RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux z13-018 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:08 UTC 2016 s390x Buildd toolchain package versions: launchpad-buildd_138 python-lpbuildd_138 sbuild_0.67.0-2ubuntu7 dpkg-dev_1.18.4ubuntu1 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10. Syncing the system clock with the buildd NTP service... 22 May 23:14:12 ntpdate[36549]: adjust time server 10.211.37.1 offset 0.000184 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-9789456', '/home/buildd/filecache-default/4c2dc15a2bd8eb52aaecab56c2b5c3013e453e5b'] Unpacking chroot for build PACKAGEBUILD-9789456 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-9789456'] Mounting chroot for build PACKAGEBUILD-9789456 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-9789456', 'deb http://ftpmaster.internal/ubuntu yakkety main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-security main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-updates main universe', 'deb http://ftpmaster.internal/ubuntu yakkety-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-9789456 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-9789456', 's390x'] Updating debian chroot for build PACKAGEBUILD-9789456 Get:1 http://ftpmaster.internal/ubuntu yakkety InRelease [247 kB] Get:2 http://ftpmaster.internal/ubuntu yakkety-security InRelease [92.2 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety-updates InRelease [92.2 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety-proposed InRelease [95.7 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main s390x Packages [1129 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main Translation-en [568 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/universe s390x Packages [7374 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/universe Translation-en [4436 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety-security/main s390x Packages [64 B] Get:10 http://ftpmaster.internal/ubuntu yakkety-security/main Translation-en [64 B] Get:11 http://ftpmaster.internal/ubuntu yakkety-security/universe s390x Packages [64 B] Get:12 http://ftpmaster.internal/ubuntu yakkety-security/universe Translation-en [64 B] Get:13 http://ftpmaster.internal/ubuntu yakkety-updates/main s390x Packages [64 B] Get:14 http://ftpmaster.internal/ubuntu yakkety-updates/main Translation-en [64 B] Get:15 http://ftpmaster.internal/ubuntu yakkety-updates/universe s390x Packages [64 B] Get:16 http://ftpmaster.internal/ubuntu yakkety-updates/universe Translation-en [64 B] Get:17 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x Packages [94.4 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety-proposed/main Translation-en [50.6 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety-proposed/universe s390x Packages [300 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety-proposed/universe Translation-en [189 kB] Fetched 14.7 MB in 31s (471 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libpng12-0 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: libpng16-16 libprocps5 The following packages will be upgraded: apt apt-transport-https bash binutils bsdutils bzip2 cpp-5 debconf dmsetup dpkg dpkg-dev g++-5 gcc-5 gcc-5-base gcc-6-base grep hostname init init-system-helpers initscripts libapt-pkg5.0 libasn1-8-heimdal libatomic1 libblkid1 libbz2-1.0 libcap2 libcap2-bin libcc1-0 libdevmapper1.02.1 libdpkg-perl libfdisk1 libgcc-5-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libitm1 libkrb5-26-heimdal libldap-2.4-2 libmount1 libperl5.22 libpng12-0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsmartcols1 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libudev1 libusb-0.1-4 libuuid1 libwind0-heimdal linux-libc-dev lsb-base make mount optipng perl perl-base perl-modules-5.22 policyrcd-script-zg2 procps sed systemd systemd-sysv sysv-rc sysvinit-utils tar tzdata ubuntu-keyring util-linux zlib1g 86 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 85.8 MB of archives. After this operation, 206 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu yakkety/main s390x bash s390x 4.3-14ubuntu2 [568 kB] Get:2 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x bsdutils s390x 1:2.28-5ubuntu1 [54.4 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety/main s390x dpkg s390x 1.18.7ubuntu1 [2151 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety/main s390x grep s390x 2.25-1 [148 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main s390x hostname s390x 3.17ubuntu1 [11.8 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main s390x perl-modules-5.22 all 5.22.2-1 [2642 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/main s390x libperl5.22 s390x 5.22.2-1 [3280 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/main s390x perl s390x 5.22.2-1 [238 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety/main s390x perl-base s390x 5.22.2-1 [1249 kB] Get:10 http://ftpmaster.internal/ubuntu yakkety/main s390x bzip2 s390x 1.0.6-8build1 [33.3 kB] Get:11 http://ftpmaster.internal/ubuntu yakkety/main s390x libbz2-1.0 s390x 1.0.6-8build1 [32.7 kB] Get:12 http://ftpmaster.internal/ubuntu yakkety/main s390x zlib1g s390x 1:1.2.8.dfsg-2ubuntu5 [51.6 kB] Get:13 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x init-system-helpers all 1.33ubuntu2 [31.9 kB] Get:14 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x init s390x 1.33ubuntu2 [4346 B] Get:15 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libsmartcols1 s390x 2.28-5ubuntu1 [61.4 kB] Get:16 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libuuid1 s390x 2.28-5ubuntu1 [15.1 kB] Get:17 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libblkid1 s390x 2.28-5ubuntu1 [100 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libfdisk1 s390x 2.28-5ubuntu1 [128 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x sysv-rc all 2.88dsf-59.4ubuntu1 [18.2 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x initscripts s390x 2.88dsf-59.4ubuntu1 [23.9 kB] Get:21 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x util-linux s390x 2.28-5ubuntu1 [866 kB] Get:22 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x sysvinit-utils s390x 2.88dsf-59.4ubuntu1 [22.0 kB] Get:23 http://ftpmaster.internal/ubuntu yakkety/main s390x debconf all 1.5.59ubuntu1 [136 kB] Get:24 http://ftpmaster.internal/ubuntu yakkety/main s390x libgpg-error0 s390x 1.22-2 [33.1 kB] Get:25 http://ftpmaster.internal/ubuntu yakkety/main s390x libgcrypt20 s390x 1.7.0-2 [339 kB] Get:26 http://ftpmaster.internal/ubuntu yakkety/main s390x libsystemd0 s390x 229-6ubuntu1 [194 kB] Get:27 http://ftpmaster.internal/ubuntu yakkety/main s390x systemd s390x 229-6ubuntu1 [3295 kB] Get:28 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libcap2 s390x 1:2.25-1 [13.7 kB] Get:29 http://ftpmaster.internal/ubuntu yakkety/main s390x libselinux1 s390x 2.5-3 [62.1 kB] Get:30 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libmount1 s390x 2.28-5ubuntu1 [109 kB] Get:31 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libcap2-bin s390x 1:2.25-1 [20.4 kB] Get:32 http://ftpmaster.internal/ubuntu yakkety/main s390x lsb-base all 9.20160110ubuntu1 [13.7 kB] Get:33 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x mount s390x 2.28-5ubuntu1 [121 kB] Get:34 http://ftpmaster.internal/ubuntu yakkety/main s390x sed s390x 4.2.2-7.1 [139 kB] Get:35 http://ftpmaster.internal/ubuntu yakkety/main s390x tar s390x 1.29-1 [214 kB] Get:36 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x gcc-6-base s390x 6.1.1-4ubuntu11 [17.0 kB] Get:37 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libgcc1 s390x 1:6.1.1-4ubuntu11 [24.6 kB] Get:38 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libstdc++6 s390x 6.1.1-4ubuntu11 [402 kB] Get:39 http://ftpmaster.internal/ubuntu yakkety/main s390x libapt-pkg5.0 s390x 1.3~exp1 [665 kB] Get:40 http://ftpmaster.internal/ubuntu yakkety/main s390x ubuntu-keyring all 2016.05.13 [16.5 kB] Get:41 http://ftpmaster.internal/ubuntu yakkety/main s390x apt s390x 1.3~exp1 [1018 kB] Get:42 http://ftpmaster.internal/ubuntu yakkety/main s390x systemd-sysv s390x 229-6ubuntu1 [17.6 kB] Get:43 http://ftpmaster.internal/ubuntu yakkety/main s390x libudev1 s390x 229-6ubuntu1 [57.0 kB] Get:44 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libdevmapper1.02.1 s390x 2:1.02.124-1ubuntu1 [134 kB] Get:45 http://ftpmaster.internal/ubuntu yakkety/main s390x libsepol1 s390x 2.5-1 [198 kB] Get:46 http://ftpmaster.internal/ubuntu yakkety/main s390x libsemanage-common all 2.5-1 [6800 B] Get:47 http://ftpmaster.internal/ubuntu yakkety/main s390x libsemanage1 s390x 2.5-1 [75.1 kB] Get:48 http://ftpmaster.internal/ubuntu yakkety/main s390x libusb-0.1-4 s390x 2:0.1.12-30 [16.6 kB] Get:49 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libprocps5 s390x 2:3.3.11-3ubuntu1 [29.7 kB] Get:50 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x procps s390x 2:3.3.11-3ubuntu1 [216 kB] Get:51 http://ftpmaster.internal/ubuntu yakkety/main s390x tzdata all 2016d-2 [168 kB] Get:52 http://ftpmaster.internal/ubuntu yakkety/main s390x libtasn1-6 s390x 4.8-1 [41.1 kB] Get:53 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libgnutls30 s390x 3.4.11-4ubuntu1 [491 kB] Get:54 http://ftpmaster.internal/ubuntu yakkety/main s390x libslang2 s390x 2.3.0-2.3ubuntu1 [405 kB] Get:55 http://ftpmaster.internal/ubuntu yakkety/main s390x apt-transport-https s390x 1.3~exp1 [24.9 kB] Get:56 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libroken18-heimdal s390x 1.7~git20160515+dfsg-1 [39.6 kB] Get:57 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libasn1-8-heimdal s390x 1.7~git20160515+dfsg-1 [147 kB] Get:58 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libheimbase1-heimdal s390x 1.7~git20160515+dfsg-1 [27.6 kB] Get:59 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libhcrypto4-heimdal s390x 1.7~git20160515+dfsg-1 [84.2 kB] Get:60 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libwind0-heimdal s390x 1.7~git20160515+dfsg-1 [48.0 kB] Get:61 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libhx509-5-heimdal s390x 1.7~git20160515+dfsg-1 [99.3 kB] Get:62 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libkrb5-26-heimdal s390x 1.7~git20160515+dfsg-1 [187 kB] Get:63 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libheimntlm0-heimdal s390x 1.7~git20160515+dfsg-1 [14.6 kB] Get:64 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libgssapi3-heimdal s390x 1.7~git20160515+dfsg-1 [88.8 kB] Get:65 http://ftpmaster.internal/ubuntu yakkety/main s390x libsasl2-modules-db s390x 2.1.26.dfsg1-15 [14.0 kB] Get:66 http://ftpmaster.internal/ubuntu yakkety/main s390x libsasl2-2 s390x 2.1.26.dfsg1-15 [46.8 kB] Get:67 http://ftpmaster.internal/ubuntu yakkety/main s390x libldap-2.4-2 s390x 2.4.42+dfsg-2ubuntu4 [151 kB] Get:68 http://ftpmaster.internal/ubuntu yakkety/main s390x libpng16-16 s390x 1.6.21-5 [170 kB] Get:69 http://ftpmaster.internal/ubuntu yakkety/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-1 [51.8 kB] Get:70 http://ftpmaster.internal/ubuntu yakkety/main s390x binutils s390x 2.26-9ubuntu1 [1056 kB] Get:71 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libgomp1 s390x 6.1.1-4ubuntu11 [71.1 kB] Get:72 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libitm1 s390x 6.1.1-4ubuntu11 [27.3 kB] Get:73 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libatomic1 s390x 6.1.1-4ubuntu11 [8172 B] Get:74 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x g++-5 s390x 5.3.1-20ubuntu1 [27.2 MB] Get:75 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x gcc-5 s390x 5.3.1-20ubuntu1 [6917 kB] Get:76 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libstdc++-5-dev s390x 5.3.1-20ubuntu1 [1353 kB] Get:77 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libgcc-5-dev s390x 5.3.1-20ubuntu1 [245 kB] Get:78 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x libcc1-0 s390x 6.1.1-4ubuntu11 [31.0 kB] Get:79 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x cpp-5 s390x 5.3.1-20ubuntu1 [25.2 MB] Get:80 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x gcc-5-base s390x 5.3.1-20ubuntu1 [16.9 kB] Get:81 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x dmsetup s390x 2:1.02.124-1ubuntu1 [69.4 kB] Get:82 http://ftpmaster.internal/ubuntu yakkety/main s390x dpkg-dev all 1.18.7ubuntu1 [666 kB] Get:83 http://ftpmaster.internal/ubuntu yakkety/main s390x libdpkg-perl all 1.18.7ubuntu1 [202 kB] Get:84 http://ftpmaster.internal/ubuntu yakkety/main s390x make s390x 4.1-9 [149 kB] Get:85 http://ftpmaster.internal/ubuntu yakkety/universe s390x libpng12-0 s390x 1.2.54-6ubuntu1 [113 kB] Get:86 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x linux-libc-dev s390x 4.4.0-23.41 [830 kB] Get:87 http://ftpmaster.internal/ubuntu yakkety/main s390x optipng s390x 0.7.6-1build1 [81.5 kB] Get:88 http://ftpmaster.internal/ubuntu yakkety/main s390x policyrcd-script-zg2 all 0.1-3 [5610 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 85.8 MB in 55s (1553 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11908 files and directories currently installed.) Preparing to unpack .../bash_4.3-14ubuntu2_s390x.deb ... Unpacking bash (4.3-14ubuntu2) over (4.3-14ubuntu1) ... Setting up bash (4.3-14ubuntu2) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 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Unpacking perl-base (5.22.2-1) over (5.22.1-9) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up perl-base (5.22.2-1) ... (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 ... 11919 files and directories currently installed.) Preparing to unpack .../bzip2_1.0.6-8build1_s390x.deb ... Unpacking bzip2 (1.0.6-8build1) over (1.0.6-8) ... Preparing to unpack .../libbz2-1.0_1.0.6-8build1_s390x.deb ... Unpacking libbz2-1.0:s390x (1.0.6-8build1) over (1.0.6-8) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libbz2-1.0:s390x (1.0.6-8build1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (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 ... 11919 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.8.dfsg-2ubuntu5_s390x.deb ... Unpacking zlib1g:s390x (1:1.2.8.dfsg-2ubuntu5) over (1:1.2.8.dfsg-2ubuntu4) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up zlib1g:s390x (1:1.2.8.dfsg-2ubuntu5) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (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 ... 11919 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.33ubuntu2_all.deb ... Unpacking init-system-helpers (1.33ubuntu2) over (1.29ubuntu1) ... Setting up init-system-helpers (1.33ubuntu2) ... (Reading database ... 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Unpacking sysvinit-utils (2.88dsf-59.4ubuntu1) over (2.88dsf-59.3ubuntu2) ... Preparing to unpack .../util-linux_2.28-5ubuntu1_s390x.deb ... Unpacking util-linux (2.28-5ubuntu1) over (2.27.1-6ubuntu3) ... Setting up util-linux (2.28-5ubuntu1) ... Processing triggers for systemd (229-4ubuntu4) ... (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 ... 11924 files and directories currently installed.) Preparing to unpack .../debconf_1.5.59ubuntu1_all.deb ... Unpacking debconf (1.5.59ubuntu1) over (1.5.58ubuntu1) ... Setting up debconf (1.5.59ubuntu1) ... (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 ... 11924 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.22-2_s390x.deb ... Unpacking libgpg-error0:s390x (1.22-2) over (1.21-2ubuntu1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libgpg-error0:s390x (1.22-2) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (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 ... 11924 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.7.0-2_s390x.deb ... Unpacking libgcrypt20:s390x (1.7.0-2) over (1.6.5-2) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libgcrypt20:s390x (1.7.0-2) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11927 files and directories currently installed.) Preparing to unpack .../libstdc++6_6.1.1-4ubuntu11_s390x.deb ... Unpacking libstdc++6:s390x (6.1.1-4ubuntu11) over (5.3.1-14ubuntu2) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libstdc++6:s390x (6.1.1-4ubuntu11) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (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 ... 11927 files and directories currently installed.) Preparing to unpack .../libapt-pkg5.0_1.3~exp1_s390x.deb ... Unpacking libapt-pkg5.0:s390x (1.3~exp1) over (1.2.10ubuntu1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libapt-pkg5.0:s390x (1.3~exp1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (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 ... 11927 files and directories currently installed.) Preparing to unpack .../ubuntu-keyring_2016.05.13_all.deb ... Unpacking ubuntu-keyring (2016.05.13) over (2012.05.19) ... Setting up ubuntu-keyring (2016.05.13) ... gpg: key 437D05B5: "Ubuntu Archive Automatic Signing Key " not changed gpg: key FBB75451: "Ubuntu CD Image Automatic Signing Key " not changed gpg: key C0B21F32: "Ubuntu Archive Automatic Signing Key (2012) " not changed gpg: key EFE21092: "Ubuntu CD Image Automatic Signing Key (2012) " not changed gpg: Total number processed: 4 gpg: unchanged: 4 (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 ... 11927 files and directories currently installed.) Preparing to unpack .../apt_1.3~exp1_s390x.deb ... Unpacking apt (1.3~exp1) over (1.2.10ubuntu1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up apt (1.3~exp1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (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 ... 11927 files and directories currently installed.) Preparing to unpack .../systemd-sysv_229-6ubuntu1_s390x.deb ... Unpacking systemd-sysv (229-6ubuntu1) over (229-4ubuntu4) ... Setting up systemd-sysv (229-6ubuntu1) ... (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 ... 11927 files and directories currently installed.) Preparing to unpack .../libudev1_229-6ubuntu1_s390x.deb ... Unpacking libudev1:s390x (229-6ubuntu1) over (229-4ubuntu4) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libudev1:s390x (229-6ubuntu1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (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 ... 11927 files and directories currently installed.) Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.124-1ubuntu1_s390x.deb ... Unpacking libdevmapper1.02.1:s390x (2:1.02.124-1ubuntu1) over (2:1.02.110-1ubuntu10) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libdevmapper1.02.1:s390x (2:1.02.124-1ubuntu1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (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 ... 11927 files and directories currently installed.) Preparing to unpack .../libsepol1_2.5-1_s390x.deb ... Unpacking libsepol1:s390x (2.5-1) over (2.4-2) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libsepol1:s390x (2.5-1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (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 ... 11927 files and directories currently installed.) Preparing to unpack .../libsemanage-common_2.5-1_all.deb ... Unpacking libsemanage-common (2.5-1) over (2.3-1build3) ... Setting up libsemanage-common (2.5-1) ... Installing new version of config file /etc/selinux/semanage.conf ... (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 ... 11927 files and directories currently installed.) Preparing to unpack .../libsemanage1_2.5-1_s390x.deb ... Unpacking libsemanage1:s390x (2.5-1) over (2.3-1build3) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libsemanage1:s390x (2.5-1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... (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 ... 11927 files and directories currently installed.) Preparing to unpack .../libusb-0.1-4_2%3a0.1.12-30_s390x.deb ... Unpacking libusb-0.1-4:s390x (2:0.1.12-30) over (2:0.1.12-28) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up libusb-0.1-4:s390x (2:0.1.12-30) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Selecting previously unselected package libprocps5:s390x. (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 ... 11927 files and directories currently installed.) Preparing to unpack .../libprocps5_2%3a3.3.11-3ubuntu1_s390x.deb ... Unpacking libprocps5:s390x (2:3.3.11-3ubuntu1) ... Preparing to unpack .../procps_2%3a3.3.11-3ubuntu1_s390x.deb ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of stop. Unpacking procps (2:3.3.11-3ubuntu1) over (2:3.3.10-4ubuntu2) ... Preparing to unpack .../tzdata_2016d-2_all.deb ... 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Setting up initscripts (2.88dsf-59.4ubuntu1) ... Installing new version of config file /etc/init.d/ondemand ... Installing new version of config file /etc/init.d/sendsigs ... Installing new version of config file /etc/init.d/umountroot ... Setting up libprocps5:s390x (2:3.3.11-3ubuntu1) ... Setting up procps (2:3.3.11-3ubuntu1) ... Installing new version of config file /etc/sysctl.conf ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up tzdata (2016d-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sun May 22 23:15:58 UTC 2016. Universal Time is now: Sun May 22 23:15:58 UTC 2016. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libtasn1-6:s390x (4.8-1) ... Setting up libgnutls30:s390x (3.4.11-4ubuntu1) ... Setting up libslang2:s390x (2.3.0-2.3ubuntu1) ... Setting up apt-transport-https (1.3~exp1) ... Setting up libroken18-heimdal:s390x (1.7~git20160515+dfsg-1) ... Setting up libasn1-8-heimdal:s390x (1.7~git20160515+dfsg-1) ... Setting up libheimbase1-heimdal:s390x (1.7~git20160515+dfsg-1) ... Setting up libhcrypto4-heimdal:s390x (1.7~git20160515+dfsg-1) ... Setting up libwind0-heimdal:s390x (1.7~git20160515+dfsg-1) ... Setting up libhx509-5-heimdal:s390x (1.7~git20160515+dfsg-1) ... Setting up libkrb5-26-heimdal:s390x (1.7~git20160515+dfsg-1) ... Setting up libheimntlm0-heimdal:s390x (1.7~git20160515+dfsg-1) ... Setting up libgssapi3-heimdal:s390x (1.7~git20160515+dfsg-1) ... Setting up libsasl2-modules-db:s390x (2.1.26.dfsg1-15) ... Setting up libsasl2-2:s390x (2.1.26.dfsg1-15) ... Setting up libldap-2.4-2:s390x (2.4.42+dfsg-2ubuntu4) ... Setting up libpng16-16:s390x (1.6.21-5) ... Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-1) ... Setting up binutils (2.26-9ubuntu1) ... Setting up libgomp1:s390x (6.1.1-4ubuntu11) ... Setting up libitm1:s390x (6.1.1-4ubuntu11) ... Setting up libatomic1:s390x (6.1.1-4ubuntu11) ... Setting up gcc-5-base:s390x (5.3.1-20ubuntu1) ... Setting up cpp-5 (5.3.1-20ubuntu1) ... Setting up libcc1-0:s390x (6.1.1-4ubuntu11) ... Setting up libgcc-5-dev:s390x (5.3.1-20ubuntu1) ... Setting up gcc-5 (5.3.1-20ubuntu1) ... Setting up libstdc++-5-dev:s390x (5.3.1-20ubuntu1) ... Setting up g++-5 (5.3.1-20ubuntu1) ... Setting up dmsetup (2:1.02.124-1ubuntu1) ... Setting up libdpkg-perl (1.18.7ubuntu1) ... Setting up make (4.1-9) ... Setting up dpkg-dev (1.18.7ubuntu1) ... Setting up libpng12-0:s390x (1.2.54-6ubuntu1) ... Setting up linux-libc-dev:s390x (4.4.0-23.41) ... Setting up optipng (0.7.6-1build1) ... Setting up policyrcd-script-zg2 (0.1-3) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Processing triggers for systemd (229-6ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-9789456', 's390x', 'yakkety-proposed', '-c', 'chroot:autobuild', '--arch=s390x', '--dist=yakkety-proposed', '--purge=never', '--nolog', 'rna-star_2.5.2a+dfsg-2.dsc'] Initiating build PACKAGEBUILD-9789456 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:08 UTC 2016 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on z13-018.buildd +==============================================================================+ | rna-star 2.5.2a+dfsg-2 (s390x) 22 May 2016 23:15 | +==============================================================================+ Package: rna-star Version: 2.5.2a+dfsg-2 Source Version: 2.5.2a+dfsg-2 Distribution: yakkety-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/rna-star-VctoG4/rna-star-2.5.2a+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rna-star-VctoG4' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-9789456/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- rna-star_2.5.2a+dfsg-2.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-uu3ppF/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-uu3ppF/apt_archive ./ InRelease Get:2 copy:/<>/resolver-uu3ppF/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-uu3ppF/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-uu3ppF/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-uu3ppF/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libpng12-0 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 772 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-uu3ppF/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 772 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11973 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9), libhts-dev, vim-common, zlib1g-dev Filtered Build-Depends: debhelper (>= 9), libhts-dev, vim-common, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-rna-star-dummy' in '/<>/resolver-bTH1df/apt_archive/sbuild-build-depends-rna-star-dummy.deb'. Ign:1 copy:/<>/resolver-bTH1df/apt_archive ./ InRelease Get:2 copy:/<>/resolver-bTH1df/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-bTH1df/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-bTH1df/apt_archive ./ Sources [232 B] Get:5 copy:/<>/resolver-bTH1df/apt_archive ./ Packages [553 B] Fetched 2904 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install rna-star build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libpng12-0 Use 'sudo apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasprintf0v5 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1 libicu57 libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf vim-common zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc groff libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser libmail-box-perl vim-gnome-py2 | vim-gtk-py2 | vim-gtk3-py2 | vim-athena-py2 | vim-nox-py2 Recommended packages: curl | wget | lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl vim | vim-gnome | vim-gtk | vim-gtk3 | vim-athena | vim-nox | vim-tiny The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasprintf0v5 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1 libicu57 libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf sbuild-build-depends-rna-star-dummy vim-common zlib1g-dev 0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 16.7 MB of archives. After this operation, 66.2 MB of additional disk space will be used. Get:1 copy:/<>/resolver-bTH1df/apt_archive ./ sbuild-build-depends-rna-star-dummy 0.invalid.0 [796 B] Get:2 http://ftpmaster.internal/ubuntu yakkety/main s390x groff-base s390x 1.22.3-7 [1199 kB] Get:3 http://ftpmaster.internal/ubuntu yakkety/main s390x bsdmainutils s390x 9.0.6ubuntu3 [179 kB] Get:4 http://ftpmaster.internal/ubuntu yakkety/main s390x libpipeline1 s390x 1.4.1-2 [24.8 kB] Get:5 http://ftpmaster.internal/ubuntu yakkety/main s390x man-db s390x 2.7.5-1 [850 kB] Get:6 http://ftpmaster.internal/ubuntu yakkety/main s390x libmagic1 s390x 1:5.25-2ubuntu1 [214 kB] Get:7 http://ftpmaster.internal/ubuntu yakkety/main s390x file s390x 1:5.25-2ubuntu1 [21.5 kB] Get:8 http://ftpmaster.internal/ubuntu yakkety/main s390x vim-common s390x 2:7.4.1689-3ubuntu2 [104 kB] Get:9 http://ftpmaster.internal/ubuntu yakkety/main s390x libasprintf0v5 s390x 0.19.7-2ubuntu3 [6344 B] Get:10 http://ftpmaster.internal/ubuntu yakkety/main s390x gettext-base s390x 0.19.7-2ubuntu3 [47.7 kB] Get:11 http://ftpmaster.internal/ubuntu yakkety/main s390x libglib2.0-0 s390x 2.48.1-1 [1043 kB] Get:12 http://ftpmaster.internal/ubuntu yakkety/main s390x libicu57 s390x 57.1-1 [7509 kB] Get:13 http://ftpmaster.internal/ubuntu yakkety/main s390x libxml2 s390x 2.9.3+dfsg1-1build1 [640 kB] Get:14 http://ftpmaster.internal/ubuntu yakkety/main s390x libsigsegv2 s390x 2.10-5 [13.5 kB] Get:15 http://ftpmaster.internal/ubuntu yakkety/main s390x m4 s390x 1.4.17-5 [192 kB] Get:16 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x autoconf all 2.69-10 [321 kB] Get:17 http://ftpmaster.internal/ubuntu yakkety-proposed/main s390x autotools-dev all 20160430.1 [39.6 kB] Get:18 http://ftpmaster.internal/ubuntu yakkety/main s390x automake all 1:1.15-4ubuntu1 [510 kB] Get:19 http://ftpmaster.internal/ubuntu yakkety/main s390x autopoint all 0.19.7-2ubuntu3 [406 kB] Get:20 http://ftpmaster.internal/ubuntu yakkety/main s390x libcroco3 s390x 0.6.11-1 [76.5 kB] Get:21 http://ftpmaster.internal/ubuntu yakkety/main s390x libunistring0 s390x 0.9.3-5.2ubuntu1 [262 kB] Get:22 http://ftpmaster.internal/ubuntu yakkety/main s390x gettext s390x 0.19.7-2ubuntu3 [1052 kB] Get:23 http://ftpmaster.internal/ubuntu yakkety/main s390x intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:24 http://ftpmaster.internal/ubuntu yakkety/main s390x po-debconf all 1.0.19 [234 kB] Get:25 http://ftpmaster.internal/ubuntu yakkety/main s390x libarchive-zip-perl all 1.57-1 [84.0 kB] Get:26 http://ftpmaster.internal/ubuntu yakkety/main s390x libfile-stripnondeterminism-perl all 0.016-1 [11.0 kB] Get:27 http://ftpmaster.internal/ubuntu yakkety/main s390x libtimedate-perl all 2.3000-2 [37.5 kB] Get:28 http://ftpmaster.internal/ubuntu yakkety/main s390x dh-strip-nondeterminism all 0.016-1 [4858 B] Get:29 http://ftpmaster.internal/ubuntu yakkety/main s390x libtool all 2.4.6-0.1 [193 kB] Get:30 http://ftpmaster.internal/ubuntu yakkety/main s390x dh-autoreconf all 12 [15.8 kB] Get:31 http://ftpmaster.internal/ubuntu yakkety/main s390x debhelper all 9.20160403ubuntu1 [711 kB] Get:32 http://ftpmaster.internal/ubuntu yakkety/universe s390x libhts1 s390x 1.3.1-1ubuntu1 [238 kB] Get:33 http://ftpmaster.internal/ubuntu yakkety/universe s390x libhts-dev s390x 1.3.1-1ubuntu1 [305 kB] Get:34 http://ftpmaster.internal/ubuntu yakkety/main s390x zlib1g-dev s390x 1:1.2.8.dfsg-2ubuntu5 [168 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.7 MB in 6s (2531 kB/s) Selecting previously unselected package groff-base. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11973 files and directories currently installed.) Preparing to unpack .../groff-base_1.22.3-7_s390x.deb ... Unpacking groff-base (1.22.3-7) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6ubuntu3_s390x.deb ... Unpacking bsdmainutils (9.0.6ubuntu3) ... Selecting previously unselected package libpipeline1:s390x. Preparing to unpack .../libpipeline1_1.4.1-2_s390x.deb ... Unpacking libpipeline1:s390x (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.5-1_s390x.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package libmagic1:s390x. Preparing to unpack .../libmagic1_1%3a5.25-2ubuntu1_s390x.deb ... Unpacking libmagic1:s390x (1:5.25-2ubuntu1) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.25-2ubuntu1_s390x.deb ... Unpacking file (1:5.25-2ubuntu1) ... Selecting previously unselected package vim-common. Preparing to unpack .../vim-common_2%3a7.4.1689-3ubuntu2_s390x.deb ... Unpacking vim-common (2:7.4.1689-3ubuntu2) ... Selecting previously unselected package libasprintf0v5:s390x. Preparing to unpack .../libasprintf0v5_0.19.7-2ubuntu3_s390x.deb ... Unpacking libasprintf0v5:s390x (0.19.7-2ubuntu3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.19.7-2ubuntu3_s390x.deb ... 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Selecting previously unselected package intltool-debian. Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ... Unpacking intltool-debian (0.35.0+20060710.4) ... Selecting previously unselected package po-debconf. Preparing to unpack .../po-debconf_1.0.19_all.deb ... Unpacking po-debconf (1.0.19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ... Unpacking libarchive-zip-perl (1.57-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../libfile-stripnondeterminism-perl_0.016-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (0.016-1) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ... Unpacking libtimedate-perl (2.3000-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../dh-strip-nondeterminism_0.016-1_all.deb ... Unpacking dh-strip-nondeterminism (0.016-1) ... Selecting previously unselected package libtool. Preparing to unpack .../libtool_2.4.6-0.1_all.deb ... Unpacking libtool (2.4.6-0.1) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../dh-autoreconf_12_all.deb ... Unpacking dh-autoreconf (12) ... Selecting previously unselected package debhelper. Preparing to unpack .../debhelper_9.20160403ubuntu1_all.deb ... Unpacking debhelper (9.20160403ubuntu1) ... Selecting previously unselected package libhts1:s390x. Preparing to unpack .../libhts1_1.3.1-1ubuntu1_s390x.deb ... Unpacking libhts1:s390x (1.3.1-1ubuntu1) ... Selecting previously unselected package libhts-dev:s390x. Preparing to unpack .../libhts-dev_1.3.1-1ubuntu1_s390x.deb ... Unpacking libhts-dev:s390x (1.3.1-1ubuntu1) ... Selecting previously unselected package zlib1g-dev:s390x. Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2ubuntu5_s390x.deb ... Unpacking zlib1g-dev:s390x (1:1.2.8.dfsg-2ubuntu5) ... Selecting previously unselected package sbuild-build-depends-rna-star-dummy. Preparing to unpack .../sbuild-build-depends-rna-star-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-rna-star-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... Setting up groff-base (1.22.3-7) ... Setting up bsdmainutils (9.0.6ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libpipeline1:s390x (1.4.1-2) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libmagic1:s390x (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up vim-common (2:7.4.1689-3ubuntu2) ... Setting up libasprintf0v5:s390x (0.19.7-2ubuntu3) ... Setting up gettext-base (0.19.7-2ubuntu3) ... Setting up libglib2.0-0:s390x (2.48.1-1) ... No schema files found: doing nothing. Setting up libicu57:s390x (57.1-1) ... Setting up libxml2:s390x (2.9.3+dfsg1-1build1) ... Setting up libsigsegv2:s390x (2.10-5) ... Setting up m4 (1.4.17-5) ... Setting up autoconf (2.69-10) ... Setting up autotools-dev (20160430.1) ... Setting up automake (1:1.15-4ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up autopoint (0.19.7-2ubuntu3) ... Setting up libcroco3:s390x (0.6.11-1) ... Setting up libunistring0:s390x (0.9.3-5.2ubuntu1) ... Setting up gettext (0.19.7-2ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.19) ... Setting up libarchive-zip-perl (1.57-1) ... Setting up libfile-stripnondeterminism-perl (0.016-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libtool (2.4.6-0.1) ... Setting up libhts1:s390x (1.3.1-1ubuntu1) ... Setting up libhts-dev:s390x (1.3.1-1ubuntu1) ... Setting up zlib1g-dev:s390x (1:1.2.8.dfsg-2ubuntu5) ... Setting up dh-autoreconf (12) ... Setting up debhelper (9.20160403ubuntu1) ... Setting up sbuild-build-depends-rna-star-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (0.016-1) ... Processing triggers for libc-bin (2.23-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-22-generic s390x (s390x) Toolchain package versions: binutils_2.26-9ubuntu1 dpkg-dev_1.18.7ubuntu1 g++-5_5.3.1-20ubuntu1 gcc-5_5.3.1-20ubuntu1 libc6-dev_2.23-0ubuntu3 libstdc++-5-dev_5.3.1-20ubuntu1 libstdc++6_6.1.1-4ubuntu11 linux-libc-dev_4.4.0-23.41 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.3~exp1 apt-transport-https_1.3~exp1 autoconf_2.69-10 automake_1:1.15-4ubuntu1 autopoint_0.19.7-2ubuntu3 autotools-dev_20160430.1 base-files_9.6ubuntu1 base-passwd_3.5.39 bash_4.3-14ubuntu2 binutils_2.26-9ubuntu1 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.28-5ubuntu1 build-essential_12.1ubuntu2 bzip2_1.0.6-8build1 ca-certificates_20160104ubuntu1 coreutils_8.25-2ubuntu2 cpp_4:5.3.1-1ubuntu1 cpp-5_5.3.1-20ubuntu1 dash_0.5.8-2.1ubuntu2 debconf_1.5.59ubuntu1 debhelper_9.20160403ubuntu1 debianutils_4.7 dh-autoreconf_12 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.124-1ubuntu1 dpkg_1.18.7ubuntu1 dpkg-dev_1.18.7ubuntu1 e2fslibs_1.42.13-1ubuntu1 e2fsprogs_1.42.13-1ubuntu1 fakeroot_1.20.2-1ubuntu1 file_1:5.25-2ubuntu1 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1ubuntu1 g++-5_5.3.1-20ubuntu1 gcc_4:5.3.1-1ubuntu1 gcc-5_5.3.1-20ubuntu1 gcc-5-base_5.3.1-20ubuntu1 gcc-6-base_6.1.1-4ubuntu11 gettext_0.19.7-2ubuntu3 gettext-base_0.19.7-2ubuntu3 gnupg_1.4.20-1ubuntu3 gpgv_1.4.20-1ubuntu3 grep_2.25-1 groff-base_1.22.3-7 gzip_1.6-4ubuntu1 hostname_3.17ubuntu1 init_1.33ubuntu2 init-system-helpers_1.33ubuntu2 initscripts_2.88dsf-59.4ubuntu1 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapparmor1_2.10.95-0ubuntu2 libapt-pkg5.0_1.3~exp1 libarchive-zip-perl_1.57-1 libasn1-8-heimdal_1.7~git20160515+dfsg-1 libasprintf0v5_0.19.7-2ubuntu3 libatomic1_6.1.1-4ubuntu11 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1ubuntu2 libaudit1_1:2.4.5-1ubuntu2 libblkid1_2.28-5ubuntu1 libbz2-1.0_1.0.6-8build1 libc-bin_2.23-0ubuntu3 libc-dev-bin_2.23-0ubuntu3 libc6_2.23-0ubuntu3 libc6-dev_2.23-0ubuntu3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-4ubuntu11 libcomerr2_1.42.13-1ubuntu1 libcroco3_0.6.11-1 libcryptsetup4_2:1.6.6-5ubuntu2 libcurl3-gnutls_7.47.0-1ubuntu2 libdb5.3_5.3.28-11 libdebconfclient0_0.198ubuntu1 libdevmapper1.02.1_2:1.02.124-1ubuntu1 libdpkg-perl_1.18.7ubuntu1 libfakeroot_1.20.2-1ubuntu1 libfdisk1_2.28-5ubuntu1 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libgcc-5-dev_5.3.1-20ubuntu1 libgcc1_1:6.1.1-4ubuntu11 libgcrypt20_1.7.0-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.48.1-1 libgmp10_2:6.1.0+dfsg-2 libgnutls30_3.4.11-4ubuntu1 libgomp1_6.1.1-4ubuntu11 libgpg-error0_1.22-2 libgssapi-krb5-2_1.13.2+dfsg-5 libgssapi3-heimdal_1.7~git20160515+dfsg-1 libhcrypto4-heimdal_1.7~git20160515+dfsg-1 libheimbase1-heimdal_1.7~git20160515+dfsg-1 libheimntlm0-heimdal_1.7~git20160515+dfsg-1 libhogweed4_3.2-1 libhts-dev_1.3.1-1ubuntu1 libhts1_1.3.1-1ubuntu1 libhx509-5-heimdal_1.7~git20160515+dfsg-1 libicu57_57.1-1 libidn11_1.32-3ubuntu1 libisl15_0.16.1-1 libitm1_6.1.1-4ubuntu11 libk5crypto3_1.13.2+dfsg-5 libkeyutils1_1.5.9-8ubuntu1 libkmod2_22-1ubuntu4 libkrb5-26-heimdal_1.7~git20160515+dfsg-1 libkrb5-3_1.13.2+dfsg-5 libkrb5support0_1.13.2+dfsg-5 libldap-2.4-2_2.4.42+dfsg-2ubuntu4 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.1.1alpha+20120614-2ubuntu2 libmagic1_1:5.25-2ubuntu1 libmount1_2.28-5ubuntu1 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160213-1ubuntu1 libncursesw5_6.0+20160213-1ubuntu1 libnettle6_3.2-1 libp11-kit0_0.23.2-3 libpam-modules_1.1.8-3.2ubuntu2 libpam-modules-bin_1.1.8-3.2ubuntu2 libpam-runtime_1.1.8-3.2ubuntu2 libpam0g_1.1.8-3.2ubuntu2 libpcre3_2:8.38-3.1 libperl5.22_5.22.2-1 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6ubuntu1 libpng16-16_1.6.21-5 libprocps4_2:3.3.10-4ubuntu2 libprocps5_2:3.3.11-3ubuntu1 libreadline6_6.3-8ubuntu2 libroken18-heimdal_1.7~git20160515+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.2.3-3ubuntu3 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libslang2_2.3.0-2.3ubuntu1 libsmartcols1_2.28-5ubuntu1 libsqlite3-0_3.11.0-1ubuntu1 libss2_1.42.13-1ubuntu1 libssl1.0.0_1.0.2g-1ubuntu4 libstdc++-5-dev_5.3.1-20ubuntu1 libstdc++6_6.1.1-4ubuntu11 libsystemd0_229-6ubuntu1 libtasn1-6_4.8-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160213-1ubuntu1 libtool_2.4.6-0.1 libudev1_229-6ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28-5ubuntu1 libwind0-heimdal_1.7~git20160515+dfsg-1 libxml2_2.9.3+dfsg1-1build1 linux-libc-dev_4.4.0-23.41 lockfile-progs_0.1.17 login_1:4.2-3.1ubuntu5 lsb-base_9.20160110ubuntu1 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mount_2.28-5ubuntu1 multiarch-support_2.23-0ubuntu3 ncurses-base_6.0+20160213-1ubuntu1 ncurses-bin_6.0+20160213-1ubuntu1 openssl_1.0.2g-1ubuntu4 optipng_0.7.6-1build1 passwd_1:4.2-3.1ubuntu5 patch_2.7.5-1 perl_5.22.2-1 perl-base_5.22.2-1 perl-modules-5.22_5.22.2-1 pkg-create-dbgsym_0.72 pkgbinarymangler_129 po-debconf_1.0.19 policyrcd-script-zg2_0.1-3 procps_2:3.3.11-3ubuntu1 readline-common_6.3-8ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-rna-star-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 systemd_229-6ubuntu1 systemd-sysv_229-6ubuntu1 sysv-rc_2.88dsf-59.4ubuntu1 sysvinit-utils_2.88dsf-59.4ubuntu1 tar_1.29-1 tzdata_2016d-2 ubuntu-keyring_2016.05.13 util-linux_2.28-5ubuntu1 vim-common_2:7.4.1689-3ubuntu2 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu5 zlib1g-dev_1:1.2.8.dfsg-2ubuntu5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sun May 22 09:10:33 2016 UTC using RSA key ID F09F4872 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./rna-star_2.5.2a+dfsg-2.dsc dpkg-source: info: extracting rna-star in rna-star-2.5.2a+dfsg dpkg-source: info: unpacking rna-star_2.5.2a+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.5.2a+dfsg-2.debian.tar.xz dpkg-source: info: applying donotuse_own_htslib.patch dpkg-source: info: applying mips_shm_noreserve.patch dpkg-source: info: applying reproducible.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<>/rna-star-2.5.2a+dfsg SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>/rna-star-2.5.2a+dfsg' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.5.2a+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build rna-star-2.5.2a+dfsg dpkg-buildpackage: info: host architecture s390x fakeroot debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/rna-star-2.5.2a+dfsg' cd source && /usr/bin/make clean make[2]: Entering directory '/<>/rna-star-2.5.2a+dfsg/source' rm -f *.o STAR STARstatic STARlong Depend.list make[2]: Leaving directory '/<>/rna-star-2.5.2a+dfsg/source' rm -f source/parametersDefault.xxd make[1]: Leaving directory '/<>/rna-star-2.5.2a+dfsg' dh_clean debian/rules build-arch dh build-arch dh_testdir -a dh_update_autotools_config -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>/rna-star-2.5.2a+dfsg' cd source && /usr/bin/make CCFLAGS_common_add="-flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>/rna-star-2.5.2a+dfsg/source' Makefile:89: Depend.list: No such file or directory xxd -i parametersDefault > parametersDefault.xxd echo OutSJ.cpp sjdbLoadFromFiles.cpp blocksOverlap.cpp sjdbPrepare.cpp genomeScanFastaFiles.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp STAR.cpp readLoad.cpp binarySearch2.cpp sjdbInsertJunctions.cpp genomeParametersWrite.cpp funCompareUintAndSuffixes.cpp BAMbinSortByCoordinate.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_stitchPieces.cpp extendAlign.cpp ReadAlign_oneRead.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp GlobalVariables.cpp signalFromBAM.cpp genomeGenerate.cpp Parameters_closeReadsFiles.cpp stitchWindowAligns.cpp Parameters.cpp sjSplitAlign.cpp Transcriptome.cpp ReadAlign_chimericDetection.cpp outputSJ.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp ThreadControl.cpp Genome.cpp BAMbinSortUnmapped.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp BAMoutput.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp genomeSAindex.cpp stringSubstituteAll.cpp Transcriptome_geneCountsAddAlign.cpp sysRemoveDir.cpp ReadAlign_storeAligns.cpp bamRemoveDuplicates.cpp InOutStreams.cpp SharedMemory.cpp Genome_insertSequences.cpp Transcript.cpp SuffixArrayFuns.cpp sjdbLoadFromStream.cpp alignSmithWaterman.cpp ReadAlign_createExtendWindowsWithAlign.cpp SequenceFuns.cpp sortSuffixesBucket.cpp BAMfunctions.cpp bam_cat.c OutSJ.cpp sjdbLoadFromFiles.cpp blocksOverlap.cpp sjdbPrepare.cpp genomeScanFastaFiles.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp STAR.cpp readLoad.cpp binarySearch2.cpp sjdbInsertJunctions.cpp genomeParametersWrite.cpp funCompareUintAndSuffixes.cpp BAMbinSortByCoordinate.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_stitchPieces.cpp extendAlign.cpp ReadAlign_oneRead.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp GlobalVariables.cpp signalFromBAM.cpp genomeGenerate.cpp Parameters_closeReadsFiles.cpp stitchWindowAligns.cpp Parameters.cpp sjSplitAlign.cpp Transcriptome.cpp ReadAlign_chimericDetection.cpp outputSJ.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp ThreadControl.cpp Genome.cpp BAMbinSortUnmapped.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp BAMoutput.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp genomeSAindex.cpp stringSubstituteAll.cpp Transcriptome_geneCountsAddAlign.cpp sysRemoveDir.cpp ReadAlign_storeAligns.cpp bamRemoveDuplicates.cpp InOutStreams.cpp SharedMemory.cpp Genome_insertSequences.cpp Transcript.cpp SuffixArrayFuns.cpp sjdbLoadFromStream.cpp alignSmithWaterman.cpp ReadAlign_createExtendWindowsWithAlign.cpp SequenceFuns.cpp sortSuffixesBucket.cpp BAMfunctions.cpp bam_cat.c /bin/rm -f ./Depend.list g++ -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM OutSJ.cpp sjdbLoadFromFiles.cpp blocksOverlap.cpp sjdbPrepare.cpp genomeScanFastaFiles.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp STAR.cpp readLoad.cpp binarySearch2.cpp sjdbInsertJunctions.cpp genomeParametersWrite.cpp funCompareUintAndSuffixes.cpp BAMbinSortByCoordinate.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp ReadAlign_alignBAM.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_stitchPieces.cpp extendAlign.cpp ReadAlign_oneRead.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp GlobalVariables.cpp signalFromBAM.cpp genomeGenerate.cpp Parameters_closeReadsFiles.cpp stitchWindowAligns.cpp Parameters.cpp sjSplitAlign.cpp Transcriptome.cpp ReadAlign_chimericDetection.cpp outputSJ.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp ThreadControl.cpp Genome.cpp BAMbinSortUnmapped.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp BAMoutput.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp genomeSAindex.cpp stringSubstituteAll.cpp Transcriptome_geneCountsAddAlign.cpp sysRemoveDir.cpp ReadAlign_storeAligns.cpp bamRemoveDuplicates.cpp InOutStreams.cpp SharedMemory.cpp Genome_insertSequences.cpp Transcript.cpp SuffixArrayFuns.cpp sjdbLoadFromStream.cpp alignSmithWaterman.cpp ReadAlign_createExtendWindowsWithAlign.cpp SequenceFuns.cpp sortSuffixesBucket.cpp BAMfunctions.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' STAR.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:299:49: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(P->inOut->outBAMfileUnsorted); ^ STAR.cpp:303:46: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(P->inOut->outQuantBAMfile); ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sysRemoveDir.cpp sysRemoveDir.cpp:7:58: warning: unused parameter ‘sb’ [-Wunused-parameter] int removeFileOrDir(const char *fpath,const struct stat *sb, int typeflag, struct FTW *ftwbuf) { ^ sysRemoveDir.cpp:7:88: warning: unused parameter ‘ftwbuf’ [-Wunused-parameter] int removeFileOrDir(const char *fpath,const struct stat *sb, int typeflag, struct FTW *ftwbuf) { ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' alignSmithWaterman.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sortSuffixesBucket.cpp sortSuffixesBucket.cpp: In function ‘void sortSuffixesBucket(char*, void*, int, int)’: sortSuffixesBucket.cpp:27:43: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] uint64_t iprev=*(uint64_t*)(ind+0*indSkip); ^ sortSuffixesBucket.cpp:31:37: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] if (*(uint64_t*)(ind+id*indSkip)==iprev) ^ sortSuffixesBucket.cpp:43:43: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] iprev=*(uint64_t*)(ind+id*indSkip); ^ sortSuffixesBucket.cpp:62:49: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] charCount[G[*(uint64_t*)(ind+id*indSkip+8) + charShift]]++;//TODO can template uint64_t ^ sortSuffixesBucket.cpp:62:57: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] charCount[G[*(uint64_t*)(ind+id*indSkip+8) + charShift]]++;//TODO can template uint64_t ^ sortSuffixesBucket.cpp:62:72: warning: array subscript has type ‘char’ [-Wchar-subscripts] charCount[G[*(uint64_t*)(ind+id*indSkip+8) + charShift]]++;//TODO can template uint64_t ^ sortSuffixesBucket.cpp:85:50: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] char c=G[*(uint64_t*)(ind+id*indSkip+8) + charShift]; ^ sortSuffixesBucket.cpp:85:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] char c=G[*(uint64_t*)(ind+id*indSkip+8) + charShift]; ^ sortSuffixesBucket.cpp:86:44: warning: array subscript has type ‘char’ [-Wchar-subscripts] memcpy(ind1+charStart[c]*indSkip, ind+id*indSkip, indSkip); ^ sortSuffixesBucket.cpp:86:62: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] memcpy(ind1+charStart[c]*indSkip, ind+id*indSkip, indSkip); ^ sortSuffixesBucket.cpp:87:32: warning: array subscript has type ‘char’ [-Wchar-subscripts] charStart[c]++; ^ sortSuffixesBucket.cpp:89:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] memcpy(ind+uB1[iu]*indSkip, ind1+uB1[iu]*indSkip, (uB2[iu]-uB1[iu])*indSkip); ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' funCompareUintAndSuffixesMemcmp.cpp funCompareUintAndSuffixesMemcmp.cpp: In function ‘int funCompareUintAndSuffixesMemcmp(const void*, const void*)’: funCompareUintAndSuffixesMemcmp.cpp:21:15: warning: unused variable ‘p5’ [-Wunused-variable] char *p5=g_funCompareUintAndSuffixesMemcmp_G+va[1]+g_funCompareUintAndSuffixesMemcmp_L; ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' loadGTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMoutput.cpp BAMoutput.cpp: In member function ‘void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)’: BAMoutput.cpp:62:47: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfBAM,bamArray,binBytes1); ^ BAMoutput.cpp: In member function ‘void BAMoutput::unsortedFlush()’: BAMoutput.cpp:75:43: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfBAM,bamArray,binBytes1); ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMfunctions.cpp BAMfunctions.cpp: In function ‘void outBAMwriteHeader(BGZF*, const string&, const std::vector >&, const std::vector&)’: BAMfunctions.cpp:76:31: 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,"BAM\001",4); ^ BAMfunctions.cpp:78:46: 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,(char*) &hlen,sizeof(hlen)); ^ BAMfunctions.cpp:79:37: 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,samh.c_str(),hlen); ^ BAMfunctions.cpp:81:46: 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,(char*) &nchr,sizeof(nchr)); ^ BAMfunctions.cpp:85:50: 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,(char*) &rlen,sizeof(rlen)); ^ BAMfunctions.cpp:86:47: 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,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string ^ BAMfunctions.cpp:87:50: 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,(char*) &slen,sizeof(slen)); ^ BAMfunctions.cpp:89:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(fp); ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMbinSortByCoordinate.cpp BAMbinSortByCoordinate.cpp: In function ‘void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::__cxx11::string, Parameters*)’: BAMbinSortByCoordinate.cpp:56:64: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfBin,ib, *((uint32*) ib)+sizeof(uint32) ); ^ BAMbinSortByCoordinate.cpp:59:24: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(bgzfBin); ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bamRemoveDuplicates.cpp bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::__cxx11::string, std::__cxx11::string, Parameters*)’: bamRemoveDuplicates.cpp:125:38: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result] bam_hdr_write(bgzfOut, bamHeader); ^ bamRemoveDuplicates.cpp:152:48: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfOut,bamRaw,bamS); ^ bamRemoveDuplicates.cpp:233:41: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfOut,bamRaw,bamLength); ^ bamRemoveDuplicates.cpp:234:24: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(bgzfOut); ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMbinSortUnmapped.cpp BAMbinSortUnmapped.cpp:5:78: warning: unused parameter ‘bgzfBAM’ [-Wunused-parameter] void BAMbinSortUnmapped(uint32 iBin, uint nThreads, string dirBAMsort, BGZF *bgzfBAM, Parameters *P) { ^ BAMbinSortUnmapped.cpp: In function ‘void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::__cxx11::string, BGZF*, Parameters*)’: BAMbinSortUnmapped.cpp:45:59: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfBin, bamIn[it], bamSize.at(it)); ^ BAMbinSortUnmapped.cpp:62:24: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(bgzfBin); ^ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -Wall -Wextra -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bam_cat.c bam_cat.c: In function ‘int bam_cat(int, char* const*, const bam_hdr_t*, const char*)’: bam_cat.c:80:32: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result] if (h) bam_hdr_write(fp, h); ^ bam_cat.c:96:53: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result] if (h == 0 && i == 0) bam_hdr_write(fp, old); ^ bam_cat.c:99:123: 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, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); ^ bam_cat.c:100:27: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(fp); ^ bam_cat.c:111:46: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_raw_write(fp, ebuf, len); ^ bam_cat.c:115:54: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] if(j!=0) bgzf_raw_write(fp, ebuf, es); ^ bam_cat.c:118:45: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_raw_write(fp, buf, len); ^ bam_cat.c:131:45: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] bgzf_raw_write(fp, ebuf, es); ^ g++ -o STAR -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security SharedMemory.o PackedArray.o SuffixArrayFuns.o STAR.o Parameters.o InOutStreams.o SequenceFuns.o Genome.o Stats.o Transcript.o Transcript_alignScore.o ReadAlign.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputAlignments.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_chimericDetection.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o sortSuffixesBucket.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o bam_cat.o GlobalVariables.cpp -pthread -Bstatic -lhts -Bdynamic -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now Parameters_openReadsFiles.cpp: In member function ‘void Parameters::openReadsFiles()’: Parameters_openReadsFiles.cpp:58:97: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(("ls -lL " + file1 + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); ^ Parameters_openReadsFiles.cpp: In member function ‘openReadsFiles’: Parameters_openReadsFiles.cpp:30:20: warning: variable ‘imate’ might be clobbered by ‘longjmp’ or ‘vfork’ [-Wclobbered] for (uint imate=0;imate>/rna-star-2.5.2a+dfsg/source' make[1]: Leaving directory '/<>/rna-star-2.5.2a+dfsg' dh_auto_test -a fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>/rna-star-2.5.2a+dfsg' dh_compress --exclude=.pdf make[1]: Leaving directory '/<>/rna-star-2.5.2a+dfsg' dh_fixperms -a dh_strip -a dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform s390x: rna-star dh_strip debug symbol extraction: packages to act on: rna-star dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform s390x: rna-star dh_gencontrol debug symbol wrapper: packages to act on: rna-star dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package rna-star (pkgdir debian/rna-star, ddeb package dir debian/rna-star-dbgsym) dh_gencontrol debug symbol wrapper: building rna-star-dbgsym_2.5.2a+dfsg-2_s390x.ddeb dpkg-deb: building package 'rna-star-dbgsym' in '../rna-star-dbgsym_2.5.2a+dfsg-2_s390x.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile rna-star-dbgsym_2.5.2a+dfsg-2_s390x.ddeb science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 129 pkgstriptranslations: processing rna-star (in debian/rna-star); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/rna-star/DEBIAN/control, package rna-star, directory debian/rna-star pkgstripfiles: Running PNG optimization (using 4 cpus) for package rna-star ... pkgstripfiles: No PNG files. dpkg-deb: building package 'rna-star' in '../rna-star_2.5.2a+dfsg-2_s390x.deb'. dpkg-genchanges --build=any -mLaunchpad Build Daemon >../rna-star_2.5.2a+dfsg-2_s390x.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build rna-star-2.5.2a+dfsg dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20160522-2317 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ rna-star_2.5.2a+dfsg-2_s390x.changes: ------------------------------------- Format: 1.8 Date: Sat, 21 May 2016 20:53:28 +0000 Source: rna-star Binary: rna-star Architecture: s390x Version: 2.5.2a+dfsg-2 Distribution: yakkety-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Sascha Steinbiss Description: rna-star - ultrafast universal RNA-seq aligner Changes: rna-star (2.5.2a+dfsg-2) unstable; urgency=medium . * Team upload. * Make build reproducible. - Stop recording build environment in binary. * Enable full hardening. Checksums-Sha1: 2d7ffcee3db10c09ee7c69956c48863703fb5847 678596 rna-star-dbgsym_2.5.2a+dfsg-2_s390x.ddeb 113095e77130cb040134cda76ace675d52644327 344872 rna-star_2.5.2a+dfsg-2_s390x.deb Checksums-Sha256: ea17d3e7423758f02e86267a020a781bfd4f338f56703dc1e2c4ad229f89f37a 678596 rna-star-dbgsym_2.5.2a+dfsg-2_s390x.ddeb 53e10a681956f2d7a0709b78341e587c45c4564eebfa6a48937e95b91c63d696 344872 rna-star_2.5.2a+dfsg-2_s390x.deb Files: 74502afda599884557fb668f5d16a4df 678596 science extra rna-star-dbgsym_2.5.2a+dfsg-2_s390x.ddeb f2d6f3713b6e9a147c4ba0d3ff381d06 344872 science optional rna-star_2.5.2a+dfsg-2_s390x.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ rna-star_2.5.2a+dfsg-2_s390x.deb -------------------------------- new debian package, version 2.0. size 344872 bytes: control archive=1339 bytes. 1450 bytes, 25 lines control 602 bytes, 9 lines md5sums Package: rna-star Version: 2.5.2a+dfsg-2 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 795 Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.3.1), libgomp1 (>= 4.9), libhts1 (>= 1.0), libstdc++6 (>= 5.2) Section: science Priority: optional Homepage: https://github.com/alexdobin/STAR/ Description: ultrafast universal RNA-seq aligner Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, the authors experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. drwxr-xr-x root/root 0 2016-05-22 23:17 ./ drwxr-xr-x root/root 0 2016-05-22 23:17 ./usr/ drwxr-xr-x root/root 0 2016-05-22 23:17 ./usr/bin/ -rwxr-xr-x root/root 535768 2016-05-22 23:17 ./usr/bin/STAR drwxr-xr-x root/root 0 2016-05-22 23:17 ./usr/share/ drwxr-xr-x root/root 0 2016-05-22 23:17 ./usr/share/doc-base/ -rw-r--r-- root/root 1179 2016-05-21 20:57 ./usr/share/doc-base/rna-star drwxr-xr-x root/root 0 2016-05-22 23:17 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-05-22 23:17 ./usr/share/doc/rna-star/ -rw-r--r-- root/root 220 2016-05-21 20:57 ./usr/share/doc/rna-star/README.Debian -rw-r--r-- root/root 3196 2016-05-10 21:41 ./usr/share/doc/rna-star/README.md -rw-r--r-- root/root 2119 2016-05-10 21:41 ./usr/share/doc/rna-star/RELEASEnotes.md.gz -rw-r--r-- root/root 251507 2016-05-10 21:41 ./usr/share/doc/rna-star/STARmanual.pdf -rw-r--r-- root/root 849 2016-05-21 21:05 ./usr/share/doc/rna-star/changelog.Debian.gz -rw-r--r-- root/root 2444 2016-05-21 20:57 ./usr/share/doc/rna-star/copyright drwxr-xr-x root/root 0 2016-05-22 23:17 ./usr/share/man/ drwxr-xr-x root/root 0 2016-05-22 23:17 ./usr/share/man/man1/ -rw-r--r-- root/root 814 2016-05-22 23:17 ./usr/share/man/man1/STAR.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 19804 Build-Time: 53 Distribution: yakkety-proposed Host Architecture: s390x Install-Time: 12 Job: rna-star_2.5.2a+dfsg-2.dsc Machine Architecture: s390x Package: rna-star Package-Time: 66 Source-Version: 2.5.2a+dfsg-2 Space: 19804 Status: successful Version: 2.5.2a+dfsg-2 -------------------------------------------------------------------------------- Finished at 20160522-2317 Build needed 00:01:06, 19804k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-9789456'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-9789456/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-9789456'] Unmounting chroot for build PACKAGEBUILD-9789456... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-9789456'] Removing build PACKAGEBUILD-9789456