RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lgw01-41 4.4.0-93-generic #116-Ubuntu SMP Fri Aug 11 21:17:51 UTC 2017 x86_64 Buildd toolchain package versions: launchpad-buildd_151 python-lpbuildd_151 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_1:2.7.4-0ubuntu1.2 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 9 Sep 09:56:49 ntpdate[1755]: adjust time server 10.211.37.1 offset 0.012360 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-12808199 /home/buildd/filecache-default/7fe38ae672de2c40a7e6ba74a0e6690544a5bb48 Creating target for build PACKAGEBUILD-12808199 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-12808199 Starting target for build PACKAGEBUILD-12808199 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-12808199 'deb http://ftpmaster.internal/ubuntu artful main universe' 'deb http://ftpmaster.internal/ubuntu artful-security main universe' 'deb http://ftpmaster.internal/ubuntu artful-updates main universe' 'deb http://ftpmaster.internal/ubuntu artful-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-12808199 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-12808199 Updating target for build PACKAGEBUILD-12808199 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:3 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed InRelease [235 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main i386 Packages [1122 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main Translation-en [550 kB] Get:7 http://ftpmaster.internal/ubuntu artful/universe i386 Packages [8170 kB] Get:8 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4777 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main i386 Packages [131 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main Translation-en [48.5 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/universe i386 Packages [122 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/universe Translation-en [62.7 kB] Fetched 15.6 MB in 4s (3395 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: g++-6 libperl5.24 libstdc++-6-dev perl-modules-5.24 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: binutils-common binutils-i686-linux-gnu cpp-7 fdisk g++-7 gcc-7 gcc-7-base libasan4 libbinutils libgcc-7-dev libperl5.26 libstdc++-7-dev perl-modules-5.26 The following packages will be upgraded: advancecomp apt apt-transport-https base-files bash binutils bsdutils ca-certificates cpp cpp-6 debconf debianutils diffutils dmsetup dpkg dpkg-dev e2fslibs e2fsprogs findutils g++ g++-6 gcc gcc-6 gcc-6-base grep init init-system-helpers libapparmor1 libapt-pkg5.0 libasan3 libasn1-8-heimdal libassuan0 libatomic1 libaudit-common libaudit1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcilkrts5 libcomerr2 libcryptsetup4 libcurl3-gnutls libdb5.3 libdevmapper1.02.1 libdpkg-perl libfdisk1 libgcc-6-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libip4tc0 libitm1 libk5crypto3 libkmod2 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma5 libmount1 libmpfr4 libmpx2 libnpth0 libp11-kit0 libpcre3 libpng16-16 libpsl5 libquadmath0 libroken18-heimdal libsasl2-2 libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-6-dev libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 libusb-0.1-4 libuuid1 libwind0-heimdal linux-libc-dev login mount multiarch-support openssl passwd perl perl-base sensible-utils systemd systemd-sysv tar tzdata util-linux xz-utils zlib1g 117 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. Need to get 166 MB of archives. After this operation, 465 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu artful/main i386 debconf all 1.5.63 [136 kB] Get:2 http://ftpmaster.internal/ubuntu artful-proposed/main i386 perl-modules-5.26 all 5.26.0-7 [2762 kB] Get:3 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libperl5.26 i386 5.26.0-7 [3159 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed/main i386 perl i386 5.26.0-7 [202 kB] Get:5 http://ftpmaster.internal/ubuntu artful-proposed/main i386 perl-base i386 5.26.0-7 [1492 kB] Get:6 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libc6-dev i386 2.26-0ubuntu1 [2145 kB] Get:7 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libc-dev-bin i386 2.26-0ubuntu1 [67.0 kB] Get:8 http://ftpmaster.internal/ubuntu artful-proposed/main i386 linux-libc-dev i386 4.12.0-13.14 [960 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libc6 i386 2.26-0ubuntu1 [2547 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libc-bin i386 2.26-0ubuntu1 [572 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/main i386 gcc-7-base i386 7.2.0-4ubuntu1 [17.9 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libgcc1 i386 1:7.2.0-4ubuntu1 [47.0 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main i386 libdb5.3 i386 5.3.28-13.1 [738 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main i386 zlib1g i386 1:1.2.11.dfsg-0ubuntu2 [58.2 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main i386 init-system-helpers all 1.49ubuntu1 [36.4 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main i386 base-files i386 9.6ubuntu101 [59.1 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main i386 debianutils i386 4.8.2 [86.5 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main i386 bash i386 4.4-5ubuntu1 [622 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main i386 bsdutils i386 1:2.30.1-0ubuntu4 [62.4 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main i386 diffutils i386 1:3.6-1 [175 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main i386 tar i386 1.29b-2 [252 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main i386 dpkg i386 1.18.24ubuntu1 [1164 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main i386 e2fslibs i386 1.43.5-1 [183 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main i386 e2fsprogs i386 1.43.5-1 [533 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main i386 findutils i386 4.6.0+git+20170729-2 [305 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main i386 grep i386 3.1-2 [163 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main i386 login i386 1:4.2-3.2ubuntu4 [307 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main i386 libuuid1 i386 2.30.1-0ubuntu4 [15.7 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main i386 libblkid1 i386 2.30.1-0ubuntu4 [133 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main i386 libpcre3 i386 2:8.39-4 [227 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main i386 libselinux1 i386 2.6-3build2 [72.8 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main i386 libmount1 i386 2.30.1-0ubuntu4 [143 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main i386 libsmartcols1 i386 2.30.1-0ubuntu4 [85.4 kB] Get:34 http://ftpmaster.internal/ubuntu artful/main i386 libfdisk1 i386 2.30.1-0ubuntu4 [173 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main i386 fdisk i386 2.30.1-0ubuntu4 [115 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main i386 util-linux i386 2.30.1-0ubuntu4 [903 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main i386 mount i386 2.30.1-0ubuntu4 [115 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main i386 liblzma5 i386 5.2.2-1.3 [98.5 kB] Get:39 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libstdc++6 i386 7.2.0-4ubuntu1 [437 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main i386 libapt-pkg5.0 i386 1.5~rc1~ubuntu1 [849 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main i386 libtasn1-6 i386 4.12-2.1 [38.7 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main i386 libp11-kit0 i386 0.23.7-3 [188 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main i386 libgnutls30 i386 3.5.8-6ubuntu3 [695 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main i386 libk5crypto3 i386 1.15.1-2 [88.3 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main i386 libgssapi-krb5-2 i386 1.15.1-2 [129 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main i386 libkrb5-3 i386 1.15.1-2 [300 kB] Get:47 http://ftpmaster.internal/ubuntu artful/main i386 libkrb5support0 i386 1.15.1-2 [34.0 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main i386 libcomerr2 i386 1.43.5-1 [11.0 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main i386 libidn2-0 i386 2.0.2-3 [92.7 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main i386 libldap-2.4-2 i386 2.4.45+dfsg-1ubuntu1 [167 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main i386 libldap-common all 2.4.45+dfsg-1ubuntu1 [16.6 kB] Get:52 http://ftpmaster.internal/ubuntu artful/main i386 libroken18-heimdal i386 7.4.0.dfsg.1-2 [44.5 kB] Get:53 http://ftpmaster.internal/ubuntu artful/main i386 libasn1-8-heimdal i386 7.4.0.dfsg.1-2 [187 kB] Get:54 http://ftpmaster.internal/ubuntu artful/main i386 libheimbase1-heimdal i386 7.4.0.dfsg.1-2 [32.0 kB] Get:55 http://ftpmaster.internal/ubuntu artful/main i386 libhcrypto4-heimdal i386 7.4.0.dfsg.1-2 [93.3 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main i386 libwind0-heimdal i386 7.4.0.dfsg.1-2 [49.1 kB] Get:57 http://ftpmaster.internal/ubuntu artful/main i386 libhx509-5-heimdal i386 7.4.0.dfsg.1-2 [118 kB] Get:58 http://ftpmaster.internal/ubuntu artful/main i386 libsqlite3-0 i386 3.19.3-3 [525 kB] Get:59 http://ftpmaster.internal/ubuntu artful/main i386 libkrb5-26-heimdal i386 7.4.0.dfsg.1-2 [231 kB] Get:60 http://ftpmaster.internal/ubuntu artful/main i386 libheimntlm0-heimdal i386 7.4.0.dfsg.1-2 [16.6 kB] Get:61 http://ftpmaster.internal/ubuntu artful/main i386 libgssapi3-heimdal i386 7.4.0.dfsg.1-2 [108 kB] Get:62 http://ftpmaster.internal/ubuntu artful/main i386 libsasl2-modules-db i386 2.1.27~101-g0780600+dfsg-3ubuntu1 [15.5 kB] Get:63 http://ftpmaster.internal/ubuntu artful/main i386 libsasl2-2 i386 2.1.27~101-g0780600+dfsg-3ubuntu1 [52.7 kB] Get:64 http://ftpmaster.internal/ubuntu artful/main i386 libpsl5 i386 0.18.0-2 [41.3 kB] Get:65 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libcurl3-gnutls i386 7.55.1-1ubuntu1 [214 kB] Get:66 http://ftpmaster.internal/ubuntu artful/main i386 apt-transport-https i386 1.5~rc1~ubuntu1 [39.0 kB] Get:67 http://ftpmaster.internal/ubuntu artful/main i386 apt i386 1.5~rc1~ubuntu1 [1147 kB] Get:68 http://ftpmaster.internal/ubuntu artful/main i386 libip4tc0 i386 1.6.1-2ubuntu1 [20.5 kB] Get:69 http://ftpmaster.internal/ubuntu artful/main i386 libapparmor1 i386 2.11.0-2ubuntu16 [30.3 kB] Get:70 http://ftpmaster.internal/ubuntu artful/main i386 libaudit-common all 1:2.7.7-1ubuntu2 [3998 B] Get:71 http://ftpmaster.internal/ubuntu artful/main i386 libcap-ng0 i386 0.7.7-3build1 [11.1 kB] Get:72 http://ftpmaster.internal/ubuntu artful/main i386 libaudit1 i386 1:2.7.7-1ubuntu2 [39.3 kB] Get:73 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libudev1 i386 234-2ubuntu10 [56.2 kB] Get:74 http://ftpmaster.internal/ubuntu artful/main i386 libdevmapper1.02.1 i386 2:1.02.137-2ubuntu3 [145 kB] Get:75 http://ftpmaster.internal/ubuntu artful/main i386 libgpg-error0 i386 1.27-3 [39.4 kB] Get:76 http://ftpmaster.internal/ubuntu artful/main i386 libgcrypt20 i386 1.7.8-2 [375 kB] Get:77 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libcryptsetup4 i386 2:1.7.3-4ubuntu1 [85.1 kB] Get:78 http://ftpmaster.internal/ubuntu artful/main i386 libkmod2 i386 24-1ubuntu2 [46.3 kB] Get:79 http://ftpmaster.internal/ubuntu artful-proposed/main i386 systemd i386 234-2ubuntu10 [2873 kB] Get:80 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libsystemd0 i386 234-2ubuntu10 [228 kB] Get:81 http://ftpmaster.internal/ubuntu artful/main i386 init i386 1.49ubuntu1 [5438 B] Get:82 http://ftpmaster.internal/ubuntu artful-proposed/main i386 systemd-sysv i386 234-2ubuntu10 [11.9 kB] Get:83 http://ftpmaster.internal/ubuntu artful/main i386 libsemanage-common all 2.6-2build2 [6682 B] Get:84 http://ftpmaster.internal/ubuntu artful/main i386 libsemanage1 i386 2.6-2build2 [90.4 kB] Get:85 http://ftpmaster.internal/ubuntu artful/main i386 libss2 i386 1.43.5-1 [11.5 kB] Get:86 http://ftpmaster.internal/ubuntu artful/main i386 passwd i386 1:4.2-3.2ubuntu4 [790 kB] Get:87 http://ftpmaster.internal/ubuntu artful/main i386 sensible-utils all 0.0.10 [14.6 kB] Get:88 http://ftpmaster.internal/ubuntu artful/main i386 dmsetup i386 2:1.02.137-2ubuntu3 [73.2 kB] Get:89 http://ftpmaster.internal/ubuntu artful/main i386 libassuan0 i386 2.4.3-3 [36.7 kB] Get:90 http://ftpmaster.internal/ubuntu artful/main i386 libnpth0 i386 1.5-2 [7942 B] Get:91 http://ftpmaster.internal/ubuntu artful/main i386 libssl1.0.0 i386 1.0.2g-1ubuntu13 [910 kB] Get:92 http://ftpmaster.internal/ubuntu artful-proposed/main i386 multiarch-support i386 2.26-0ubuntu1 [6828 B] Get:93 http://ftpmaster.internal/ubuntu artful/main i386 tzdata all 2017b-2 [203 kB] Get:94 http://ftpmaster.internal/ubuntu artful/main i386 xz-utils i386 5.2.2-1.3 [88.6 kB] Get:95 http://ftpmaster.internal/ubuntu artful/main i386 openssl i386 1.0.2g-1ubuntu13 [506 kB] Get:96 http://ftpmaster.internal/ubuntu artful/main i386 ca-certificates all 20170717 [167 kB] Get:97 http://ftpmaster.internal/ubuntu artful/main i386 libpng16-16 i386 1.6.32-1 [185 kB] Get:98 http://ftpmaster.internal/ubuntu artful/main i386 advancecomp i386 2.0-1 [206 kB] Get:99 http://ftpmaster.internal/ubuntu artful-proposed/main i386 binutils i386 2.29-9ubuntu1 [30.5 kB] Get:100 http://ftpmaster.internal/ubuntu artful-proposed/main i386 binutils-common i386 2.29-9ubuntu1 [37.9 kB] Get:101 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libbinutils i386 2.29-9ubuntu1 [549 kB] Get:102 http://ftpmaster.internal/ubuntu artful-proposed/main i386 binutils-i686-linux-gnu i386 2.29-9ubuntu1 [2127 kB] Get:103 http://ftpmaster.internal/ubuntu artful/main i386 libmpfr4 i386 3.1.6-1 [194 kB] Get:104 http://ftpmaster.internal/ubuntu artful-proposed/main i386 cpp-7 i386 7.2.0-4ubuntu1 [31.8 MB] Get:105 http://ftpmaster.internal/ubuntu artful/main i386 cpp i386 4:7.1.0-1ubuntu3 [27.6 kB] Get:106 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libquadmath0 i386 7.2.0-4ubuntu1 [205 kB] Get:107 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libitm1 i386 7.2.0-4ubuntu1 [30.3 kB] Get:108 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libmpx2 i386 7.2.0-4ubuntu1 [13.0 kB] Get:109 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libubsan0 i386 7.2.0-4ubuntu1 [134 kB] Get:110 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libcilkrts5 i386 7.2.0-4ubuntu1 [47.3 kB] Get:111 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libgomp1 i386 7.2.0-4ubuntu1 [80.3 kB] Get:112 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libatomic1 i386 7.2.0-4ubuntu1 [9700 B] Get:113 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libasan3 i386 6.4.0-5ubuntu3 [308 kB] Get:114 http://ftpmaster.internal/ubuntu artful-proposed/universe i386 g++-6 i386 6.4.0-5ubuntu3 [7645 kB] Get:115 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libstdc++-6-dev i386 6.4.0-5ubuntu3 [1475 kB] Get:116 http://ftpmaster.internal/ubuntu artful-proposed/main i386 gcc-6 i386 6.4.0-5ubuntu3 [7487 kB] Get:117 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libgcc-6-dev i386 6.4.0-5ubuntu3 [2332 kB] Get:118 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libcc1-0 i386 7.2.0-4ubuntu1 [41.4 kB] Get:119 http://ftpmaster.internal/ubuntu artful-proposed/main i386 cpp-6 i386 6.4.0-5ubuntu3 [6817 kB] Get:120 http://ftpmaster.internal/ubuntu artful-proposed/main i386 gcc-6-base i386 6.4.0-5ubuntu3 [16.8 kB] Get:121 http://ftpmaster.internal/ubuntu artful/main i386 dpkg-dev all 1.18.24ubuntu1 [608 kB] Get:122 http://ftpmaster.internal/ubuntu artful/main i386 libdpkg-perl all 1.18.24ubuntu1 [209 kB] Get:123 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libasan4 i386 7.2.0-4ubuntu1 [354 kB] Get:124 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libgcc-7-dev i386 7.2.0-4ubuntu1 [2383 kB] Get:125 http://ftpmaster.internal/ubuntu artful-proposed/main i386 gcc-7 i386 7.2.0-4ubuntu1 [31.3 MB] Get:126 http://ftpmaster.internal/ubuntu artful/main i386 gcc i386 4:7.1.0-1ubuntu3 [5336 B] Get:127 http://ftpmaster.internal/ubuntu artful-proposed/main i386 libstdc++-7-dev i386 7.2.0-4ubuntu1 [1496 kB] Get:128 http://ftpmaster.internal/ubuntu artful-proposed/main i386 g++-7 i386 7.2.0-4ubuntu1 [34.1 MB] Get:129 http://ftpmaster.internal/ubuntu artful/main i386 g++ i386 4:7.1.0-1ubuntu3 [1490 B] Get:130 http://ftpmaster.internal/ubuntu artful/main i386 libusb-0.1-4 i386 2:0.1.12-31 [17.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 166 MB in 13s (12.4 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12465 files and directories currently installed.) Preparing to unpack .../debconf_1.5.63_all.deb ... Unpacking debconf (1.5.63) over (1.5.60ubuntu1) ... Setting up debconf (1.5.63) ... (Reading database ... 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Setting up util-linux (2.30.1-0ubuntu4) ... update-alternatives: warning: alternative /usr/bin/pg (part of link group pager) doesn't exist; removing from list of alternatives Setting up mount (2.30.1-0ubuntu4) ... Setting up systemd (234-2ubuntu10) ... Installing new version of config file /etc/systemd/resolved.conf ... Created symlink /etc/systemd/system/dbus-org.freedesktop.resolve1.service -> /lib/systemd/system/systemd-resolved.service. Created symlink /etc/systemd/system/multi-user.target.wants/systemd-resolved.service -> /lib/systemd/system/systemd-resolved.service. Created symlink /etc/systemd/system/dbus-org.freedesktop.network1.service -> /lib/systemd/system/systemd-networkd.service. Created symlink /etc/systemd/system/multi-user.target.wants/systemd-networkd.service -> /lib/systemd/system/systemd-networkd.service. Created symlink /etc/systemd/system/sockets.target.wants/systemd-networkd.socket -> /lib/systemd/system/systemd-networkd.socket. Created symlink /etc/systemd/system/network-online.target.wants/systemd-networkd-wait-online.service -> /lib/systemd/system/systemd-networkd-wait-online.service. addgroup: The group `systemd-journal' already exists as a system group. Exiting. Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.hostname1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.locale1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.login1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.network1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.resolve1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.systemd1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.timedate1.conf ... (Reading database ... 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Setting up libidn2-0:i386 (2.0.2-3) ... Setting up libssl1.0.0:i386 (1.0.2g-1ubuntu13) ... Setting up libasan4:i386 (7.2.0-4ubuntu1) ... Setting up libpng16-16:i386 (1.6.32-1) ... Setting up libldap-common (2.4.45+dfsg-1ubuntu1) ... Setting up libcilkrts5:i386 (7.2.0-4ubuntu1) ... Setting up libpsl5:i386 (0.18.0-2) ... Setting up multiarch-support (2.26-0ubuntu1) ... Setting up tzdata (2017b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Sep 9 09:57:52 UTC 2017. Universal Time is now: Sat Sep 9 09:57:52 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (234-2ubuntu10) ... Setting up libubsan0:i386 (7.2.0-4ubuntu1) ... Setting up gcc-6-base:i386 (6.4.0-5ubuntu3) ... Setting up libsasl2-modules-db:i386 (2.1.27~101-g0780600+dfsg-3ubuntu1) ... Setting up linux-libc-dev:i386 (4.12.0-13.14) ... Setting up advancecomp (2.0-1) ... Setting up libsasl2-2:i386 (2.1.27~101-g0780600+dfsg-3ubuntu1) ... Setting up libroken18-heimdal:i386 (7.4.0.dfsg.1-2) ... Setting up perl-modules-5.26 (5.26.0-7) ... Setting up libkrb5support0:i386 (1.15.1-2) ... Setting up binutils-common:i386 (2.29-9ubuntu1) ... Setting up libmpx2:i386 (7.2.0-4ubuntu1) ... Processing triggers for libc-bin (2.26-0ubuntu1) ... Setting up libperl5.26:i386 (5.26.0-7) ... Setting up xz-utils (5.2.2-1.3) ... Setting up libheimbase1-heimdal:i386 (7.4.0.dfsg.1-2) ... Setting up openssl (1.0.2g-1ubuntu13) ... Setting up libsqlite3-0:i386 (3.19.3-3) ... Setting up libmpfr4:i386 (3.1.6-1) ... Setting up dmsetup (2:1.02.137-2ubuntu3) ... Setting up cpp-6 (6.4.0-5ubuntu3) ... Setting up libc-dev-bin (2.26-0ubuntu1) ... Setting up ca-certificates (20170717) ... Updating certificates in /etc/ssl/certs... 7 added, 32 removed; done. Setting up libc6-dev:i386 (2.26-0ubuntu1) ... Setting up libassuan0:i386 (2.4.3-3) ... Setting up libusb-0.1-4:i386 (2:0.1.12-31) ... Setting up libitm1:i386 (7.2.0-4ubuntu1) ... 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Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-12808199 i386 artful-proposed -c chroot:build-PACKAGEBUILD-12808199 --arch=i386 --dist=artful-proposed --nolog pbbam_0.7.4+ds-1build1.dsc Initiating build PACKAGEBUILD-12808199 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-93-generic #116-Ubuntu SMP Fri Aug 11 21:17:51 UTC 2017 i686 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-41.buildd +==============================================================================+ | pbbam 0.7.4+ds-1build1 (i386) 09 Sep 2017 09:57 | +==============================================================================+ Package: pbbam Version: 0.7.4+ds-1build1 Source Version: 0.7.4+ds-1build1 Distribution: artful-proposed Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/pbbam-H2BSfN/pbbam-0.7.4+ds' with '<>' I: NOTICE: Log filtering will replace 'build/pbbam-H2BSfN' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-12808199/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- pbbam_0.7.4+ds-1build1.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-CRYiHl/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-CRYiHl/apt_archive ./ InRelease Get:2 copy:/<>/resolver-CRYiHl/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-CRYiHl/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-CRYiHl/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-CRYiHl/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (279 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 packages were automatically installed and are no longer required: g++-6 libperl5.24 libstdc++-6-dev perl-modules-5.24 Use 'apt autoremove' to remove them. 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 778 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-CRYiHl/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [778 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 778 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 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Merged Build-Depends: debhelper (>= 10), dh-exec, cmake, python, libboost-dev (>= 1.54), zlib1g-dev, libssl-dev, libhts-dev, python-cram, samtools Filtered Build-Depends: debhelper (>= 10), dh-exec, cmake, python, libboost-dev (>= 1.54), zlib1g-dev, libssl-dev, libhts-dev, python-cram, samtools dpkg-deb: building package 'sbuild-build-depends-pbbam-dummy' in '/<>/resolver-CzCTiR/apt_archive/sbuild-build-depends-pbbam-dummy.deb'. Ign:1 copy:/<>/resolver-CzCTiR/apt_archive ./ InRelease Get:2 copy:/<>/resolver-CzCTiR/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-CzCTiR/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-CzCTiR/apt_archive ./ Sources [264 B] Get:5 copy:/<>/resolver-CzCTiR/apt_archive ./ Packages [585 B] Fetched 2968 B in 0s (248 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install pbbam build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: g++-6 libperl5.24 perl-modules-5.24 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-exec dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libboost-dev libboost1.62-dev libbsd0 libcroco3 libcurl3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts2 libicu57 libjsoncpp1 liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib librhash0 libsigsegv2 libssl-dev libtimedate-perl libtool libuv1 libxml2 m4 man-db mime-support po-debconf python python-cram python-minimal python2.7 python2.7-minimal samtools tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libboost-doc libboost1.62-doc libboost-atomic1.62-dev libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev libboost-filesystem1.62-dev libboost-graph1.62-dev libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev libboost-program-options1.62-dev libboost-python1.62-dev libboost-random1.62-dev libboost-regex1.62-dev libboost-serialization1.62-dev libboost-signals1.62-dev libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev libboost1.62-tools-dev libmpfrc++-dev libntl-dev liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libssl-doc libltdl-dev xml-core libmail-sendmail-perl The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-exec dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libboost-dev libboost1.62-dev libbsd0 libcroco3 libcurl3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts2 libicu57 libjsoncpp1 liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib librhash0 libsigsegv2 libssl-dev libtimedate-perl libtool libuv1 libxml2 m4 man-db mime-support po-debconf python python-cram python-minimal python2.7 python2.7-minimal samtools sbuild-build-depends-pbbam-dummy tabix zlib1g-dev 0 upgraded, 58 newly installed, 1 to remove and 0 not upgraded. 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artful/main i386 dh-strip-nondeterminism all 0.038-1 [5026 B] Get:43 http://ftpmaster.internal/ubuntu artful/main i386 libcroco3 i386 0.6.12-1 [87.5 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main i386 gettext i386 0.19.8.1-4ubuntu1 [1097 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main i386 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main i386 po-debconf all 1.0.20 [232 kB] Get:47 http://ftpmaster.internal/ubuntu artful/main i386 debhelper all 10.7.2ubuntu2 [877 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main i386 libboost1.62-dev i386 1.62.0+dfsg-4build3 [7030 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main i386 libboost-dev i386 1.62.0.1 [3072 B] Get:50 http://ftpmaster.internal/ubuntu artful/universe i386 libhts2 i386 1.5-1 [304 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main i386 liblzma-dev i386 5.2.2-1.3 [154 kB] Get:52 http://ftpmaster.internal/ubuntu artful/universe i386 tabix i386 1.5-1 [335 kB] Get:53 http://ftpmaster.internal/ubuntu artful/universe i386 libhts-dev i386 1.5-1 [411 kB] Get:54 http://ftpmaster.internal/ubuntu artful/main i386 zlib1g-dev i386 1:1.2.11.dfsg-0ubuntu2 [178 kB] Get:55 http://ftpmaster.internal/ubuntu artful/main i386 libssl-dev i386 1.0.2g-1ubuntu13 [1129 kB] Get:56 http://ftpmaster.internal/ubuntu artful/universe i386 python-cram all 0.7-1 [16.7 kB] Get:57 http://ftpmaster.internal/ubuntu artful/universe i386 samtools i386 1.4.1-1build1 [267 kB] Get:58 http://ftpmaster.internal/ubuntu artful/main i386 dh-exec i386 0.23build1 [24.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 35.9 MB in 0s (43.5 MB/s) (Reading database ... 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Setting up libjsoncpp1:i386 (1.7.4-3) ... Setting up gettext (0.19.8.1-4ubuntu1) ... Setting up libarchive13:i386 (3.2.2-2) ... Setting up libhts-dev:i386 (1.5-1) ... Setting up libssl-dev:i386 (1.0.2g-1ubuntu13) ... Setting up python2.7 (2.7.14~rc1-3ubuntu1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.32-1) ... Setting up libpython-stdlib:i386 (2.7.13-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15-6ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up samtools (1.4.1-1build1) ... Setting up cmake (3.9.1-1) ... Setting up python (2.7.13-2) ... Setting up libtool (2.4.6-2) ... Setting up python-cram (0.7-1) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.038-1) ... Setting up debhelper (10.7.2ubuntu2) ... 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Processing triggers for libc-bin (2.26-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-93-generic amd64 (i686) Toolchain package versions: binutils_2.29-9ubuntu1 dpkg-dev_1.18.24ubuntu1 g++-6_6.4.0-5ubuntu3 g++-7_7.2.0-4ubuntu1 gcc-6_6.4.0-5ubuntu3 gcc-7_7.2.0-4ubuntu1 libc6-dev_2.26-0ubuntu1 libstdc++-6-dev_6.4.0-5ubuntu3 libstdc++-7-dev_7.2.0-4ubuntu1 libstdc++6_7.2.0-4ubuntu1 linux-libc-dev_4.12.0-13.14 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 apt_1.5~rc1~ubuntu1 apt-transport-https_1.5~rc1~ubuntu1 autoconf_2.69-11 automake_1:1.15-6ubuntu1 autopoint_0.19.8.1-4ubuntu1 autotools-dev_20161112.1 base-files_9.6ubuntu101 base-passwd_3.5.43 bash_4.4-5ubuntu1 binutils_2.29-9ubuntu1 binutils-common_2.29-9ubuntu1 binutils-i686-linux-gnu_2.29-9ubuntu1 bsdmainutils_9.0.12+nmu1ubuntu1 bsdutils_1:2.30.1-0ubuntu4 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20170717 cmake_3.9.1-1 cmake-data_3.9.1-1 coreutils_8.26-3ubuntu3 cpp_4:7.1.0-1ubuntu3 cpp-6_6.4.0-5ubuntu3 cpp-7_7.2.0-4ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.63 debhelper_10.7.2ubuntu2 debianutils_4.8.2 dh-autoreconf_14 dh-exec_0.23build1 dh-strip-nondeterminism_0.038-1 diffutils_1:3.6-1 dmsetup_2:1.02.137-2ubuntu3 dpkg_1.18.24ubuntu1 dpkg-dev_1.18.24ubuntu1 e2fslibs_1.43.5-1 e2fsprogs_1.43.5-1 fakeroot_1.21-1ubuntu2 fdisk_2.30.1-0ubuntu4 file_1:5.32-1 findutils_4.6.0+git+20170729-2 g++_4:7.1.0-1ubuntu3 g++-6_6.4.0-5ubuntu3 g++-7_7.2.0-4ubuntu1 gcc_4:7.1.0-1ubuntu3 gcc-6_6.4.0-5ubuntu3 gcc-6-base_6.4.0-5ubuntu3 gcc-7_7.2.0-4ubuntu1 gcc-7-base_7.2.0-4ubuntu1 gettext_0.19.8.1-4ubuntu1 gettext-base_0.19.8.1-4ubuntu1 gnupg_2.1.15-1ubuntu7 gnupg-agent_2.1.15-1ubuntu7 gpgv_2.1.15-1ubuntu7 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5ubuntu1 hostname_3.18 init_1.49ubuntu1 init-system-helpers_1.49ubuntu1 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu16 libapt-pkg5.0_1.5~rc1~ubuntu1 libarchive-zip-perl_1.59-1 libarchive13_3.2.2-2 libasan3_6.4.0-5ubuntu3 libasan4_7.2.0-4ubuntu1 libasn1-8-heimdal_7.4.0.dfsg.1-2 libassuan0_2.4.3-3 libatomic1_7.2.0-4ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.7.7-1ubuntu2 libaudit1_1:2.7.7-1ubuntu2 libbinutils_2.29-9ubuntu1 libblkid1_2.30.1-0ubuntu4 libboost-dev_1.62.0.1 libboost1.62-dev_1.62.0+dfsg-4build3 libbsd0_0.8.6-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.26-0ubuntu1 libc-dev-bin_2.26-0ubuntu1 libc6_2.26-0ubuntu1 libc6-dev_2.26-0ubuntu1 libcap-ng0_0.7.7-3build1 libcap2_1:2.25-1 libcc1-0_7.2.0-4ubuntu1 libcilkrts5_7.2.0-4ubuntu1 libcomerr2_1.43.5-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.3-4ubuntu1 libcurl3_7.55.1-1ubuntu1 libcurl3-gnutls_7.55.1-1ubuntu1 libdb5.3_5.3.28-13.1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.137-2ubuntu3 libdpkg-perl_1.18.24ubuntu1 libexpat1_2.2.3-1 libfakeroot_1.21-1ubuntu2 libfdisk1_2.30.1-0ubuntu4 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-6-dev_6.4.0-5ubuntu3 libgcc-7-dev_7.2.0-4ubuntu1 libgcc1_1:7.2.0-4ubuntu1 libgcrypt20_1.7.8-2 libgdbm3_1.8.3-14 libglib2.0-0_2.53.6-1ubuntu2 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.8-6ubuntu3 libgomp1_7.2.0-4ubuntu1 libgpg-error0_1.27-3 libgssapi-krb5-2_1.15.1-2 libgssapi3-heimdal_7.4.0.dfsg.1-2 libhcrypto4-heimdal_7.4.0.dfsg.1-2 libheimbase1-heimdal_7.4.0.dfsg.1-2 libheimntlm0-heimdal_7.4.0.dfsg.1-2 libhogweed4_3.3-1 libhts-dev_1.5-1 libhts2_1.5-1 libhx509-5-heimdal_7.4.0.dfsg.1-2 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_2.0.2-3 libip4tc0_1.6.1-2ubuntu1 libisl15_0.18-1 libitm1_7.2.0-4ubuntu1 libjsoncpp1_1.7.4-3 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9ubuntu1 libkmod2_24-1ubuntu2 libkrb5-26-heimdal_7.4.0.dfsg.1-2 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1ubuntu1 libldap-common_2.4.45+dfsg-1ubuntu1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 liblz4-1_0.0~r131-2ubuntu2 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 liblzo2-2_2.08-1.2 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.1-0ubuntu4 libmpc3_1.0.3-1 libmpfr4_3.1.6-1 libmpx2_7.2.0-4ubuntu1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-1 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.2ubuntu3 libpam-modules-bin_1.1.8-3.2ubuntu3 libpam-runtime_1.1.8-3.2ubuntu3 libpam0g_1.1.8-3.2ubuntu3 libpcre3_2:8.39-4 libperl5.24_5.24.1-2ubuntu1 libperl5.26_5.26.0-7 libpipeline1_1.4.2-1 libpng16-16_1.6.32-1 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.18.0-2 libpython-stdlib_2.7.13-2 libpython2.7-minimal_2.7.14~rc1-3ubuntu1 libpython2.7-stdlib_2.7.14~rc1-3ubuntu1 libquadmath0_7.2.0-4ubuntu1 libreadline7_7.0-0ubuntu2 librhash0_1.3.4-3 libroken18-heimdal_7.4.0.dfsg.1-2 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu1 libseccomp2_2.3.1-2.1ubuntu1 libselinux1_2.6-3build2 libsemanage-common_2.6-2build2 libsemanage1_2.6-2build2 libsepol1_2.6-2 libsigsegv2_2.11-1 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.30.1-0ubuntu4 libsqlite3-0_3.19.3-3 libss2_1.43.5-1 libssl-dev_1.0.2g-1ubuntu13 libssl1.0.0_1.0.2g-1ubuntu13 libstdc++-6-dev_6.4.0-5ubuntu3 libstdc++-7-dev_7.2.0-4ubuntu1 libstdc++6_7.2.0-4ubuntu1 libsystemd0_234-2ubuntu10 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libubsan0_7.2.0-4ubuntu1 libudev1_234-2ubuntu10 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.30.1-0ubuntu4 libuv1_1.9.1-3 libwind0-heimdal_7.4.0.dfsg.1-2 libxml2_2.9.4+dfsg1-3.1 linux-libc-dev_4.12.0-13.14 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu4 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17ubuntu2 mime-support_3.60ubuntu1 mount_2.30.1-0ubuntu4 multiarch-support_2.26-0ubuntu1 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu13 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu4 patch_2.7.5-1build1 perl_5.26.0-7 perl-base_5.26.0-7 perl-modules-5.24_5.24.1-2ubuntu1 perl-modules-5.26_5.26.0-7 pinentry-curses_1.0.0-2 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 python_2.7.13-2 python-cram_0.7-1 python-minimal_2.7.13-2 python2.7_2.7.14~rc1-3ubuntu1 python2.7-minimal_2.7.14~rc1-3ubuntu1 readline-common_7.0-0ubuntu2 samtools_1.4.1-1build1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbbam-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_234-2ubuntu10 systemd-sysv_234-2ubuntu10 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tabix_1.5-1 tar_1.29b-2 tzdata_2017b-2 ubuntu-keyring_2016.10.27 util-linux_2.30.1-0ubuntu4 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 Jun 26 07:29:41 2017 UTC gpgv: using RSA key gpgv: issuer "steve.langasek@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pbbam_0.7.4+ds-1build1.dsc dpkg-source: info: extracting pbbam in pbbam-0.7.4+ds dpkg-source: info: unpacking pbbam_0.7.4+ds.orig.tar.gz dpkg-source: info: unpacking pbbam_0.7.4+ds-1build1.debian.tar.xz dpkg-source: info: applying ssl-md5.patch dpkg-source: info: applying remove-bam2sam.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-12808199 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-12808199 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-12808199 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 0.7.4+ds-1build1 dpkg-buildpackage: info: source distribution artful dpkg-source --before-build pbbam-0.7.4+ds dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/pbbam-0.7.4+ds' dh_auto_clean find -name "*.deb.t" -delete rm -f -r /<>/pbbam-0.7.4+ds/gendata make[1]: Leaving directory '/<>/pbbam-0.7.4+ds' dh_autoreconf_clean dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/pbbam-0.7.4+ds' dh_auto_configure -- \ -DPacBioBAM_build_shared=ON \ -DPacBioBAM_build_tests=OFF \ -DCMAKE_LIBRARY_PATH=i386-linux-gnu \ -DCMAKE_SKIP_RPATH=ON \ -DHTSLIB_INCLUDE_DIRS=/usr/include \ -DHTSLIB_LIBRARIES="-lssl -lcrypto -lhts" \ -DCMAKE_SHARED_LINKER_FLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DPacBioBAM_build_shared=ON -DPacBioBAM_build_tests=OFF -DCMAKE_LIBRARY_PATH=i386-linux-gnu -DCMAKE_SKIP_RPATH=ON -DHTSLIB_INCLUDE_DIRS=/usr/include "-DHTSLIB_LIBRARIES=-lssl -lcrypto -lhts" "-DCMAKE_SHARED_LINKER_FLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro" -- The CXX compiler identification is GNU 7.2.0 -- The C compiler identification is GNU 7.2.0 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS -- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS - Success -- Performing Test HAS_NO_SIGN_COMPARE -- Performing Test HAS_NO_SIGN_COMPARE - Success -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Boost version: 1.62.0 -- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found version "1.2.11") -- Performing Test HAS_NO_UNUSED_PRIVATE_FIELD -- Performing Test HAS_NO_UNUSED_PRIVATE_FIELD - Success -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu make[1]: Leaving directory '/<>/pbbam-0.7.4+ds' dh_auto_build -a make -j4 make[1]: Entering directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' /usr/bin/cmake -H/<>/pbbam-0.7.4+ds -B/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/CMakeFiles /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' make -f src/CMakeFiles/pbbam.dir/build.make src/CMakeFiles/pbbam.dir/depend make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/pbbam-0.7.4+ds /<>/pbbam-0.7.4+ds/src /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src/CMakeFiles/pbbam.dir/DependInfo.cmake --color= Scanning dependencies of target pbbam make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' make -f src/CMakeFiles/pbbam.dir/build.make src/CMakeFiles/pbbam.dir/build make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' [ 1%] Building CXX object src/CMakeFiles/pbbam.dir/Accuracy.cpp.o [ 3%] Building CXX object src/CMakeFiles/pbbam.dir/AlignmentPrinter.cpp.o [ 3%] Building CXX object src/CMakeFiles/pbbam.dir/AssertUtils.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/AlignmentPrinter.cpp.o -c /<>/pbbam-0.7.4+ds/src/AlignmentPrinter.cpp cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/AssertUtils.cpp.o -c /<>/pbbam-0.7.4+ds/src/AssertUtils.cpp cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Accuracy.cpp.o -c /<>/pbbam-0.7.4+ds/src/Accuracy.cpp [ 4%] Building CXX object src/CMakeFiles/pbbam.dir/BaiIndexedBamReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BaiIndexedBamReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/BaiIndexedBamReader.cpp [ 5%] Building CXX object src/CMakeFiles/pbbam.dir/BamFile.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamFile.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamFile.cpp [ 6%] Building CXX object src/CMakeFiles/pbbam.dir/BamHeader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamHeader.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamHeader.cpp [ 8%] Building CXX object src/CMakeFiles/pbbam.dir/BamReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamReader.cpp [ 9%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecord.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamRecord.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamRecord.cpp [ 10%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecordBuilder.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamRecordBuilder.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamRecordBuilder.cpp [ 11%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecordImpl.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamRecordImpl.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamRecordImpl.cpp [ 12%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecordTags.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamRecordTags.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamRecordTags.cpp [ 13%] Building CXX object src/CMakeFiles/pbbam.dir/BamTagCodec.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamTagCodec.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamTagCodec.cpp [ 14%] Building CXX object src/CMakeFiles/pbbam.dir/BamWriter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BamWriter.cpp.o -c /<>/pbbam-0.7.4+ds/src/BamWriter.cpp /<>/pbbam-0.7.4+ds/src/BamWriter.cpp: In member function ‘void PacBio::BAM::internal::BamWriterPrivate::Write(const PacBio::BAM::BamRecord&, int64_t*)’: /<>/pbbam-0.7.4+ds/src/BamWriter.cpp:143:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(bgzf); ~~~~~~~~~~^~~~~~ /<>/pbbam-0.7.4+ds/src/BamWriter.cpp: In destructor ‘PacBio::BAM::BamWriter::~BamWriter()’: /<>/pbbam-0.7.4+ds/src/BamWriter.cpp:182:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(d_->file_.get()->fp.bgzf); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ [ 16%] Building CXX object src/CMakeFiles/pbbam.dir/BarcodeQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/BarcodeQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/BarcodeQuery.cpp [ 17%] Building CXX object src/CMakeFiles/pbbam.dir/ChemistryTable.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ChemistryTable.cpp.o -c /<>/pbbam-0.7.4+ds/src/ChemistryTable.cpp [ 18%] Building CXX object src/CMakeFiles/pbbam.dir/Cigar.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Cigar.cpp.o -c /<>/pbbam-0.7.4+ds/src/Cigar.cpp [ 19%] Building CXX object src/CMakeFiles/pbbam.dir/CigarOperation.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/CigarOperation.cpp.o -c /<>/pbbam-0.7.4+ds/src/CigarOperation.cpp [ 20%] Building CXX object src/CMakeFiles/pbbam.dir/Compare.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Compare.cpp.o -c /<>/pbbam-0.7.4+ds/src/Compare.cpp [ 21%] Building CXX object src/CMakeFiles/pbbam.dir/Config.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Config.cpp.o -c /<>/pbbam-0.7.4+ds/src/Config.cpp [ 22%] Building CXX object src/CMakeFiles/pbbam.dir/DataSet.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSet.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSet.cpp [ 24%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetBaseTypes.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSetBaseTypes.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSetBaseTypes.cpp [ 25%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetElement.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSetElement.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSetElement.cpp [ 26%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetIO.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSetIO.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSetIO.cpp [ 27%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetTypes.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSetTypes.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSetTypes.cpp [ 28%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetXsd.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/DataSetXsd.cpp.o -c /<>/pbbam-0.7.4+ds/src/DataSetXsd.cpp [ 29%] Building CXX object src/CMakeFiles/pbbam.dir/EntireFileQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/EntireFileQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/EntireFileQuery.cpp [ 31%] Building CXX object src/CMakeFiles/pbbam.dir/FastaReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/FastaReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/FastaReader.cpp [ 32%] Building CXX object src/CMakeFiles/pbbam.dir/FileProducer.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/FileProducer.cpp.o -c /<>/pbbam-0.7.4+ds/src/FileProducer.cpp [ 33%] Building CXX object src/CMakeFiles/pbbam.dir/FileUtils.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/FileUtils.cpp.o -c /<>/pbbam-0.7.4+ds/src/FileUtils.cpp [ 34%] Building CXX object src/CMakeFiles/pbbam.dir/FofnReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/FofnReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/FofnReader.cpp [ 35%] Building CXX object src/CMakeFiles/pbbam.dir/Frames.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Frames.cpp.o -c /<>/pbbam-0.7.4+ds/src/Frames.cpp [ 36%] Building CXX object src/CMakeFiles/pbbam.dir/GenomicInterval.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/GenomicInterval.cpp.o -c /<>/pbbam-0.7.4+ds/src/GenomicInterval.cpp [ 37%] Building CXX object src/CMakeFiles/pbbam.dir/GenomicIntervalQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/GenomicIntervalQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/GenomicIntervalQuery.cpp [ 39%] Building CXX object src/CMakeFiles/pbbam.dir/IndexedFastaReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/IndexedFastaReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/IndexedFastaReader.cpp [ 40%] Building CXX object src/CMakeFiles/pbbam.dir/IRecordWriter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/IRecordWriter.cpp.o -c /<>/pbbam-0.7.4+ds/src/IRecordWriter.cpp [ 41%] Building CXX object src/CMakeFiles/pbbam.dir/MD5.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/MD5.cpp.o -c /<>/pbbam-0.7.4+ds/src/MD5.cpp [ 42%] Building CXX object src/CMakeFiles/pbbam.dir/MemoryUtils.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/MemoryUtils.cpp.o -c /<>/pbbam-0.7.4+ds/src/MemoryUtils.cpp [ 43%] Building CXX object src/CMakeFiles/pbbam.dir/PbiBuilder.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiBuilder.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiBuilder.cpp [ 44%] Building CXX object src/CMakeFiles/pbbam.dir/PbiFile.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiFile.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiFile.cpp [ 45%] Building CXX object src/CMakeFiles/pbbam.dir/PbiFilter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiFilter.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiFilter.cpp [ 47%] Building CXX object src/CMakeFiles/pbbam.dir/PbiFilterQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiFilterQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiFilterQuery.cpp [ 48%] Building CXX object src/CMakeFiles/pbbam.dir/PbiFilterTypes.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiFilterTypes.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiFilterTypes.cpp [ 49%] Building CXX object src/CMakeFiles/pbbam.dir/PbiIndex.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiIndex.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiIndex.cpp [ 50%] Building CXX object src/CMakeFiles/pbbam.dir/PbiIndexedBamReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiIndexedBamReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiIndexedBamReader.cpp [ 51%] Building CXX object src/CMakeFiles/pbbam.dir/PbiIndexIO.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiIndexIO.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp [ 52%] Building CXX object src/CMakeFiles/pbbam.dir/PbiRawData.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/PbiRawData.cpp.o -c /<>/pbbam-0.7.4+ds/src/PbiRawData.cpp [ 54%] Building CXX object src/CMakeFiles/pbbam.dir/ProgramInfo.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ProgramInfo.cpp.o -c /<>/pbbam-0.7.4+ds/src/ProgramInfo.cpp [ 55%] Building CXX object src/CMakeFiles/pbbam.dir/QNameQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/QNameQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/QNameQuery.cpp [ 56%] Building CXX object src/CMakeFiles/pbbam.dir/QualityValue.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/QualityValue.cpp.o -c /<>/pbbam-0.7.4+ds/src/QualityValue.cpp [ 57%] Building CXX object src/CMakeFiles/pbbam.dir/ReadAccuracyQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ReadAccuracyQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/ReadAccuracyQuery.cpp In file included from /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:38:0: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = short int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &data[0], numReads*sizeof(T)); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = signed char]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadHeader(PacBio::BAM::PbiRawData&, BGZF*)’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:237:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &version, sizeof(version)); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:238:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, §ions, sizeof(sections)); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:239:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &numReads, sizeof(numReads)); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:38:0: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &data[0], numReads*sizeof(T)); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = unsigned int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = unsigned char]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadReferenceData(PacBio::BAM::PbiRawReferenceData&, BGZF*)’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:293:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &numRefs, 4); ~~~~~~~~~^~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:302:18: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &entry.tId_, 4); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:303:18: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &entry.beginRow_, 4); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:304:18: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &entry.endRow_, 4); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:38:0: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = float]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_read(fp, &data[0], numReads*sizeof(T)); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector&, uint32_t) [with T = long long int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:121:14: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = short int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &output[0], data.size()*sizeof(T)); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = signed char]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteHeader(const PacBio::BAM::PbiRawData&, BGZF*)’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:380:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, magic, 4); ~~~~~~~~~~^~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:391:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &version, 4); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:392:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &pbi_flags, 2); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:393:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &numReads, 4); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:398:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, reserved, 18); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:38:0: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &output[0], data.size()*sizeof(T)); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = unsigned int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = unsigned char]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteReferenceData(const PacBio::BAM::PbiRawReferenceData&, BGZF*)’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:434:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &numRefs, 4); ~~~~~~~~~~^~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:448:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &tId, 4); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:449:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &beginRow, 4); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:450:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &endRow, 4); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /<>/pbbam-0.7.4+ds/src/PbiIndexIO.cpp:38:0: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = float]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(fp, &output[0], data.size()*sizeof(T)); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector&) [with T = long long int]’: /<>/pbbam-0.7.4+ds/src/PbiIndexIO.h:158:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] [ 58%] Building CXX object src/CMakeFiles/pbbam.dir/ReadGroupInfo.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ReadGroupInfo.cpp.o -c /<>/pbbam-0.7.4+ds/src/ReadGroupInfo.cpp [ 59%] Building CXX object src/CMakeFiles/pbbam.dir/SamTagCodec.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/SamTagCodec.cpp.o -c /<>/pbbam-0.7.4+ds/src/SamTagCodec.cpp [ 60%] Building CXX object src/CMakeFiles/pbbam.dir/SamWriter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/SamWriter.cpp.o -c /<>/pbbam-0.7.4+ds/src/SamWriter.cpp [ 62%] Building CXX object src/CMakeFiles/pbbam.dir/SequenceInfo.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/SequenceInfo.cpp.o -c /<>/pbbam-0.7.4+ds/src/SequenceInfo.cpp [ 63%] Building CXX object src/CMakeFiles/pbbam.dir/SubreadLengthQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/SubreadLengthQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/SubreadLengthQuery.cpp [ 64%] Building CXX object src/CMakeFiles/pbbam.dir/Tag.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Tag.cpp.o -c /<>/pbbam-0.7.4+ds/src/Tag.cpp [ 65%] Building CXX object src/CMakeFiles/pbbam.dir/TagCollection.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/TagCollection.cpp.o -c /<>/pbbam-0.7.4+ds/src/TagCollection.cpp [ 66%] Building CXX object src/CMakeFiles/pbbam.dir/Validator.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Validator.cpp.o -c /<>/pbbam-0.7.4+ds/src/Validator.cpp [ 67%] Building CXX object src/CMakeFiles/pbbam.dir/ValidationErrors.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ValidationErrors.cpp.o -c /<>/pbbam-0.7.4+ds/src/ValidationErrors.cpp [ 68%] Building CXX object src/CMakeFiles/pbbam.dir/ValidationException.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ValidationException.cpp.o -c /<>/pbbam-0.7.4+ds/src/ValidationException.cpp [ 70%] Building CXX object src/CMakeFiles/pbbam.dir/Version.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/Version.cpp.o -c /<>/pbbam-0.7.4+ds/src/Version.cpp [ 71%] Building CXX object src/CMakeFiles/pbbam.dir/VirtualZmwBamRecord.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/VirtualZmwBamRecord.cpp.o -c /<>/pbbam-0.7.4+ds/src/VirtualZmwBamRecord.cpp [ 72%] Building CXX object src/CMakeFiles/pbbam.dir/VirtualZmwCompositeReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/VirtualZmwCompositeReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/VirtualZmwCompositeReader.cpp [ 73%] Building CXX object src/CMakeFiles/pbbam.dir/VirtualZmwReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/VirtualZmwReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/VirtualZmwReader.cpp [ 74%] Building CXX object src/CMakeFiles/pbbam.dir/VirtualRegionTypeMap.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/VirtualRegionTypeMap.cpp.o -c /<>/pbbam-0.7.4+ds/src/VirtualRegionTypeMap.cpp [ 75%] Building CXX object src/CMakeFiles/pbbam.dir/XmlReader.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/XmlReader.cpp.o -c /<>/pbbam-0.7.4+ds/src/XmlReader.cpp [ 77%] Building CXX object src/CMakeFiles/pbbam.dir/XmlWriter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/XmlWriter.cpp.o -c /<>/pbbam-0.7.4+ds/src/XmlWriter.cpp [ 78%] Building CXX object src/CMakeFiles/pbbam.dir/WhitelistedZmwReadStitcher.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/WhitelistedZmwReadStitcher.cpp.o -c /<>/pbbam-0.7.4+ds/src/WhitelistedZmwReadStitcher.cpp [ 79%] Building CXX object src/CMakeFiles/pbbam.dir/ZmwGroupQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ZmwGroupQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/ZmwGroupQuery.cpp [ 80%] Building CXX object src/CMakeFiles/pbbam.dir/ZmwReadStitcher.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ZmwReadStitcher.cpp.o -c /<>/pbbam-0.7.4+ds/src/ZmwReadStitcher.cpp [ 81%] Building CXX object src/CMakeFiles/pbbam.dir/ZmwQuery.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ZmwQuery.cpp.o -c /<>/pbbam-0.7.4+ds/src/ZmwQuery.cpp [ 82%] Building CXX object src/CMakeFiles/pbbam.dir/ZmwTypeMap.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/ZmwTypeMap.cpp.o -c /<>/pbbam-0.7.4+ds/src/ZmwTypeMap.cpp [ 83%] Building CXX object src/CMakeFiles/pbbam.dir/pugixml/pugixml.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -fPIC -std=gnu++11 -o CMakeFiles/pbbam.dir/pugixml/pugixml.cpp.o -c /<>/pbbam-0.7.4+ds/src/pugixml/pugixml.cpp [ 85%] Linking CXX shared library ../lib/libpbbam.so cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbbam.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libpbbam.so -o ../lib/libpbbam.so CMakeFiles/pbbam.dir/Accuracy.cpp.o CMakeFiles/pbbam.dir/AlignmentPrinter.cpp.o CMakeFiles/pbbam.dir/AssertUtils.cpp.o CMakeFiles/pbbam.dir/BaiIndexedBamReader.cpp.o CMakeFiles/pbbam.dir/BamFile.cpp.o CMakeFiles/pbbam.dir/BamHeader.cpp.o CMakeFiles/pbbam.dir/BamReader.cpp.o CMakeFiles/pbbam.dir/BamRecord.cpp.o CMakeFiles/pbbam.dir/BamRecordBuilder.cpp.o CMakeFiles/pbbam.dir/BamRecordImpl.cpp.o CMakeFiles/pbbam.dir/BamRecordTags.cpp.o CMakeFiles/pbbam.dir/BamTagCodec.cpp.o CMakeFiles/pbbam.dir/BamWriter.cpp.o CMakeFiles/pbbam.dir/BarcodeQuery.cpp.o CMakeFiles/pbbam.dir/ChemistryTable.cpp.o CMakeFiles/pbbam.dir/Cigar.cpp.o CMakeFiles/pbbam.dir/CigarOperation.cpp.o CMakeFiles/pbbam.dir/Compare.cpp.o CMakeFiles/pbbam.dir/Config.cpp.o CMakeFiles/pbbam.dir/DataSet.cpp.o CMakeFiles/pbbam.dir/DataSetBaseTypes.cpp.o CMakeFiles/pbbam.dir/DataSetElement.cpp.o CMakeFiles/pbbam.dir/DataSetIO.cpp.o CMakeFiles/pbbam.dir/DataSetTypes.cpp.o CMakeFiles/pbbam.dir/DataSetXsd.cpp.o CMakeFiles/pbbam.dir/EntireFileQuery.cpp.o CMakeFiles/pbbam.dir/FastaReader.cpp.o CMakeFiles/pbbam.dir/FileProducer.cpp.o CMakeFiles/pbbam.dir/FileUtils.cpp.o CMakeFiles/pbbam.dir/FofnReader.cpp.o CMakeFiles/pbbam.dir/Frames.cpp.o CMakeFiles/pbbam.dir/GenomicInterval.cpp.o CMakeFiles/pbbam.dir/GenomicIntervalQuery.cpp.o CMakeFiles/pbbam.dir/IndexedFastaReader.cpp.o CMakeFiles/pbbam.dir/IRecordWriter.cpp.o CMakeFiles/pbbam.dir/MD5.cpp.o CMakeFiles/pbbam.dir/MemoryUtils.cpp.o CMakeFiles/pbbam.dir/PbiBuilder.cpp.o CMakeFiles/pbbam.dir/PbiFile.cpp.o CMakeFiles/pbbam.dir/PbiFilter.cpp.o CMakeFiles/pbbam.dir/PbiFilterQuery.cpp.o CMakeFiles/pbbam.dir/PbiFilterTypes.cpp.o CMakeFiles/pbbam.dir/PbiIndex.cpp.o CMakeFiles/pbbam.dir/PbiIndexedBamReader.cpp.o CMakeFiles/pbbam.dir/PbiIndexIO.cpp.o CMakeFiles/pbbam.dir/PbiRawData.cpp.o CMakeFiles/pbbam.dir/ProgramInfo.cpp.o CMakeFiles/pbbam.dir/QNameQuery.cpp.o CMakeFiles/pbbam.dir/QualityValue.cpp.o CMakeFiles/pbbam.dir/ReadAccuracyQuery.cpp.o CMakeFiles/pbbam.dir/ReadGroupInfo.cpp.o CMakeFiles/pbbam.dir/SamTagCodec.cpp.o CMakeFiles/pbbam.dir/SamWriter.cpp.o CMakeFiles/pbbam.dir/SequenceInfo.cpp.o CMakeFiles/pbbam.dir/SubreadLengthQuery.cpp.o CMakeFiles/pbbam.dir/Tag.cpp.o CMakeFiles/pbbam.dir/TagCollection.cpp.o CMakeFiles/pbbam.dir/Validator.cpp.o CMakeFiles/pbbam.dir/ValidationErrors.cpp.o CMakeFiles/pbbam.dir/ValidationException.cpp.o CMakeFiles/pbbam.dir/Version.cpp.o CMakeFiles/pbbam.dir/VirtualZmwBamRecord.cpp.o CMakeFiles/pbbam.dir/VirtualZmwCompositeReader.cpp.o CMakeFiles/pbbam.dir/VirtualZmwReader.cpp.o CMakeFiles/pbbam.dir/VirtualRegionTypeMap.cpp.o CMakeFiles/pbbam.dir/XmlReader.cpp.o CMakeFiles/pbbam.dir/XmlWriter.cpp.o CMakeFiles/pbbam.dir/WhitelistedZmwReadStitcher.cpp.o CMakeFiles/pbbam.dir/ZmwGroupQuery.cpp.o CMakeFiles/pbbam.dir/ZmwReadStitcher.cpp.o CMakeFiles/pbbam.dir/ZmwQuery.cpp.o CMakeFiles/pbbam.dir/ZmwTypeMap.cpp.o CMakeFiles/pbbam.dir/pugixml/pugixml.cpp.o -lssl -lcrypto -lhts -lz -lpthread make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' [ 85%] Built target pbbam make -f tools/pbindex/CMakeFiles/pbindex.dir/build.make tools/pbindex/CMakeFiles/pbindex.dir/depend make -f tools/pbindexdump/CMakeFiles/pbindexdump.dir/build.make tools/pbindexdump/CMakeFiles/pbindexdump.dir/depend make -f tools/pbmerge/CMakeFiles/pbmerge.dir/build.make tools/pbmerge/CMakeFiles/pbmerge.dir/depend make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/pbbam-0.7.4+ds /<>/pbbam-0.7.4+ds/tools/pbindex /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/tools/pbindex /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/tools/pbindex/CMakeFiles/pbindex.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/pbbam-0.7.4+ds /<>/pbbam-0.7.4+ds/tools/pbmerge /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/tools/pbmerge /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/tools/pbmerge/CMakeFiles/pbmerge.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/pbbam-0.7.4+ds /<>/pbbam-0.7.4+ds/tools/pbindexdump /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/tools/pbindexdump /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/tools/pbindexdump/CMakeFiles/pbindexdump.dir/DependInfo.cmake --color= Scanning dependencies of target pbindex make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' make -f tools/pbindex/CMakeFiles/pbindex.dir/build.make tools/pbindex/CMakeFiles/pbindex.dir/build make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' Scanning dependencies of target pbindexdump make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' make -f tools/pbindexdump/CMakeFiles/pbindexdump.dir/build.make tools/pbindexdump/CMakeFiles/pbindexdump.dir/build make[3]: Entering directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' Scanning dependencies of target pbmerge make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' make -f tools/pbmerge/CMakeFiles/pbmerge.dir/build.make tools/pbmerge/CMakeFiles/pbmerge.dir/build [ 87%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/__/common/OptionParser.cpp.o [ 87%] Building CXX object tools/pbindex/CMakeFiles/pbindex.dir/__/common/OptionParser.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/tools/pbindex && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindex.dir/__/common/OptionParser.cpp.o -c /<>/pbbam-0.7.4+ds/tools/common/OptionParser.cpp cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/tools/pbindexdump && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindexdump.dir/__/common/OptionParser.cpp.o -c /<>/pbbam-0.7.4+ds/tools/common/OptionParser.cpp [ 88%] Building CXX object tools/pbindex/CMakeFiles/pbindex.dir/src/main.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/tools/pbindex && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindex.dir/src/main.cpp.o -c /<>/pbbam-0.7.4+ds/tools/pbindex/src/main.cpp 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindex.dir/src/PbIndex.cpp.o -c /<>/pbbam-0.7.4+ds/tools/pbindex/src/PbIndex.cpp [ 91%] Building CXX object tools/pbmerge/CMakeFiles/pbmerge.dir/src/main.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/tools/pbmerge && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbmerge.dir/src/main.cpp.o -c /<>/pbbam-0.7.4+ds/tools/pbmerge/src/main.cpp [ 93%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/src/CppFormatter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/tools/pbindexdump && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindexdump.dir/src/CppFormatter.cpp.o -c /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/CppFormatter.cpp [ 94%] Linking CXX executable ../../bin/pbindex cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/tools/pbindex && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbindex.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -Wl,-Bsymbolic-functions -Wl,-z,relro -rdynamic CMakeFiles/pbindex.dir/__/common/OptionParser.cpp.o CMakeFiles/pbindex.dir/src/main.cpp.o CMakeFiles/pbindex.dir/src/PbIndex.cpp.o -o ../../bin/pbindex ../../lib/libpbbam.so -lssl -lcrypto -lhts -lz -lpthread make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' [ 94%] Built target pbindex [ 95%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/src/JsonFormatter.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/tools/pbindexdump && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindexdump.dir/src/JsonFormatter.cpp.o -c /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/JsonFormatter.cpp [ 96%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/src/PbIndexDump.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/tools/pbindexdump && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -std=gnu++11 -o CMakeFiles/pbindexdump.dir/src/PbIndexDump.cpp.o -c /<>/pbbam-0.7.4+ds/tools/pbindexdump/src/PbIndexDump.cpp [ 97%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/src/main.cpp.o cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/tools/pbindexdump && /usr/bin/c++ -I/<>/pbbam-0.7.4+ds/tools/common -I/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/generated -I/<>/pbbam-0.7.4+ds/include -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-lpthread make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' [ 98%] Built target pbindexdump [100%] Linking CXX executable ../../bin/pbmerge cd /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/tools/pbmerge && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbmerge.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/pbbam-0.7.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -Wl,-Bsymbolic-functions -Wl,-z,relro -rdynamic CMakeFiles/pbmerge.dir/__/common/OptionParser.cpp.o CMakeFiles/pbmerge.dir/src/main.cpp.o -o ../../bin/pbmerge ../../lib/libpbbam.so -lssl -lcrypto -lhts -lz -lpthread make[3]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' [100%] Built target pbmerge make[2]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/pbbam-0.7.4+ds/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/pbbam-0.7.4+ds/obj-i686-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/pbbam-0.7.4+ds' sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbmerge_pacbio_ordering.t.in > tests/src/cram/pbmerge_pacbio_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbmerge_mixed_ordering.t.in > tests/src/cram/pbmerge_mixed_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbmerge_aligned_ordering.t.in > tests/src/cram/pbmerge_aligned_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbindexdump_json.t.in > tests/src/cram/pbindexdump_json.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbindexdump_cpp.t.in > tests/src/cram/pbindexdump_cpp.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbmerge_fofn.t.in > tests/src/cram/pbmerge_fofn.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.7.4+ds/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.7.4|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.7.4+ds/gendata|g' \ tests/src/cram/pbmerge_dataset.t.in > tests/src/cram/pbmerge_dataset.deb.t mkdir -p /<>/pbbam-0.7.4+ds/gendata python tests/scripts/generate_data.py /<>/pbbam-0.7.4+ds/tests/data /<>/pbbam-0.7.4+ds/gendata Generating test data in /<>/pbbam-0.7.4+ds/gendata - Creating file: truncated.bam...done. - Creating file: normal.fa...done. - Creating file: chunking_missingfilters.subreadset.xml...done. - Creating file: chunking_emptyfilters.subreadset.xml...done. - Creating symlink: missing_pbi.bam...done. - Creating symlink: aligned.bam.bai...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done. - Creating symlink: aligned2.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi...done. - Creating symlink: aligned2.bam.bai...done. - Creating symlink: aligned2.bam...done. - Creating symlink: aligned.bam...done. - Creating symlink: aligned.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam...done. BINDIR=`find $PWD -name bin -type d`; \ LIBDIR=`find $PWD -name lib -type d`; \ PATH="$BINDIR:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" LD_LIBRARY_PATH="$LIBDIR:" \ cram -v tests/src/cram/pbmerge_pacbio_ordering.deb.t tests/src/cram/pbmerge_mixed_ordering.deb.t tests/src/cram/pbmerge_aligned_ordering.deb.t tests/src/cram/pbindexdump_json.deb.t tests/src/cram/pbindexdump_cpp.deb.t tests/src/cram/pbmerge_fofn.deb.t tests/src/cram/pbmerge_dataset.deb.t tests/src/cram/pbmerge_pacbio_ordering.deb.t: passed tests/src/cram/pbmerge_mixed_ordering.deb.t: passed tests/src/cram/pbmerge_aligned_ordering.deb.t: failed --- tests/src/cram/pbmerge_aligned_ordering.deb.t +++ tests/src/cram/pbmerge_aligned_ordering.deb.t.err @@ -122,41 +122,28 @@ Explicit Output Filename (also enables PBI): $ $PBMERGE -o $MERGED_BAM $INPUT_1 $INPUT_2 + pbmerge: /<>/pbbam-0.7.4+ds/src/PbiBuilder.cpp:327: bool PacBio::BAM::internal::PbiBuilderPrivate::HasBarcodeData() const: Assertion `bcForward.size() == rawData_.NumReads()' failed. + Aborted (core dumped) + [134] $ samtools view -H $MERGED_BAM - @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc) - @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc) - @RG\tID:a9a22406c5\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc) - @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc) - @PG\tID:pbmerge-0.7.4\tPN:pbmerge\tVN:0.7.4 (esc) + [E::hts_open_format] Failed to open file /<>/pbbam-0.7.4+ds/gendata/aligned_ordering_merged.bam + samtools view: failed to open "/<>/pbbam-0.7.4+ds/gendata/aligned_ordering_merged.bam" for reading: No such file or directory + [1] $ samtools view $MERGED_BAM | cut -f 1,3,4 | head -n 20 - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/0_344\tlambda_NEB3011\t676 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/9936_10187\tlambda_NEB3011\t2171 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/9936_10187\tlambda_NEB3011\t2171 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/10232_10394\tlambda_NEB3011\t2204 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/10232_10394\tlambda_NEB3011\t2204 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7468_8906\tlambda_NEB3011\t3573 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7468_8906\tlambda_NEB3011\t3573 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/5557_7235\tlambda_NEB3011\t4507 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/5557_7235\tlambda_NEB3011\t4507 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/7285_8657\tlambda_NEB3011\t4508 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/7285_8657\tlambda_NEB3011\t4508 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/426_1045\tlambda_NEB3011\t4593 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/426_1045\tlambda_NEB3011\t4593 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7064_7421\tlambda_NEB3011\t4670 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7064_7421\tlambda_NEB3011\t4670 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/0_382\tlambda_NEB3011\t4843 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/0_382\tlambda_NEB3011\t4843 (esc) - m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/7247/7338_7831\tlambda_NEB3011\t4904 (esc) + [E::hts_open_format] Failed to open file /<>/pbbam-0.7.4+ds/gendata/aligned_ordering_merged.bam + samtools view: failed to open "/<>/pbbam-0.7.4+ds/gendata/aligned_ordering_merged.bam" for reading: No such file or directory $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" - Found + Not found $ rm $MERGED_BAM + rm: cannot remove '/<>/pbbam-0.7.4+ds/gendata/aligned_ordering_merged.bam': No such file or directory + [1] $ rm $MERGED_BAM_PBI + rm: cannot remove '/<>/pbbam-0.7.4+ds/gendata/aligned_ordering_merged.bam.pbi': No such file or directory + [1] Explicit Output Filename (with disabled PBI): tests/src/cram/pbindexdump_json.deb.t: passed tests/src/cram/pbindexdump_cpp.deb.t: passed tests/src/cram/pbmerge_fofn.deb.t: passed tests/src/cram/pbmerge_dataset.deb.t: passed # Ran 7 tests, 0 skipped, 1 failed. debian/rules:26: recipe for target 'override_dh_auto_test' failed make[1]: *** [override_dh_auto_test] Error 1 make[1]: Leaving directory '/<>/pbbam-0.7.4+ds' debian/rules:11: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 20170909-1000 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: i386 Build-Space: 124592 Build-Time: 130 Distribution: artful-proposed Fail-Stage: build Host Architecture: i386 Install-Time: 18 Job: pbbam_0.7.4+ds-1build1.dsc Machine Architecture: amd64 Package: pbbam Package-Time: 149 Source-Version: 0.7.4+ds-1build1 Space: 124592 Status: attempted Version: 0.7.4+ds-1build1 -------------------------------------------------------------------------------- Finished at 20170909-1000 Build needed 00:02:29, 124592k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-12808199 Scanning for processes to kill in build PACKAGEBUILD-12808199 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-12808199 Stopping target for build PACKAGEBUILD-12808199 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=artful --arch=i386 PACKAGEBUILD-12808199 Removing build PACKAGEBUILD-12808199