpp.o' -c ../utils/PulseToFasta.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:19, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:13, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../utils/PulseToFasta.cpp:5: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition In file included from ../utils/PulseToFasta.cpp:8: /usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’: /usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] } catch (DataSetIException e) { ^ In file included from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../utils/PulseToFasta.cpp:5: /usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’: ../utils/PulseToFasta.cpp:157:41: required from here /usr/include/pbseq/hdf/HDFBasReader.hpp:760:11: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ /usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = FASTASequence]’: /usr/include/pbseq/hdf/HDFBasReader.hpp:726:25: required from ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’ ../utils/PulseToFasta.cpp:157:41: required from here /usr/include/pbseq/hdf/HDFBasReader.hpp:647:11: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ [20/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SamFilter.cpp.o' -MF 'blasr_impl@sta/utils_SamFilter.cpp.o.d' -o 'blasr_impl@sta/utils_SamFilter.cpp.o' -c ../utils/SamFilter.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13, from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6, from ../utils/SamFilter.cpp:32: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition [21/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_LoadPulses.cpp.o' -MF 'blasr_impl@sta/utils_LoadPulses.cpp.o.d' -o 'blasr_impl@sta/utils_LoadPulses.cpp.o' -c ../utils/LoadPulses.cpp In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4, from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13, from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6, from /usr/include/pbseq/alignment/datastructures/alignment/ByteAlignment.h:6, from ../utils/LoadPulses.cpp:11: /usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined #define USE_PBBAM : note: this is the location of the previous definition In file included from ../utils/LoadPulses.cpp:19: /usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’: /usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] } catch (DataSetIException e) { ^ In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:13, from ../utils/LoadPulses.cpp:16: /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = std::__cxx11::basic_string; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:9: required from ‘void HDFArray::Write(const T*, int) [with T = std::__cxx11::basic_string]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:36:43: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:9: required from ‘void HDFArray::Write(const T*, int) [with T = unsigned int]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:44:29: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = float; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = float; UInt = unsigned int]’ /usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp:81:60: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from ../utils/LoadPulses.cpp:16: /usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’: /usr/include/pbseq/hdf/HDFBasReader.hpp:135:28: required from ‘DNALength T_HDFBasReader::GetReadAt(UInt, SMRTSequence&) [with T_Sequence = FASTASequence; DNALength = unsigned int; UInt = unsigned int]’ ../utils/LoadPulses.cpp:680:59: required from here /usr/include/pbseq/hdf/HDFBasReader.hpp:760:11: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:13, from ../utils/LoadPulses.cpp:16: /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = unsigned char; UInt = unsigned int]’ ../utils/LoadPulses.cpp:1525:62: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = char; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = char; UInt = unsigned int]’ ../utils/LoadPulses.cpp:1537:64: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = short unsigned int; UInt = unsigned int]’ ../utils/LoadPulses.cpp:1547:76: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from ../utils/LoadPulses.cpp:16: /usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = FASTASequence]’: /usr/include/pbseq/hdf/HDFBasReader.hpp:726:25: required from ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’ /usr/include/pbseq/hdf/HDFBasReader.hpp:135:28: required from ‘DNALength T_HDFBasReader::GetReadAt(UInt, SMRTSequence&) [with T_Sequence = FASTASequence; DNALength = unsigned int; UInt = unsigned int]’ ../utils/LoadPulses.cpp:680:59: required from here /usr/include/pbseq/hdf/HDFBasReader.hpp:647:11: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] } catch (H5::DataSetIException e) { ^~~~~ [22/25] rm -f libblasr_impl.a && gcc-ar csrD libblasr_impl.a 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' 'blasr_impl@sta/extrautils_SAModify.cpp.o' 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o' 'blasr_impl@sta/extrautils_SALS.cpp.o' 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' 'blasr_impl@sta/extrautils_Evolve.cpp.o' 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' 'blasr_impl@sta/utils_SamToM4.cpp.o' 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' 'blasr_impl@sta/utils_SDPMatcher.cpp.o' 'blasr_impl@sta/utils_LoadPulses.cpp.o' 'blasr_impl@sta/utils_PulseToFasta.cpp.o' 'blasr_impl@sta/utils_SamFilter.cpp.o' [23/25] c++ -o sawriter 'sawriter@exe/utils_SAWriter.cpp.o' -I/usr/include/pbseq -L/usr/lib/powerpc64le-linux-gnu -L/usr/lib/powerpc64le-linux-gnu/hdf5/serial -Wl,--no-undefined -Wl,--as-needed -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a /usr/lib/powerpc64le-linux-gnu/libpbbam.so /usr/lib/powerpc64le-linux-gnu/libhts.so -lblasr /usr/lib/powerpc64le-linux-gnu/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf -Wl,--end-group -pthread '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/<>/blasr-5.3.2+dfsg/build/ [24/25] c++ -o toAfg 'toAfg@exe/utils_ToAfg.cpp.o' -I/usr/include/pbseq -L/usr/lib/powerpc64le-linux-gnu -L/usr/lib/powerpc64le-linux-gnu/hdf5/serial -Wl,--no-undefined -Wl,--as-needed -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a /usr/lib/powerpc64le-linux-gnu/libpbbam.so /usr/lib/powerpc64le-linux-gnu/libhts.so -lblasr /usr/lib/powerpc64le-linux-gnu/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf -Wl,--end-group -pthread '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/<>/blasr-5.3.2+dfsg/build/ [25/25] c++ -o blasr 'blasr@exe/Blasr.cpp.o' -I/usr/include/pbseq -L/usr/lib/powerpc64le-linux-gnu -L/usr/lib/powerpc64le-linux-gnu/hdf5/serial -Wl,--no-undefined -Wl,--as-needed -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -fdebug-prefix-map=/<>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a /usr/lib/powerpc64le-linux-gnu/libpbbam.so /usr/lib/powerpc64le-linux-gnu/libhts.so -lblasr /usr/lib/powerpc64le-linux-gnu/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf -Wl,--end-group -pthread '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/<>/blasr-5.3.2+dfsg/build/ make[1]: Leaving directory '/<>/blasr-5.3.2+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/blasr-5.3.2+dfsg' echo Tests require data not available in the source distribution Tests require data not available in the source distribution make[1]: Leaving directory '/<>/blasr-5.3.2+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --buildsystem=meson dh_testroot -a -O--buildsystem=meson dh_prep -a -O--buildsystem=meson dh_auto_install -a -O--buildsystem=meson cd obj-powerpc64le-linux-gnu && DESTDIR=/<>/blasr-5.3.2\+dfsg/debian/blasr LC_ALL=C.UTF-8 ninja install [1/4] Generating BlasrGitHash.h with a custom command. [1/2] Installing files. Installing blasr to /<>/blasr-5.3.2+dfsg/debian/blasr/usr/bin Installing sawriter to /<>/blasr-5.3.2+dfsg/debian/blasr/usr/bin dh_install -a -O--buildsystem=meson dh_installdocs -a -O--buildsystem=meson dh_installchangelogs -a -O--buildsystem=meson dh_installman -a -O--buildsystem=meson dh_installinit -a -O--buildsystem=meson dh_installsystemduser -a -O--buildsystem=meson dh_lintian -a -O--buildsystem=meson dh_perl -a -O--buildsystem=meson dh_link -a -O--buildsystem=meson dh_strip_nondeterminism -a -O--buildsystem=meson dh_compress -a -O--buildsystem=meson dh_fixperms -a -O--buildsystem=meson dh_missing -a -O--buildsystem=meson dh_dwz -a -O--buildsystem=meson dh_strip -a -O--buildsystem=meson dh_makeshlibs -a -O--buildsystem=meson dh_shlibdeps -a -O--buildsystem=meson dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so' dh_installdeb -a -O--buildsystem=meson dh_gencontrol -a -O--buildsystem=meson dh_md5sums -a -O--buildsystem=meson dh_builddeb -a -O--buildsystem=meson INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing blasr (in debian/blasr); do_strip: , oemstrip: pkgstriptranslations: processing blasr-dbgsym (in debian/.debhelper/blasr/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/blasr/DEBIAN/control, package blasr, directory debian/blasr pkgstripfiles: processing control file: debian/.debhelper/blasr/dbgsym-root/DEBIAN/control, package blasr-dbgsym, directory debian/.debhelper/blasr/dbgsym-root dpkg-deb: building package 'blasr-dbgsym' in 'debian/.debhelper/scratch-space/build-blasr/blasr-dbgsym_5.3.2+dfsg-1.1_ppc64el.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package blasr ... pkgstripfiles: No PNG files. dpkg-deb: building package 'blasr' in '../blasr_5.3.2+dfsg-1.1_ppc64el.deb'. Renaming blasr-dbgsym_5.3.2+dfsg-1.1_ppc64el.deb to blasr-dbgsym_5.3.2+dfsg-1.1_ppc64el.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../blasr_5.3.2+dfsg-1.1_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20190206-1712 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ blasr_5.3.2+dfsg-1.1_ppc64el.changes: ------------------------------------- Format: 1.8 Date: Wed, 06 Feb 2019 09:24:24 +0200 Source: blasr Binary: blasr Architecture: ppc64el Version: 5.3.2+dfsg-1.1 Distribution: disco-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Adrian Bunk Description: blasr - mapping single-molecule sequencing reads Changes: blasr (5.3.2+dfsg-1.1) unstable; urgency=medium . * Non-maintainer upload. * Remove manual dependency on libpbbam, a proper one is already being generated. Checksums-Sha1: cf6773bb803b7521cc6bdff929e1eff8b8cc1e4c 3264476 blasr-dbgsym_5.3.2+dfsg-1.1_ppc64el.ddeb a6cc4841990903efbbf59d6d2ef68cd525a2cbe7 7834 blasr_5.3.2+dfsg-1.1_ppc64el.buildinfo b52e97a7a95e6aa26c058e9a7fa117df55d66603 226060 blasr_5.3.2+dfsg-1.1_ppc64el.deb Checksums-Sha256: b558626be9a29b33913c385ab4e06ac6d32e279cb8e358da8bcf7a3b63133b7f 3264476 blasr-dbgsym_5.3.2+dfsg-1.1_ppc64el.ddeb 4004861e857bf5ce22882fc897caa8a9a370d8f4cfba99b4b93518238b6adfce 7834 blasr_5.3.2+dfsg-1.1_ppc64el.buildinfo 94df5c97b643f68208303930e95d2ffc202ed5ac8e150aa4db97b4bb682c7136 226060 blasr_5.3.2+dfsg-1.1_ppc64el.deb Files: 418b5586f17aa6d07d0574389594df07 3264476 debug optional blasr-dbgsym_5.3.2+dfsg-1.1_ppc64el.ddeb 138cee5921922e3e6842b9baf9800640 7834 science optional blasr_5.3.2+dfsg-1.1_ppc64el.buildinfo ee69fbf929bc6ca014f046a5bc783463 226060 science optional blasr_5.3.2+dfsg-1.1_ppc64el.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ blasr_5.3.2+dfsg-1.1_ppc64el.deb -------------------------------- new debian package, version 2.0. size 226060 bytes: control archive=1080 bytes. 822 bytes, 15 lines control 635 bytes, 10 lines md5sums Package: blasr Version: 5.3.2+dfsg-1.1 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 734 Depends: libc6 (>= 2.17), libgcc1 (>= 1:3.0), libhdf5-cpp-103 (>= 1.10.1), libpbbam0.19.0 (>= 0.19.0+dfsg), libstdc++6 (>= 5.2), libpbseq (>= 0~20160912) Section: science Priority: optional Homepage: https://github.com/PacificBiosciences/blasr Description: mapping single-molecule sequencing reads Basic local alignment with successive refinement (BLASR) is a method for mapping single-molecule sequencing reads against a reference genome. Such reads are thousands of bases long, with divergence between them and the genome being dominated by insertion and deletion error. drwxr-xr-x root/root 0 2019-02-06 07:24 ./ drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/ drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/bin/ -rwxr-xr-x root/root 657784 2019-02-06 07:24 ./usr/bin/blasr -rwxr-xr-x root/root 67848 2019-02-06 07:24 ./usr/bin/sawriter drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/share/ drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/share/doc/blasr/ -rw-r--r-- root/root 373 2019-01-28 15:10 ./usr/share/doc/blasr/NEWS.Debian.gz -rw-r--r-- root/root 1587 2018-06-08 20:17 ./usr/share/doc/blasr/README.md -rw-r--r-- root/root 41 2019-01-28 15:10 ./usr/share/doc/blasr/TODO.Debian -rw-r--r-- root/root 1387 2019-02-06 07:24 ./usr/share/doc/blasr/changelog.Debian.gz -rw-r--r-- root/root 2081 2019-01-28 15:10 ./usr/share/doc/blasr/copyright drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/share/lintian/ drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 84 2019-01-28 15:10 ./usr/share/lintian/overrides/blasr drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/share/man/ drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/share/man/man1/ -rw-r--r-- root/root 1369 2019-02-06 07:24 ./usr/share/man/man1/blasr.1.gz -rw-r--r-- root/root 872 2019-02-06 07:24 ./usr/share/man/man1/sawriter.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build-Space: 188172 Build-Time: 73 Distribution: disco-proposed Host Architecture: ppc64el Install-Time: 22 Job: blasr_5.3.2+dfsg-1.1.dsc Machine Architecture: ppc64el Package: blasr Package-Time: 96 Source-Version: 5.3.2+dfsg-1.1 Space: 188172 Status: successful Version: 5.3.2+dfsg-1.1 -------------------------------------------------------------------------------- Finished at 20190206-1712 Build needed 00:01:36, 188172k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=ppc64el PACKAGEBUILD-16358884 Scanning for processes to kill in build PACKAGEBUILD-16358884