https://launchpad.net/ubuntu/+source/blasr/5.3+0-2ubuntu1/+build/15790051 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lgw01-amd64-039 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018 x86_64 Buildd toolchain package versions: launchpad-buildd_165 python-lpbuildd_165 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... 17 Dec 22:12:39 ntpdate[1807]: adjust time server 10.211.37.1 offset 0.000486 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15790051 /home/buildd/filecache-default/020b0022f770b890c357907d03d82568c584d50e Creating target for build PACKAGEBUILD-15790051 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15790051 Starting target for build PACKAGEBUILD-15790051 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15790051 '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-15790051 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15790051 Updating target for build PACKAGEBUILD-15790051 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 amd64 Packages [1006 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe amd64 Packages [8975 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5154 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 Packages [76.3 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [34.2 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 Packages [752 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [321 kB] Fetched 17.3 MB in 5s (3661 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: binutils binutils-common binutils-x86-64-linux-gnu cpp-8 dpkg dpkg-dev e2fslibs e2fsprogs g++-8 gcc-8 gcc-8-base libasan5 libassuan0 libatomic1 libbinutils libcc1-0 libcom-err2 libcomerr2 libdpkg-perl libext2fs2 libgcc-8-dev libgcc1 libgomp1 libgpg-error0 libitm1 liblsan0 libmpx2 libquadmath0 libsqlite3-0 libss2 libstdc++-8-dev libstdc++6 libtsan0 libubsan1 linux-libc-dev 35 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 35.6 MB of archives. After this operation, 87.0 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main amd64 dpkg amd64 1.19.2ubuntu2 [1101 kB] Get:2 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libext2fs2 amd64 1.44.5-1 [159 kB] Get:3 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 e2fsprogs amd64 1.44.5-1 [514 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libubsan1 amd64 8.2.0-12ubuntu2 [121 kB] Get:5 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libtsan0 amd64 8.2.0-12ubuntu2 [288 kB] Get:6 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 gcc-8-base amd64 8.2.0-12ubuntu2 [18.7 kB] Get:7 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libstdc++6 amd64 8.2.0-12ubuntu2 [398 kB] Get:8 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libgomp1 amd64 8.2.0-12ubuntu2 [76.5 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libitm1 amd64 8.2.0-12ubuntu2 [28.1 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libatomic1 amd64 8.2.0-12ubuntu2 [9088 B] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libasan5 amd64 8.2.0-12ubuntu2 [365 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 liblsan0 amd64 8.2.0-12ubuntu2 [132 kB] Get:13 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libmpx2 amd64 8.2.0-12ubuntu2 [11.7 kB] Get:14 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libquadmath0 amd64 8.2.0-12ubuntu2 [134 kB] Get:15 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 cpp-8 amd64 8.2.0-12ubuntu2 [7226 kB] Get:16 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libcc1-0 amd64 8.2.0-12ubuntu2 [39.4 kB] Get:17 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 g++-8 amd64 8.2.0-12ubuntu2 [8112 kB] Get:18 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 gcc-8 amd64 8.2.0-12ubuntu2 [7999 kB] Get:19 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libgcc-8-dev amd64 8.2.0-12ubuntu2 [2306 kB] Get:20 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libstdc++-8-dev amd64 8.2.0-12ubuntu2 [1539 kB] Get:21 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libgcc1 amd64 1:8.2.0-12ubuntu2 [40.7 kB] Get:22 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libbinutils amd64 2.31.1-11ubuntu1 [484 kB] Get:23 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 binutils-common amd64 2.31.1-11ubuntu1 [194 kB] Get:24 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 binutils amd64 2.31.1-11ubuntu1 [3396 B] Get:25 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.31.1-11ubuntu1 [1829 kB] Get:26 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libgpg-error0 amd64 1.33-3 [57.4 kB] Get:27 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libcom-err2 amd64 1.44.5-1 [9372 B] Get:28 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libss2 amd64 1.44.5-1 [11.1 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main amd64 libsqlite3-0 amd64 3.26.0-3 [530 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main amd64 dpkg-dev all 1.19.2ubuntu2 [549 kB] Get:31 http://ftpmaster.internal/ubuntu disco/main amd64 libdpkg-perl all 1.19.2ubuntu2 [227 kB] Get:32 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 e2fslibs amd64 1.44.5-1 [2704 B] Get:33 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libassuan0 amd64 2.5.2-1 [35.1 kB] Get:34 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libcomerr2 amd64 1.44.5-1 [2700 B] Get:35 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 linux-libc-dev amd64 4.19.0-9.10 [1041 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 35.6 MB in 1s (47.8 MB/s) (Reading database ... 12665 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.2ubuntu2_amd64.deb ... Unpacking dpkg (1.19.2ubuntu2) over (1.19.2ubuntu1) ... Setting up dpkg (1.19.2ubuntu2) ... (Reading database ... 12665 files and directories currently installed.) Preparing to unpack .../libext2fs2_1.44.5-1_amd64.deb ... Unpacking libext2fs2:amd64 (1.44.5-1) over (1.44.4-2ubuntu1) ... Setting up libext2fs2:amd64 (1.44.5-1) ... (Reading database ... 12664 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.44.5-1_amd64.deb ... Unpacking e2fsprogs (1.44.5-1) over (1.44.4-2ubuntu1) ... Preparing to unpack .../libubsan1_8.2.0-12ubuntu2_amd64.deb ... Unpacking libubsan1:amd64 (8.2.0-12ubuntu2) over (8.2.0-12ubuntu1) ... Preparing to unpack .../libtsan0_8.2.0-12ubuntu2_amd64.deb ... Unpacking libtsan0:amd64 (8.2.0-12ubuntu2) over (8.2.0-12ubuntu1) ... Preparing to unpack .../gcc-8-base_8.2.0-12ubuntu2_amd64.deb ... Unpacking gcc-8-base:amd64 (8.2.0-12ubuntu2) over (8.2.0-12ubuntu1) ... Setting up gcc-8-base:amd64 (8.2.0-12ubuntu2) ... (Reading database ... 12664 files and directories currently installed.) Preparing to unpack .../libstdc++6_8.2.0-12ubuntu2_amd64.deb ... Unpacking libstdc++6:amd64 (8.2.0-12ubuntu2) over (8.2.0-12ubuntu1) ... Setting up libstdc++6:amd64 (8.2.0-12ubuntu2) ... (Reading database ... 12664 files and directories currently installed.) Preparing to unpack .../00-libgomp1_8.2.0-12ubuntu2_amd64.deb ... Unpacking libgomp1:amd64 (8.2.0-12ubuntu2) over (8.2.0-12ubuntu1) ... Preparing to unpack .../01-libitm1_8.2.0-12ubuntu2_amd64.deb ... Unpacking libitm1:amd64 (8.2.0-12ubuntu2) over (8.2.0-12ubuntu1) ... Preparing to unpack .../02-libatomic1_8.2.0-12ubuntu2_amd64.deb ... Unpacking libatomic1:amd64 (8.2.0-12ubuntu2) over (8.2.0-12ubuntu1) ... Preparing to unpack .../03-libasan5_8.2.0-12ubuntu2_amd64.deb ... Unpacking libasan5:amd64 (8.2.0-12ubuntu2) over (8.2.0-12ubuntu1) ... Preparing to unpack .../04-liblsan0_8.2.0-12ubuntu2_amd64.deb ... 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Setting up binutils-common:amd64 (2.31.1-11ubuntu1) ... Setting up libmpx2:amd64 (8.2.0-12ubuntu2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up libsqlite3-0:amd64 (3.26.0-3) ... Setting up libcomerr2:amd64 (1.44.5-1) ... Setting up libasan5:amd64 (8.2.0-12ubuntu2) ... Setting up libassuan0:amd64 (2.5.2-1) ... Setting up libitm1:amd64 (8.2.0-12ubuntu2) ... Setting up libubsan1:amd64 (8.2.0-12ubuntu2) ... Setting up libbinutils:amd64 (2.31.1-11ubuntu1) ... Setting up libgcc-8-dev:amd64 (8.2.0-12ubuntu2) ... Setting up binutils-x86-64-linux-gnu (2.31.1-11ubuntu1) ... Setting up libstdc++-8-dev:amd64 (8.2.0-12ubuntu2) ... Setting up binutils (2.31.1-11ubuntu1) ... Setting up gcc-8 (8.2.0-12ubuntu2) ... Setting up g++-8 (8.2.0-12ubuntu2) ... Setting up dpkg-dev (1.19.2ubuntu2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15790051 amd64 disco-proposed -c chroot:build-PACKAGEBUILD-15790051 --arch=amd64 --dist=disco-proposed --nolog -A blasr_5.3+0-2ubuntu1.dsc Initiating build PACKAGEBUILD-15790051 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-039.buildd +==============================================================================+ | blasr 5.3+0-2ubuntu1 (amd64) 17 Dec 2018 22:13 | +==============================================================================+ Package: blasr Version: 5.3+0-2ubuntu1 Source Version: 5.3+0-2ubuntu1 Distribution: disco-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/blasr-KfhhCf/blasr-5.3+0' with '<>' I: NOTICE: Log filtering will replace 'build/blasr-KfhhCf' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15790051/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- blasr_5.3+0-2ubuntu1.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-OIetBf/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-OIetBf/apt_archive ./ InRelease Get:2 copy:/<>/resolver-OIetBf/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-OIetBf/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-OIetBf/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-OIetBf/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (222 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-OIetBf/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12667 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), python, cmake, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev (>= 0~20160912), libpbbam-dev, libpbdata-dev Filtered Build-Depends: debhelper (>= 11~), python, cmake, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev (>= 0~20160912), libpbbam-dev, libpbdata-dev dpkg-deb: building package 'sbuild-build-depends-blasr-dummy' in '/<>/resolver-4S5AV_/apt_archive/sbuild-build-depends-blasr-dummy.deb'. Ign:1 copy:/<>/resolver-4S5AV_/apt_archive ./ InRelease Get:2 copy:/<>/resolver-4S5AV_/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-4S5AV_/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-4S5AV_/apt_archive ./ Sources [271 B] Get:5 copy:/<>/resolver-4S5AV_/apt_archive ./ Packages [587 B] Fetched 2977 B in 0s (241 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 additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libasn1-8-heimdal libblasr libblasr-dev libboost-dev libboost1.67-dev libbsd0 libcroco3 libcurl3-gnutls libcurl4 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal 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 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpbbam libpbbam-dev libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpbseq-dev libpipeline1 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssl-dev libsz2 libtool libuv1 libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-minimal python2 python2-minimal python2.7 python2.7-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cmake-doc ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip 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 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 cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libasn1-8-heimdal libblasr libblasr-dev libboost-dev libboost1.67-dev libbsd0 libcroco3 libcurl3-gnutls libcurl4 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal 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 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpbbam libpbbam-dev libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpbseq-dev libpipeline1 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssl-dev libsz2 libtool libuv1 libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-minimal python2 python2-minimal python2.7 python2.7-minimal sbuild-build-depends-blasr-dummy zlib1g-dev 0 upgraded, 101 newly installed, 0 to remove and 0 not upgraded. Need to get 48.4 MB of archives. After this operation, 297 MB of additional disk space will be used. Get:1 copy:/<>/resolver-4S5AV_/apt_archive ./ sbuild-build-depends-blasr-dummy 0.invalid.0 [916 B] Get:2 http://ftpmaster.internal/ubuntu disco/main amd64 libbsd0 amd64 0.9.1-1 [44.6 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main amd64 bsdmainutils amd64 11.1.2ubuntu2 [181 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main amd64 groff-base amd64 1.22.3-10 [1153 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main amd64 libpipeline1 amd64 1.5.0-2 [25.7 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main amd64 man-db amd64 2.8.4-3 [1028 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main amd64 libpython2.7-minimal amd64 2.7.15-5 [335 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main amd64 python2.7-minimal amd64 2.7.15-5 [1308 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main amd64 python2-minimal amd64 2.7.15-3 [28.1 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main amd64 python-minimal amd64 2.7.15-3 [5996 B] Get:11 http://ftpmaster.internal/ubuntu disco/main amd64 mime-support all 3.60ubuntu1 [30.1 kB] Get:12 http://ftpmaster.internal/ubuntu disco/main amd64 libexpat1 amd64 2.2.6-1 [87.2 kB] Get:13 http://ftpmaster.internal/ubuntu disco/main amd64 libpython2.7-stdlib amd64 2.7.15-5 [1909 kB] Get:14 http://ftpmaster.internal/ubuntu disco/main amd64 python2.7 amd64 2.7.15-5 [239 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main amd64 libpython2-stdlib amd64 2.7.15-3 [7728 B] Get:16 http://ftpmaster.internal/ubuntu disco/main amd64 libpython-stdlib amd64 2.7.15-3 [5824 B] Get:17 http://ftpmaster.internal/ubuntu disco/main amd64 python2 amd64 2.7.15-3 [26.5 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main amd64 python amd64 2.7.15-3 [7828 B] Get:19 http://ftpmaster.internal/ubuntu disco/main amd64 libmagic-mgc amd64 1:5.34-2 [197 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main amd64 libmagic1 amd64 1:5.34-2 [72.3 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main amd64 file amd64 1:5.34-2 [22.8 kB] Get:22 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2.1.27~101-g0780600+dfsg-3ubuntu2 [49.2 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main amd64 libldap-common all 2.4.46+dfsg-5ubuntu3 [16.0 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main amd64 libldap-2.4-2 amd64 2.4.46+dfsg-5ubuntu3 [154 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main amd64 libnghttp2-14 amd64 1.35.1-1 [78.9 kB] Get:55 http://ftpmaster.internal/ubuntu disco/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [54.5 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main amd64 libcurl4 amd64 7.61.0-1ubuntu2.2 [217 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main amd64 libjsoncpp1 amd64 1.7.4-3 [73.6 kB] Get:58 http://ftpmaster.internal/ubuntu disco/main amd64 librhash0 amd64 1.3.6-3 [78.6 kB] Get:59 http://ftpmaster.internal/ubuntu disco/main amd64 libuv1 amd64 1.24.0-1 [69.3 kB] Get:60 http://ftpmaster.internal/ubuntu disco/main amd64 cmake amd64 3.13.2-1 [3466 kB] Get:61 http://ftpmaster.internal/ubuntu disco/main amd64 libtool all 2.4.6-6 [195 kB] Get:62 http://ftpmaster.internal/ubuntu disco/main amd64 dh-autoreconf all 19 [16.1 kB] Get:63 http://ftpmaster.internal/ubuntu disco/main amd64 libarchive-zip-perl all 1.64-1 [84.9 kB] Get:64 http://ftpmaster.internal/ubuntu disco/main amd64 libfile-stripnondeterminism-perl all 1.0.0-1 [13.9 kB] Get:65 http://ftpmaster.internal/ubuntu disco/main amd64 dh-strip-nondeterminism all 1.0.0-1 [5064 B] Get:66 http://ftpmaster.internal/ubuntu disco/main amd64 dwz amd64 0.12-3 [78.1 kB] Get:67 http://ftpmaster.internal/ubuntu disco/main amd64 libcroco3 amd64 0.6.12-2 [81.3 kB] Get:68 http://ftpmaster.internal/ubuntu disco/main amd64 gettext amd64 0.19.8.1-9 [896 kB] Get:69 http://ftpmaster.internal/ubuntu disco/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:70 http://ftpmaster.internal/ubuntu disco/main amd64 po-debconf all 1.0.21 [233 kB] Get:71 http://ftpmaster.internal/ubuntu disco/main amd64 debhelper all 11.5.3ubuntu1 [888 kB] Get:72 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amd64 libhdf5-cpp-103 amd64 1.10.4+repack-1 [121 kB] Get:82 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 libpbihdf amd64 5.3.1+dfsg-1build1 [166 kB] Get:83 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 libblasr amd64 5.3.1+dfsg-1build1 [871 kB] Get:84 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 libblasr-dev amd64 5.3.1+dfsg-1build1 [1697 kB] Get:85 http://ftpmaster.internal/ubuntu disco/main amd64 libboost1.67-dev amd64 1.67.0-11 [8362 kB] Get:86 http://ftpmaster.internal/ubuntu disco/main amd64 libboost-dev amd64 1.67.0.1 [3228 B] Get:87 http://ftpmaster.internal/ubuntu disco/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-0ubuntu2 [176 kB] Get:88 http://ftpmaster.internal/ubuntu disco/main amd64 libjpeg-turbo8 amd64 2.0.0-0ubuntu2 [117 kB] Get:89 http://ftpmaster.internal/ubuntu disco/main amd64 libjpeg-turbo8-dev amd64 2.0.0-0ubuntu2 [238 kB] Get:90 http://ftpmaster.internal/ubuntu disco/main amd64 libjpeg8 amd64 8c-2ubuntu8 [2194 B] 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libpbihdf-dev amd64 5.3.1+dfsg-1build1 [261 kB] Get:101 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 libpbseq-dev all 5.3.1+dfsg-1build1 [3224 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 48.4 MB in 1s (34.5 MB/s) Selecting previously unselected package libbsd0:amd64. 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Setting up python2.7 (2.7.15-5) ... Setting up autoconf (2.69-11) ... Setting up libhdf5-103:amd64 (1.10.4+repack-1) ... Setting up file (1:5.34-2) ... Setting up libhx509-5-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libjpeg8-dev:amd64 (8c-2ubuntu8) ... Setting up libjpeg-dev:amd64 (8c-2ubuntu8) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.4-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython2-stdlib:amd64 (2.7.15-3) ... Setting up libkrb5-3:amd64 (1.16.1-1ubuntu1) ... Setting up libkrb5-26-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libheimntlm0-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libtool (2.4.6-6) ... Setting up po-debconf (1.0.21) ... Setting up libhdf5-cpp-103:amd64 (1.10.4+repack-1) ... Setting up libhdf5-dev (1.10.4+repack-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up python2 (2.7.15-3) ... Setting up libgssapi-krb5-2:amd64 (1.16.1-1ubuntu1) ... Setting up libpython-stdlib:amd64 (2.7.15-3) ... Setting up libgssapi3-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up python (2.7.15-3) ... Setting up libldap-2.4-2:amd64 (2.4.46+dfsg-5ubuntu3) ... Setting up libcurl3-gnutls:amd64 (7.61.0-1ubuntu2.2) ... Setting up libcurl4:amd64 (7.61.0-1ubuntu2.2) ... Setting up cmake (3.13.2-1) ... Setting up libhts2:amd64 (1.9-6) ... Setting up libhts-dev:amd64 (1.9-6) ... Setting up libpbbam:amd64 (0.7.4+ds-1build2) ... Setting up libpbbam-dev (0.7.4+ds-1build2) ... Setting up libpbdata:amd64 (5.3.1+dfsg-1build1) ... Setting up libpbihdf:amd64 (5.3.1+dfsg-1build1) ... Setting up libblasr:amd64 (5.3.1+dfsg-1build1) ... Setting up libpbihdf-dev:amd64 (5.3.1+dfsg-1build1) ... Setting up libpbdata-dev:amd64 (5.3.1+dfsg-1build1) ... Setting up libblasr-dev:amd64 (5.3.1+dfsg-1build1) ... Setting up libpbseq-dev (5.3.1+dfsg-1build1) ... Setting up dh-autoreconf (19) ... Setting up debhelper (11.5.3ubuntu1) ... Setting up sbuild-build-depends-blasr-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (1.0.0-1) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-140-generic amd64 (x86_64) Toolchain package versions: binutils_2.31.1-11ubuntu1 dpkg-dev_1.19.2ubuntu2 g++-8_8.2.0-12ubuntu2 gcc-8_8.2.0-12ubuntu2 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-12ubuntu2 libstdc++6_8.2.0-12ubuntu2 linux-libc-dev_4.19.0-9.10 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.8.0~alpha2ubuntu1 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_4.4.18-2ubuntu3 binutils_2.31.1-11ubuntu1 binutils-common_2.31.1-11ubuntu1 binutils-x86-64-linux-gnu_2.31.1-11ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu2 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20180409 cmake_3.13.2-1 cmake-data_3.13.2-1 coreutils_8.28-1ubuntu2 cpp_4:8.2.0-2ubuntu2 cpp-8_8.2.0-12ubuntu2 dash_0.5.10.2-2 debconf_1.5.69 debhelper_11.5.3ubuntu1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_1.0.0-1 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_2.32-0.1ubuntu2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2ubuntu2 g++-8_8.2.0-12ubuntu2 gcc_4:8.2.0-2ubuntu2 gcc-8_8.2.0-12ubuntu2 gcc-8-base_8.2.0-12ubuntu2 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpg_2.2.8-3ubuntu1 gpg-agent_2.2.8-3ubuntu1 gpgconf_2.2.8-3ubuntu1 gpgv_2.2.8-3ubuntu1 grep_3.1-3 groff-base_1.22.3-10 gzip_1.6-5ubuntu2 hdf5-helpers_1.10.4+repack-1 hostname_3.21 init_1.56 init-system-helpers_1.56 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 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~alpha2ubuntu1 libarchive-zip-perl_1.64-1 libarchive13_3.3.3-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-12ubuntu2 libasn1-8-heimdal_7.5.0+dfsg-2.1 libassuan0_2.5.2-1 libatomic1_8.2.0-12ubuntu2 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu3 libaudit1_1:2.8.3-1ubuntu3 libbinutils_2.31.1-11ubuntu1 libblasr_5.3.1+dfsg-1build1 libblasr-dev_5.3.1+dfsg-1build1 libblkid1_2.32-0.1ubuntu2 libboost-dev_1.67.0.1 libboost1.67-dev_1.67.0-11 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_0.7.9-1build1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-12ubuntu2 libcom-err2_1.44.5-1 libcomerr2_1.44.5-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2ubuntu2 libcurl3-gnutls_7.61.0-1ubuntu2.2 libcurl4_7.61.0-1ubuntu2.2 libdb5.3_5.3.28+dfsg1-0.2 libdebconfclient0_0.244ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu4 libdpkg-perl_1.19.2ubuntu2 libelf1_0.175-1 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.32-0.1ubuntu2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libgcc-8-dev_8.2.0-12ubuntu2 libgcc1_1:8.2.0-12ubuntu2 libgcrypt20_1.8.4-3ubuntu1 libgdbm-compat4_1.18.1-2 libgdbm6_1.18.1-2 libgfortran5_8.2.0-12ubuntu2 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.4-2ubuntu2 libgomp1_8.2.0-12ubuntu2 libgpg-error0_1.33-3 libgssapi-krb5-2_1.16.1-1ubuntu1 libgssapi3-heimdal_7.5.0+dfsg-2.1 libhcrypto4-heimdal_7.5.0+dfsg-2.1 libhdf5-103_1.10.4+repack-1 libhdf5-cpp-103_1.10.4+repack-1 libhdf5-dev_1.10.4+repack-1 libheimbase1-heimdal_7.5.0+dfsg-2.1 libheimntlm0-heimdal_7.5.0+dfsg-2.1 libhogweed4_3.4.1~rc1-1 libhts-dev_1.9-6 libhts2_1.9-6 libhx509-5-heimdal_7.5.0+dfsg-2.1 libicu63_63.1-5 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.5-1 libip4tc0_1.6.1-2ubuntu3 libisl19_0.20-2 libitm1_8.2.0-12ubuntu2 libjpeg-dev_8c-2ubuntu8 libjpeg-turbo8_2.0.0-0ubuntu2 libjpeg-turbo8-dev_2.0.0-0ubuntu2 libjpeg8_8c-2ubuntu8 libjpeg8-dev_8c-2ubuntu8 libjson-c3_0.12.1-1.3 libjsoncpp1_1.7.4-3 libk5crypto3_1.16.1-1ubuntu1 libkeyutils1_1.5.9-9.3 libkmod2_25-1ubuntu2 libkrb5-26-heimdal_7.5.0+dfsg-2.1 libkrb5-3_1.16.1-1ubuntu1 libkrb5support0_1.16.1-1ubuntu1 libldap-2.4-2_2.4.46+dfsg-5ubuntu3 libldap-common_2.4.46+dfsg-5ubuntu3 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblsan0_8.2.0-12ubuntu2 liblz4-1_1.8.2-1ubuntu1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32-0.1ubuntu2 libmpc3_1.1.0-1 libmpfr6_4.0.1-2 libmpx2_8.2.0-12ubuntu2 libncurses6_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4.1~rc1-1 libnghttp2-14_1.35.1-1 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_0.7.4+ds-1build2 libpbbam-dev_0.7.4+ds-1build2 libpbdata_5.3.1+dfsg-1build1 libpbdata-dev_5.3.1+dfsg-1build1 libpbihdf_5.3.1+dfsg-1build1 libpbihdf-dev_5.3.1+dfsg-1build1 libpbseq-dev_5.3.1+dfsg-1build1 libpcre3_2:8.39-11 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libpng16-16_1.6.34-2 libprocps7_2:3.3.15-2ubuntu1 libpsl5_0.20.2-2 libpython-stdlib_2.7.15-3 libpython2-stdlib_2.7.15-3 libpython2.7-minimal_2.7.15-5 libpython2.7-stdlib_2.7.15-5 libquadmath0_8.2.0-12ubuntu2 libreadline7_7.0-5 librhash0_1.3.6-3 libroken18-heimdal_7.5.0+dfsg-2.1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2 libseccomp2_2.3.3-3ubuntu2 libselinux1_2.8-1build2 libsemanage-common_2.8-1build2 libsemanage1_2.8-1build2 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.32-0.1ubuntu2 libsqlite3-0_3.26.0-3 libss2_1.44.5-1 libssl-dev_1.1.1a-1ubuntu2 libssl1.1_1.1.1a-1ubuntu2 libstdc++-8-dev_8.2.0-12ubuntu2 libstdc++6_8.2.0-12ubuntu2 libsystemd0_239-7ubuntu15 libsz2_1.0.2-1 libtasn1-6_4.13-3 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-6 libtsan0_8.2.0-12ubuntu2 libubsan1_8.2.0-12ubuntu2 libudev1_239-7ubuntu15 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libuuid1_2.32-0.1ubuntu2 libuv1_1.24.0-1 libwind0-heimdal_7.5.0+dfsg-2.1 libxml2_2.9.4+dfsg1-7ubuntu3 libzstd1_1.3.5+dfsg-1ubuntu1 linux-libc-dev_4.19.0-9.10 lockfile-progs_0.1.18 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.4-3 mawk_1.3.3-17ubuntu3 mime-support_3.60ubuntu1 mount_2.32-0.1ubuntu2 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.1a-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1build2 pkgbinarymangler_143 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 python_2.7.15-3 python-minimal_2.7.15-3 python2_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-5 python2.7-minimal_2.7.15-5 readline-common_7.0-5 sbuild-build-depends-blasr-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.5-2 sensible-utils_0.0.12 systemd_239-7ubuntu15 systemd-sysv_239-7ubuntu15 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tar_1.30+dfsg-3 tzdata_2018g-1 ubuntu-keyring_2018.09.18.1 util-linux_2.32-0.1ubuntu2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Mon Dec 17 22:11:05 2018 UTC gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./blasr_5.3+0-2ubuntu1.dsc dpkg-source: info: extracting blasr in blasr-5.3+0 dpkg-source: info: unpacking blasr_5.3+0.orig.tar.gz dpkg-source: info: unpacking blasr_5.3+0-2ubuntu1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable-gtest.patch dpkg-source: info: applying cmake-utils.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-15790051 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15790051 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15790051 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+0-2ubuntu1 dpkg-buildpackage: info: source distribution disco dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/blasr-5.3+0' ./configure.py --shared `uname` Linux writing to '/<>/blasr-5.3+0/defines.mk': """ HTSLIB_INC ?= /usr/include/htslib HDF5_INC ?= /usr/include/hdf5/serial PBBAM_INC ?= /usr/include CXXFLAGS ?= -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 LIBPBDATA_LIBFLAGS ?= -lpbdata LIBPBIHDF_LIB ?= /usr/lib/x86_64-linux-gnu SHELL ?= bash LIBPBDATA_INC ?= /usr/include/pbseq/pbdata PBBAM_LIBFLAGS ?= -lpbbam LIBPBIHDF_INC ?= /usr/include/pbseq/hdf RT_LIBFLAGS ?= -lrt ZLIB_LIBFLAGS ?= -lz HTSLIB_LIB ?= /usr/lib/x86_64-linux-gnu PTHREAD_LIBFLAGS ?= -lpthread LIBBLASR_LIBFLAGS ?= -lblasr LIBPBDATA_LIB ?= /usr/lib/x86_64-linux-gnu HTSLIB_LIBFLAGS ?= -lhts HDF5_LIB ?= /usr/lib/x86_64-linux-gnu/hdf5/serial HDF5_LIBFLAGS ?= -lhdf5_cpp -lhdf5 DL_LIBFLAGS ?= -ldl LIBPBIHDF_LIBFLAGS ?= -lpbihdf LIBBLASR_INC ?= /usr/include/pbseq/alignment LIBBLASR_LIB ?= /usr/lib/x86_64-linux-gnu PBBAM_LIB ?= /usr/lib/x86_64-linux-gnu BOOST_INC ?= /usr/include/boost """ ---- /usr/bin/make clean make[2]: Entering directory '/<>/blasr-5.3+0' make[2]: git: Command not found rm -f blasr Blasr.o Blasr.d blasr.d /usr/bin/make -C utils clean make[3]: Entering directory '/<>/blasr-5.3+0/utils' make[4]: Entering directory '/<>/blasr-5.3+0/utils/bam2bax' make[4]: Leaving directory '/<>/blasr-5.3+0/utils/bam2bax' make[4]: Entering directory '/<>/blasr-5.3+0/utils/bax2bam' make[4]: Leaving directory '/<>/blasr-5.3+0/utils/bax2bam' make[3]: Leaving directory '/<>/blasr-5.3+0/utils' /usr/bin/make -C extrautils clean make[3]: Entering directory '/<>/blasr-5.3+0/extrautils' ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. make[3]: Leaving directory '/<>/blasr-5.3+0/extrautils' make[2]: Leaving directory '/<>/blasr-5.3+0' /usr/bin/make -C utils/bam2bax clean make[2]: Entering directory '/<>/blasr-5.3+0/utils/bam2bax' make[2]: Leaving directory '/<>/blasr-5.3+0/utils/bam2bax' /usr/bin/make -C utils/bax2bam clean make[2]: Entering directory '/<>/blasr-5.3+0/utils/bax2bam' make[2]: Leaving directory '/<>/blasr-5.3+0/utils/bax2bam' # This is created by configure.py rm -f defines.mk make[1]: Leaving directory '/<>/blasr-5.3+0' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/blasr-5.3+0' ./configure.py --shared `uname` Linux writing to '/<>/blasr-5.3+0/defines.mk': """ HTSLIB_INC ?= /usr/include/htslib HDF5_INC ?= /usr/include/hdf5/serial PBBAM_INC ?= /usr/include CXXFLAGS ?= -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 LIBPBDATA_LIBFLAGS ?= -lpbdata LIBPBIHDF_LIB ?= /usr/lib/x86_64-linux-gnu SHELL ?= bash LIBPBDATA_INC ?= /usr/include/pbseq/pbdata PBBAM_LIBFLAGS ?= -lpbbam LIBPBIHDF_INC ?= /usr/include/pbseq/hdf RT_LIBFLAGS ?= -lrt ZLIB_LIBFLAGS ?= -lz HTSLIB_LIB ?= /usr/lib/x86_64-linux-gnu PTHREAD_LIBFLAGS ?= -lpthread LIBBLASR_LIBFLAGS ?= -lblasr LIBPBDATA_LIB ?= /usr/lib/x86_64-linux-gnu HTSLIB_LIBFLAGS ?= -lhts HDF5_LIB ?= /usr/lib/x86_64-linux-gnu/hdf5/serial HDF5_LIBFLAGS ?= -lhdf5_cpp -lhdf5 DL_LIBFLAGS ?= -ldl LIBPBIHDF_LIBFLAGS ?= -lpbihdf LIBBLASR_INC ?= /usr/include/pbseq/alignment LIBBLASR_LIB ?= /usr/lib/x86_64-linux-gnu PBBAM_LIB ?= /usr/lib/x86_64-linux-gnu BOOST_INC ?= /usr/include/boost """ ---- make[1]: Leaving directory '/<>/blasr-5.3+0' debian/rules override_dh_auto_build make[1]: Entering directory '/<>/blasr-5.3+0' dh_auto_build make V=1 -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/blasr-5.3+0' make[2]: git: Command not found g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o Blasr.o Blasr.cpp make -C utils make[3]: Entering directory '/<>/blasr-5.3+0/utils' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o LoadPulses.o LoadPulses.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o PulseToFasta.o PulseToFasta.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o SamToCmpH5.o SamToCmpH5.cpp In file included from iblasr/BlasrMiscs.hpp:4, from Blasr.cpp:3: iblasr/BlasrHeaders.h:24:10: fatal error: libconfig.h: No such file or directory #include ^~~~~~~~~~~~~ compilation terminated. make[2]: *** [: Blasr.o] Error 1 make[2]: *** Waiting for unfinished jobs.... g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o SamToM4.o SamToM4.cpp SamToM4.cpp: In function ‘int main(int, char**)’: SamToM4.cpp:34:5: error: ‘string’ was not declared in this scope string program = "samtom4"; ^~~~~~ SamToM4.cpp:34:5: note: suggested alternative: In file included from /usr/include/c++/8/iosfwd:39, from /usr/include/c++/8/ios:38, from /usr/include/c++/8/ostream:38, from /usr/include/c++/8/iostream:39, from SamToM4.cpp:18: /usr/include/c++/8/bits/stringfwd.h:74:33: note: ‘std::__cxx11::string’ typedef basic_string string; ^~~~~~ SamToM4.cpp:35:11: error: expected ‘;’ before ‘versionString’ string versionString = VERSION; ^~~~~~~~~~~~~~ ; SamToM4.cpp:36:55: error: ‘versionString’ was not declared in this scope AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionString); ^~~~~~~~~~~~~ SamToM4.cpp:38:11: error: expected ‘;’ before ‘samFileName’ string samFileName, refFileName, outFileName; ^~~~~~~~~~~~ ; SamToM4.cpp:44:24: error: ‘program’ was not declared in this scope clp.SetProgramName(program); ^~~~~~~ SamToM4.cpp:47:48: error: ‘samFileName’ was not declared in this scope clp.RegisterStringOption("in.sam", &samFileName, ^~~~~~~~~~~ SamToM4.cpp:47:48: note: suggested alternative: ‘samFile’ clp.RegisterStringOption("in.sam", &samFileName, ^~~~~~~~~~~ samFile SamToM4.cpp:49:50: error: ‘refFileName’ was not declared in this scope clp.RegisterStringOption("reference.fasta", &refFileName, ^~~~~~~~~~~ SamToM4.cpp:51:50: error: ‘outFileName’ was not declared in this scope clp.RegisterStringOption("out.m4", &outFileName, ^~~~~~~~~~~ SamToM4.cpp:64:5: error: ‘ostream’ was not declared in this scope ostream * outFilePtr = &cout; ^~~~~~~ SamToM4.cpp:64:5: note: suggested alternative: In file included from /usr/include/c++/8/ios:38, from /usr/include/c++/8/ostream:38, from /usr/include/c++/8/iostream:39, from SamToM4.cpp:18: /usr/include/c++/8/iosfwd:141:33: note: ‘std::ostream’ typedef basic_ostream ostream; ^~~~~~~ SamToM4.cpp:64:15: error: ‘outFilePtr’ was not declared in this scope ostream * outFilePtr = &cout; ^~~~~~~~~~ SamToM4.cpp:64:29: error: ‘cout’ was not declared in this scope ostream * outFilePtr = &cout; ^~~~ SamToM4.cpp:64:29: note: suggested alternative: In file included from SamToM4.cpp:18: /usr/include/c++/8/iostream:61:18: note: ‘std::cout’ extern ostream cout; /// Linked to standard output ^~~~ SamToM4.cpp:65:2: error: ‘ofstream’ was not declared in this scope ofstream outFileStrm; ^~~~~~~~ SamToM4.cpp:65:2: note: suggested alternative: In file included from /usr/include/c++/8/ios:38, from /usr/include/c++/8/ostream:38, from /usr/include/c++/8/iostream:39, from SamToM4.cpp:18: /usr/include/c++/8/iosfwd:165:34: note: ‘std::ofstream’ typedef basic_ofstream ofstream; ^~~~~~~~ SamToM4.cpp:67:28: error: ‘outFileStrm’ was not declared in this scope CrucialOpen(outFileName, outFileStrm, std::ios::out); ^~~~~~~~~~~ SamToM4.cpp:83:11: error: expected ‘;’ before ‘command’ string command; ^~~~~~~~ ; SamToM4.cpp:84:56: error: ‘command’ was not declared in this scope CommandLineParser::CommandLineToString(argc, argv, command); ^~~~~~~ SamToM4.cpp:89:5: error: ‘vector’ was not declared in this scope vector references; ^~~~~~ SamToM4.cpp:89:5: note: suggested alternative: In file included from /usr/include/c++/8/vector:64, from /usr/include/pbbam/Frames.h:46, from /usr/include/pbbam/BamRecord.h:46, from /usr/include/pbseq/pbdata/DNASequence.hpp:17, from /usr/include/pbseq/pbdata/FASTASequence.hpp:13, from SamToM4.cpp:19: /usr/include/c++/8/bits/stl_vector.h:339:11: note: ‘std::vector’ class vector : protected _Vector_base<_Tp, _Alloc> ^~~~~~ SamToM4.cpp:89:25: error: expected primary-expression before ‘>’ token vector references; ^ SamToM4.cpp:89:27: error: ‘references’ was not declared in this scope vector references; ^~~~~~~~~~ SamToM4.cpp:107:5: error: ‘map’ was not declared in this scope map shortRefNameToFull; ^~~ SamToM4.cpp:107:5: note: suggested alternative: In file included from /usr/include/c++/8/map:61, from /usr/include/boost/detail/container_fwd.hpp:94, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/variant/variant.hpp:21, from /usr/include/boost/variant.hpp:17, from /usr/include/pbbam/Tag.h:46, from /usr/include/pbbam/TagCollection.h:46, from /usr/include/pbbam/BamRecordImpl.h:50, from /usr/include/pbbam/BamRecord.h:47, from /usr/include/pbseq/pbdata/DNASequence.hpp:17, from /usr/include/pbseq/pbdata/FASTASequence.hpp:13, from SamToM4.cpp:19: /usr/include/c++/8/bits/stl_map.h:100:11: note: ‘std::map’ class map ^~~ SamToM4.cpp:107:25: error: ‘shortRefNameToFull’ was not declared in this scope map shortRefNameToFull; ^~~~~~~~~~~~~~~~~~ SamToM4.cpp:107:25: note: suggested alternative: ‘useShortRefName’ map shortRefNameToFull; ^~~~~~~~~~~~~~~~~~ useShortRefName SamToM4.cpp:108:26: error: ‘::iterator’ has not been declared map::iterator it; ^~~~~~~~ SamToM4.cpp:108:26: note: suggested alternatives: In file included from /usr/include/c++/8/bits/stl_algobase.h:65, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/ios:40, from /usr/include/c++/8/ostream:38, from /usr/include/c++/8/iostream:39, from SamToM4.cpp:18: /usr/include/c++/8/bits/stl_iterator_base_types.h:118:12: note: ‘std::iterator’ struct iterator ^~~~~~~~ /usr/include/c++/8/bits/stl_iterator_base_types.h:118:12: note: ‘std::iterator’ SamToM4.cpp:112:19: error: expected ‘;’ before ‘shortRefName’ string shortRefName = alignmentSet.references[i].GetSequenceName(); ^~~~~~~~~~~~~ ; SamToM4.cpp:113:19: error: expected ‘;’ before ‘fullRefName’ string fullRefName(references[i].title); ^~~~~~~~~~~~ ; SamToM4.cpp:114:41: error: ‘shortRefName’ was not declared in this scope if (shortRefNameToFull.find(shortRefName) != shortRefNameToFull.end()) { ^~~~~~~~~~~~ SamToM4.cpp:114:41: note: suggested alternative: ‘useShortRefName’ if (shortRefNameToFull.find(shortRefName) != shortRefNameToFull.end()) { ^~~~~~~~~~~~ useShortRefName SamToM4.cpp:115:103: error: ‘endl’ was not declared in this scope cout << "ERROR, Found more than one reference " << shortRefName << "in sam header" << endl; ^~~~ SamToM4.cpp:115:103: note: suggested alternative: In file included from /usr/include/c++/8/iostream:39, from SamToM4.cpp:18: /usr/include/c++/8/ostream:590:5: note: ‘std::endl’ endl(basic_ostream<_CharT, _Traits>& __os) ^~~~ SamToM4.cpp:118:32: error: ‘shortRefName’ was not declared in this scope shortRefNameToFull[shortRefName] = fullRefName; ^~~~~~~~~~~~ SamToM4.cpp:118:32: note: suggested alternative: ‘useShortRefName’ shortRefNameToFull[shortRefName] = fullRefName; ^~~~~~~~~~~~ useShortRefName SamToM4.cpp:118:48: error: ‘fullRefName’ was not declared in this scope shortRefNameToFull[shortRefName] = fullRefName; ^~~~~~~~~~~ SamToM4.cpp:124:17: error: expected primary-expression before ‘int’ map refNameToIndex; ^~~ SamToM4.cpp:126:15: error: expected ‘;’ before ‘refName’ string refName = alignmentSet.references[i].GetSequenceName(); ^~~~~~~~ ; SamToM4.cpp:127:9: error: ‘refNameToIndex’ was not declared in this scope refNameToIndex[refName] = i; ^~~~~~~~~~~~~~ SamToM4.cpp:127:24: error: ‘refName’ was not declared in this scope refNameToIndex[refName] = i; ^~~~~~~ SamToM4.cpp:127:24: note: suggested alternative: ‘rename’ refNameToIndex[refName] = i; ^~~~~~~ rename SamToM4.cpp:157:13: error: ‘it’ was not declared in this scope it = shortRefNameToFull.find(samAlignment.rName); ^~ SamToM4.cpp:157:13: note: suggested alternative: ‘Fit’ it = shortRefNameToFull.find(samAlignment.rName); ^~ Fit SamToM4.cpp:159:110: error: ‘endl’ was not declared in this scope cout << "ERROR, Could not find " << samAlignment.rName << " in the reference repository." << endl; ^~~~ SamToM4.cpp:159:110: note: suggested alternative: In file included from /usr/include/c++/8/iostream:39, from SamToM4.cpp:18: /usr/include/c++/8/ostream:590:5: note: ‘std::endl’ endl(basic_ostream<_CharT, _Traits>& __os) ^~~~ SamToM4.cpp:166:45: error: ‘string’ is not a class, namespace, or enumeration if (samAlignment.cigar.find('P') != string::npos) { ^~~~~~ SamToM4.cpp:168:21: error: ‘endl’ was not declared in this scope << endl; ^~~~ SamToM4.cpp:168:21: note: suggested alternative: In file included from /usr/include/c++/8/iostream:39, from SamToM4.cpp:18: /usr/include/c++/8/ostream:590:5: note: ‘std::endl’ endl(basic_ostream<_CharT, _Traits>& __os) ^~~~ SamToM4.cpp:172:37: error: expected primary-expression before ‘>’ token vector > convertedAlignments; ^ SamToM4.cpp:172:39: error: ‘convertedAlignments’ was not declared in this scope vector > convertedAlignments; ^~~~~~~~~~~~~~~~~~~ SamToM4.cpp:181:61: error: ‘refNameToIndex’ was not declared in this scope SAMAlignmentsToCandidates(samAlignment, references, refNameToIndex, ^~~~~~~~~~~~~~ SamToM4.cpp:186:84: error: ‘endl’ was not declared in this scope cout << "WARNING. Ignore an alignment which has multiple segments." << endl; ^~~~ SamToM4.cpp:186:84: note: suggested alternative: In file included from /usr/include/c++/8/iostream:39, from SamToM4.cpp:18: /usr/include/c++/8/ostream:590:5: note: ‘std::endl’ endl(basic_ostream<_CharT, _Traits>& __os) ^~~~ SamToM4.cpp:219:3: error: ‘outFileStrm’ was not declared in this scope outFileStrm.close(); ^~~~~~~~~~~ In file included from LoadPulses.cpp:5: /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 PulseToFasta.cpp:5: /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) { ^ SamToCmpH5.cpp: In function ‘int main(int, char**)’: SamToCmpH5.cpp:19:3: error: ‘string’ was not declared in this scope string program = "samtoh5"; ^~~~~~ SamToCmpH5.cpp:19:3: note: suggested alternative: In file included from /usr/include/c++/8/iosfwd:39, from /usr/include/c++/8/ios:38, from /usr/include/c++/8/ostream:38, from /usr/include/c++/8/iostream:39, from SamToCmpH5.cpp:1: /usr/include/c++/8/bits/stringfwd.h:74:33: note: ‘std::__cxx11::string’ typedef basic_string string; ^~~~~~ SamToCmpH5.cpp:20:9: error: expected ‘;’ before ‘versionString’ string versionString = VERSION; ^~~~~~~~~~~~~~ ; SamToCmpH5.cpp:21:53: error: ‘versionString’ was not declared in this scope AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionString); ^~~~~~~~~~~~~ SamToCmpH5.cpp:22:9: error: expected ‘;’ before ‘samFileName’ string samFileName, cmpFileName, refFileName; ^~~~~~~~~~~~ ; SamToCmpH5.cpp:27:9: error: expected ‘;’ before ‘readType’ string readType = "standard"; ^~~~~~~~~ ; SamToCmpH5.cpp:30:22: error: ‘program’ was not declared in this scope clp.SetProgramName(program); ^~~~~~~ SamToCmpH5.cpp:34:39: error: ‘samFileName’ was not declared in this scope clp.RegisterStringOption("in.sam", &samFileName, ^~~~~~~~~~~ SamToCmpH5.cpp:34:39: note: suggested alternative: ‘samFile’ clp.RegisterStringOption("in.sam", &samFileName, ^~~~~~~~~~~ samFile SamToCmpH5.cpp:36:48: error: ‘refFileName’ was not declared in this scope clp.RegisterStringOption("reference.fasta", &refFileName, ^~~~~~~~~~~ SamToCmpH5.cpp:38:43: error: ‘cmpFileName’ was not declared in this scope clp.RegisterStringOption("out.cmp.h5", &cmpFileName, ^~~~~~~~~~~ SamToCmpH5.cpp:38:43: note: suggested alternative: ‘CmpFile’ clp.RegisterStringOption("out.cmp.h5", &cmpFileName, ^~~~~~~~~~~ CmpFile SamToCmpH5.cpp:50:41: error: ‘readType’ was not declared in this scope clp.RegisterStringOption("readType", &readType, ^~~~~~~~ SamToCmpH5.cpp:50:41: note: suggested alternative: ‘ReadType’ clp.RegisterStringOption("readType", &readType, ^~~~~~~~ ReadType SamToCmpH5.cpp:64:9: error: expected ‘;’ before ‘description’ string description = ("Because SAM has optional tags that have different " ^~~~~~~~~~~~ ; SamToCmpH5.cpp:72:19: error: ‘description’ was not declared in this scope clp.SetExamples(description); ^~~~~~~~~~~ SamToCmpH5.cpp:72:19: note: suggested alternatives: In file included from /usr/include/pbseq/pbdata/reads/RegionTable.hpp:15, from /usr/include/pbseq/pbdata/SMRTSequence.hpp:14, from /usr/include/pbseq/hdf/HDFCmpFile.hpp:25, from SamToCmpH5.cpp:6: /usr/include/pbseq/pbdata/PacBioDefs.h:72:26: note: ‘PacBio::AttributeNames::Common::description’ static const std::string description = "Description"; ^~~~~~~~~~~ /usr/include/pbseq/pbdata/PacBioDefs.h:107:26: note: ‘PacBio::AttributeValues::ZMW::HoleNumber::description’ static const std::string description = "Hole number on chip array"; ^~~~~~~~~~~ /usr/include/pbseq/pbdata/PacBioDefs.h:111:26: note: ‘PacBio::AttributeValues::ZMW::HoleStatus::description’ static const std::string description = "Type of data coming from ZMW"; ^~~~~~~~~~~ /usr/include/pbseq/pbdata/PacBioDefs.h:121:26: note: ‘PacBio::AttributeValues::ZMW::HoleXY::description’ static const std::string description = "Coordinates of ZMW on Chip"; ^~~~~~~~~~~ /usr/include/pbseq/pbdata/PacBioDefs.h:125:26: note: ‘PacBio::AttributeValues::ZMW::BaseLineSigma::description’ static const std::string description = "Estimated baseline sigma (std dev) over trace"; ^~~~~~~~~~~ /usr/include/pbseq/pbdata/PacBioDefs.h:145:26: note: ‘PacBio::AttributeValues::ZMWMetrics::HQRegionSNR::description’ static const std::string description = "HQRegion average signal to noise ratio"; ^~~~~~~~~~~ /usr/include/pbseq/pbdata/PacBioDefs.h:148:26: note: ‘PacBio::AttributeValues::ZMWMetrics::ReadScore::description’ static const std::string description = "Read raw accuracy prediction"; ^~~~~~~~~~~ /usr/include/pbseq/pbdata/PacBioDefs.h:151:26: note: ‘PacBio::AttributeValues::ZMWMetrics::Productivity::description’ static const std::string description = "ZMW productivity classification"; ^~~~~~~~~~~ SamToCmpH5.cpp:78:5: error: ‘cout’ was not declared in this scope cout << "ERROR. Read type '" << readType ^~~~ SamToCmpH5.cpp:78:5: note: suggested alternative: In file included from SamToCmpH5.cpp:1: /usr/include/c++/8/iostream:61:18: note: ‘std::cout’ extern ostream cout; /// Linked to standard output ^~~~ SamToCmpH5.cpp:80:13: error: ‘endl’ was not declared in this scope << endl; ^~~~ SamToCmpH5.cpp:80:13: note: suggested alternative: In file included from /usr/include/c++/8/iostream:39, from SamToCmpH5.cpp:1: /usr/include/c++/8/ostream:590:5: note: ‘std::endl’ endl(basic_ostream<_CharT, _Traits>& __os) ^~~~ SamToCmpH5.cpp:84:3: error: ‘cerr’ was not declared in this scope cerr << "[INFO] " << GetTimestamp() << " [" << program << "] started." << endl; ^~~~ SamToCmpH5.cpp:84:3: note: suggested alternative: In file included from SamToCmpH5.cpp:1: /usr/include/c++/8/iostream:62:18: note: ‘std::cerr’ extern ostream cerr; /// Linked to standard error (unbuffered) ^~~~ SamToCmpH5.cpp:84:77: error: ‘endl’ was not declared in this scope cerr << "[INFO] " << GetTimestamp() << " [" << program << "] started." << endl; ^~~~ SamToCmpH5.cpp:84:77: note: suggested alternative: In file included from /usr/include/c++/8/iostream:39, from SamToCmpH5.cpp:1: /usr/include/c++/8/ostream:590:5: note: ‘std::endl’ endl(basic_ostream<_CharT, _Traits>& __os) ^~~~ SamToCmpH5.cpp:100:9: error: expected ‘;’ before ‘command’ string command; ^~~~~~~~ ; SamToCmpH5.cpp:101:54: error: ‘command’ was not declared in this scope CommandLineParser::CommandLineToString(argc, argv, command); ^~~~~~~ SamToCmpH5.cpp:102:9: error: expected ‘;’ before ‘log’ string log = "Convert sam to cmp.h5"; ^~~~ ; SamToCmpH5.cpp:114:3: error: ‘vector’ was not declared in this scope vector references; ^~~~~~ SamToCmpH5.cpp:114:3: note: suggested alternative: In file included from /usr/include/c++/8/vector:64, from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:5, from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, from SamToCmpH5.cpp:3: /usr/include/c++/8/bits/stl_vector.h:339:11: note: ‘std::vector’ class vector : protected _Vector_base<_Tp, _Alloc> ^~~~~~ SamToCmpH5.cpp:114:23: error: expected primary-expression before ‘>’ token vector references; ^ SamToCmpH5.cpp:114:25: error: ‘references’ was not declared in this scope vector references; ^~~~~~~~~~ SamToCmpH5.cpp:114:25: note: suggested alternative: ‘H5Rdereference1’ vector references; ^~~~~~~~~~ H5Rdereference1 SamToCmpH5.cpp:146:3: error: ‘map’ was not declared in this scope map shortRefNameToFull; ^~~ SamToCmpH5.cpp:146:3: note: suggested alternative: In file included from /usr/include/c++/8/map:61, from /usr/include/boost/detail/container_fwd.hpp:94, from /usr/include/boost/container_hash/extensions.hpp:22, from /usr/include/boost/container_hash/hash.hpp:760, from /usr/include/boost/type_index/stl_type_index.hpp:43, from /usr/include/boost/type_index.hpp:29, from /usr/include/boost/variant/variant.hpp:21, from /usr/include/boost/variant.hpp:17, from /usr/include/pbbam/Tag.h:46, from /usr/include/pbbam/TagCollection.h:46, from /usr/include/pbbam/BamRecordImpl.h:50, from /usr/include/pbbam/BamRecord.h:47, from /usr/include/pbseq/pbdata/DNASequence.hpp:17, from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:9, from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, from SamToCmpH5.cpp:3: /usr/include/c++/8/bits/stl_map.h:100:11: note: ‘std::map’ class map ^~~ SamToCmpH5.cpp:146:23: error: ‘shortRefNameToFull’ was not declared in this scope map shortRefNameToFull; ^~~~~~~~~~~~~~~~~~ SamToCmpH5.cpp:146:23: note: suggested alternative: ‘useShortRefName’ map shortRefNameToFull; ^~~~~~~~~~~~~~~~~~ useShortRefName SamToCmpH5.cpp:147:24: error: ‘::iterator’ has not been declared map::iterator it; ^~~~~~~~ SamToCmpH5.cpp:147:24: note: suggested alternatives: In file included from /usr/include/c++/8/bits/stl_algobase.h:65, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/ios:40, from /usr/include/c++/8/ostream:38, from /usr/include/c++/8/iostream:39, from SamToCmpH5.cpp:1: /usr/include/c++/8/bits/stl_iterator_base_types.h:118:12: note: ‘std::iterator’ struct iterator ^~~~~~~~ /usr/include/c++/8/bits/stl_iterator_base_types.h:118:12: note: ‘std::iterator’ SamToCmpH5.cpp:151:17: error: expected ‘;’ before ‘shortRefName’ string shortRefName = alignmentSet.references[i].GetSequenceName(); ^~~~~~~~~~~~~ ; SamToCmpH5.cpp:152:17: error: expected ‘;’ before ‘fullRefName’ string fullRefName(references[i].title); ^~~~~~~~~~~~ ; SamToCmpH5.cpp:153:39: error: ‘shortRefName’ was not declared in this scope if (shortRefNameToFull.find(shortRefName) != shortRefNameToFull.end()) { ^~~~~~~~~~~~ SamToCmpH5.cpp:153:39: note: suggested alternative: ‘useShortRefName’ if (shortRefNameToFull.find(shortRefName) != shortRefNameToFull.end()) { ^~~~~~~~~~~~ useShortRefName SamToCmpH5.cpp:154:15: error: ‘cout’ was not declared in this scope cout << "ERROR, Found more than one reference " << shortRefName << "in sam header" << endl; ^~~~ SamToCmpH5.cpp:154:15: note: suggested alternative: In file included from SamToCmpH5.cpp:1: /usr/include/c++/8/iostream:61:18: note: ‘std::cout’ extern ostream cout; /// Linked to standard output ^~~~ SamToCmpH5.cpp:157:30: error: ‘shortRefName’ was not declared in this scope shortRefNameToFull[shortRefName] = fullRefName; ^~~~~~~~~~~~ SamToCmpH5.cpp:157:30: note: suggested alternative: ‘useShortRefName’ shortRefNameToFull[shortRefName] = fullRefName; ^~~~~~~~~~~~ useShortRefName SamToCmpH5.cpp:157:46: error: ‘fullRefName’ was not declared in this scope shortRefNameToFull[shortRefName] = fullRefName; ^~~~~~~~~~~ SamToCmpH5.cpp:179:9: error: ‘it’ was not declared in this scope it = shortRefNameToFull.find(samAlignment.rName); ^~ SamToCmpH5.cpp:179:9: note: suggested alternative: ‘Fit’ it = shortRefNameToFull.find(samAlignment.rName); ^~ Fit SamToCmpH5.cpp:181:13: error: ‘cout’ was not declared in this scope cout << "ERROR, Could not find " << samAlignment.rName << " in the reference repository." << endl; ^~~~ SamToCmpH5.cpp:181:13: note: suggested alternative: In file included from SamToCmpH5.cpp:1: /usr/include/c++/8/iostream:61:18: note: ‘std::cout’ extern ostream cout; /// Linked to standard output ^~~~ SamToCmpH5.cpp:186:33: error: expected primary-expression before ‘>’ token vector > convertedAlignments; ^ SamToCmpH5.cpp:186:35: error: ‘convertedAlignments’ was not declared in this scope vector > convertedAlignments; ^~~~~~~~~~~~~~~~~~~ SamToCmpH5.cpp:186:35: note: suggested alternative: ‘ByteAlignment’ vector > convertedAlignments; ^~~~~~~~~~~~~~~~~~~ ByteAlignment SamToCmpH5.cpp:188:7: error: ‘cout’ was not declared in this scope cout << "Storing alignment for " << samAlignment.qName << endl; ^~~~ SamToCmpH5.cpp:188:7: note: suggested alternative: In file included from SamToCmpH5.cpp:1: /usr/include/c++/8/iostream:61:18: note: ‘std::cout’ extern ostream cout; /// Linked to standard output ^~~~ 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 SamToCmpH5.cpp:6: /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 /usr/include/pbseq/hdf/HDFPlsReader.hpp:12, from PulseToFasta.cpp:5: /usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’: PulseToFasta.cpp:145:41: 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) { ^~~~~ 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 LoadPulses.cpp:3: /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 LoadPulses.cpp:4: /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]’ LoadPulses.cpp:701:59: 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/HDFAlnGroupGroup.hpp:6, from /usr/include/pbseq/hdf/HDFCmpFile.hpp:12, from LoadPulses.cpp:3: /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]’ LoadPulses.cpp:1565:62: 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]’ LoadPulses.cpp:1577:64: 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]’ LoadPulses.cpp:1588:76: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] make[3]: *** [: SamToM4.o] Error 1 make[3]: *** Waiting for unfinished jobs.... In file included from LoadPulses.cpp:4: /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]’ LoadPulses.cpp:701:59: 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) { ^~~~~ /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]’ PulseToFasta.cpp:145:41: 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) { ^~~~~ make[3]: *** [: SamToCmpH5.o] Error 1 make[3]: Leaving directory '/<>/blasr-5.3+0/utils' make[2]: *** [makefile:67: makeutils] Error 2 make[2]: Leaving directory '/<>/blasr-5.3+0' dh_auto_build: make V=1 -j4 "INSTALL=install --strip-program=true" returned exit code 2 make[1]: *** [debian/rules:42: main] Error 2 make[1]: Leaving directory '/<>/blasr-5.3+0' make: *** [debian/rules:33: build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20181217-2214 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 30032 Build-Time: 44 Distribution: disco-proposed Fail-Stage: build Host Architecture: amd64 Install-Time: 28 Job: blasr_5.3+0-2ubuntu1.dsc Machine Architecture: amd64 Package: blasr Package-Time: 73 Source-Version: 5.3+0-2ubuntu1 Space: 30032 Status: attempted Version: 5.3+0-2ubuntu1 -------------------------------------------------------------------------------- Finished at 20181217-2214 Build needed 00:01:13, 30032k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15790051 Scanning for processes to kill in build PACKAGEBUILD-15790051