RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux bos01-ppc64el-012 4.2.0-23-generic #28-Ubuntu SMP Sun Dec 27 17:46:45 UTC 2015 ppc64le Buildd toolchain package versions: launchpad-buildd_136 python-lpbuildd_136 sbuild_0.65.2-1ubuntu2+ubuntu15.10.2 bzr-builder_0.7.3-0ubuntu1 bzr_2.6.0+bzr6602-2ubuntu4 dpkg-dev_1.18.2ubuntu5.1 python-debian_0.1.27ubuntu1. Syncing the system clock with the buildd NTP service... 18 Jan 17:10:02 ntpdate[1550]: adjust time server 10.211.37.1 offset 0.300219 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-8865980', '/home/buildd/filecache-default/64ba6963cee521707036a0c48846d736532c58ef'] Unpacking chroot for build PACKAGEBUILD-8865980 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-8865980'] Mounting chroot for build PACKAGEBUILD-8865980 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-8865980', 'deb http://ftpmaster.internal/ubuntu xenial main universe', 'deb http://ftpmaster.internal/ubuntu xenial-security main universe', 'deb http://ftpmaster.internal/ubuntu xenial-updates main universe', 'deb http://ftpmaster.internal/ubuntu xenial-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-8865980 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-8865980', 'ppc64el'] Updating debian chroot for build PACKAGEBUILD-8865980 Get:1 http://ftpmaster.internal xenial InRelease [227 kB] Get:2 http://ftpmaster.internal xenial-security InRelease [73.5 kB] Get:3 http://ftpmaster.internal xenial-updates InRelease [73.5 kB] Get:4 http://ftpmaster.internal xenial-proposed InRelease [227 kB] Get:5 http://ftpmaster.internal xenial/main ppc64el Packages [1428 kB] Get:6 http://ftpmaster.internal xenial/universe ppc64el Packages [6962 kB] Get:7 http://ftpmaster.internal xenial/main Translation-en [852 kB] Get:8 http://ftpmaster.internal xenial/universe Translation-en [4811 kB] Get:9 http://ftpmaster.internal xenial-security/main ppc64el Packages [28 B] Get:10 http://ftpmaster.internal xenial-security/universe ppc64el Packages [28 B] Get:11 http://ftpmaster.internal xenial-security/main Translation-en [28 B] Get:12 http://ftpmaster.internal xenial-security/universe Translation-en [28 B] Get:13 http://ftpmaster.internal xenial-updates/main ppc64el Packages [28 B] Get:14 http://ftpmaster.internal xenial-updates/universe ppc64el Packages [28 B] Get:15 http://ftpmaster.internal xenial-updates/main Translation-en [28 B] Get:16 http://ftpmaster.internal xenial-updates/universe Translation-en [28 B] Get:17 http://ftpmaster.internal xenial-proposed/main ppc64el Packages [49.3 kB] Get:18 http://ftpmaster.internal xenial-proposed/universe ppc64el Packages [297 kB] Get:19 http://ftpmaster.internal xenial-proposed/main Translation-en [31.6 kB] Get:20 http://ftpmaster.internal xenial-proposed/universe Translation-en [166 kB] Fetched 15.2 MB in 5s (2746 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 libprocps3 udev Use 'apt-get autoremove' to remove them. The following packages will be REMOVED: perl-modules* The following NEW packages will be installed: libapt-pkg5.0 libisl15 libperl5.22 libprocps4 perl-modules-5.22 The following packages will be upgraded: advancecomp apt apt-transport-https base-files base-passwd binutils bsdutils cpp cpp-5 debconf diffutils dmsetup dpkg dpkg-dev e2fslibs e2fsprogs findutils g++ g++-5 gcc gcc-5 gcc-5-base gnupg gpgv grep hostname init initscripts libapparmor1 libasan2 libatomic1 libaudit-common libaudit1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcap2-bin libcc1-0 libcomerr2 libcurl3-gnutls libdbus-1-3 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfdisk1 libffi6 libgcc-5-dev libgcc1 libgcrypt20 libgmp10 libgnutls-deb0-28 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn11 libitm1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libmount1 libmpfr4 libncurses5 libncursesw5 libnih-dbus1 libnih1 libp11-kit0 libpcre3 libpng12-0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libubsan0 libudev1 libusb-0.1-4 libuuid1 linux-libc-dev lsb-base make mount multiarch-support ncurses-base ncurses-bin openssl perl perl-base pkg-create-dbgsym pkgbinarymangler procps systemd systemd-sysv sysv-rc sysvinit-utils tar udev util-linux 111 upgraded, 5 newly installed, 1 to remove and 0 not upgraded. Need to get 129 MB of archives. After this operation, 331 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ xenial/main base-files ppc64el 9.4ubuntu3 [67.8 kB] Get:2 http://ftpmaster.internal/ubuntu/ xenial/main bsdutils ppc64el 1:2.27.1-1ubuntu3 [50.1 kB] Get:3 http://ftpmaster.internal/ubuntu/ xenial/main diffutils ppc64el 1:3.3-3 [158 kB] Get:4 http://ftpmaster.internal/ubuntu/ xenial/main dpkg ppc64el 1.18.4ubuntu1 [2099 kB] Get:5 http://ftpmaster.internal/ubuntu/ xenial/main libc6-dev ppc64el 2.21-0ubuntu5 [1994 kB] Get:6 http://ftpmaster.internal/ubuntu/ xenial/main libc-dev-bin ppc64el 2.21-0ubuntu5 [64.9 kB] Get:7 http://ftpmaster.internal/ubuntu/ xenial-proposed/main linux-libc-dev ppc64el 4.3.0-6.17 [810 kB] Get:8 http://ftpmaster.internal/ubuntu/ xenial/main libcap2 ppc64el 1:2.24-12 [13.3 kB] Get:9 http://ftpmaster.internal/ubuntu/ xenial/main libc-bin ppc64el 2.21-0ubuntu5 [1168 kB] Get:10 http://ftpmaster.internal/ubuntu/ xenial/main libgomp1 ppc64el 5.3.1-6ubuntu1 [50.3 kB] Get:11 http://ftpmaster.internal/ubuntu/ xenial/main libitm1 ppc64el 5.3.1-6ubuntu1 [27.3 kB] Get:12 http://ftpmaster.internal/ubuntu/ xenial/main libatomic1 ppc64el 5.3.1-6ubuntu1 [7950 B] Get:13 http://ftpmaster.internal/ubuntu/ xenial/main libasan2 ppc64el 5.3.1-6ubuntu1 [237 kB] Get:14 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5-base ppc64el 5.3.1-6ubuntu1 [16.5 kB] Get:15 http://ftpmaster.internal/ubuntu/ xenial/main libgcc1 ppc64el 1:5.3.1-6ubuntu1 [27.5 kB] Get:16 http://ftpmaster.internal/ubuntu/ xenial/main libubsan0 ppc64el 5.3.1-6ubuntu1 [95.9 kB] Get:17 http://ftpmaster.internal/ubuntu/ xenial/main libisl15 ppc64el 0.15-3 [497 kB] Get:18 http://ftpmaster.internal/ubuntu/ xenial/main cpp-5 ppc64el 5.3.1-6ubuntu1 [27.9 MB] Get:19 http://ftpmaster.internal/ubuntu/ xenial/main libcc1-0 ppc64el 5.3.1-6ubuntu1 [43.6 kB] Get:20 http://ftpmaster.internal/ubuntu/ xenial/main binutils ppc64el 2.25.90.20160101-1ubuntu2 [2206 kB] Get:21 http://ftpmaster.internal/ubuntu/ xenial/main g++-5 ppc64el 5.3.1-6ubuntu1 [30.1 MB] Get:22 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5 ppc64el 5.3.1-6ubuntu1 [28.3 MB] Get:23 http://ftpmaster.internal/ubuntu/ xenial/main libgcc-5-dev ppc64el 5.3.1-6ubuntu1 [583 kB] Get:24 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++-5-dev ppc64el 5.3.1-6ubuntu1 [1416 kB] Get:25 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++6 ppc64el 5.3.1-6ubuntu1 [410 kB] Get:26 http://ftpmaster.internal/ubuntu/ xenial/main libgmp10 ppc64el 2:6.1.0+dfsg-2 [226 kB] Get:27 http://ftpmaster.internal/ubuntu/ xenial/main libmpfr4 ppc64el 3.1.3-2 [184 kB] Get:28 http://ftpmaster.internal/ubuntu/ xenial/main libc6 ppc64el 2.21-0ubuntu5 [5184 kB] Get:29 http://ftpmaster.internal/ubuntu/ xenial/main e2fslibs ppc64el 1.42.13-1ubuntu1 [192 kB] Get:30 http://ftpmaster.internal/ubuntu/ xenial/main e2fsprogs ppc64el 1.42.13-1ubuntu1 [763 kB] Get:31 http://ftpmaster.internal/ubuntu/ xenial/main findutils ppc64el 4.6.0-2 [289 kB] Get:32 http://ftpmaster.internal/ubuntu/ xenial-proposed/main grep ppc64el 2.22-1 [143 kB] Get:33 http://ftpmaster.internal/ubuntu/ xenial/main hostname ppc64el 3.16ubuntu2 [11.4 kB] Get:34 http://ftpmaster.internal/ubuntu/ xenial/main init ppc64el 1.24ubuntu2 [3970 B] Get:35 http://ftpmaster.internal/ubuntu/ xenial/main libsmartcols1 ppc64el 2.27.1-1ubuntu3 [58.0 kB] Get:36 http://ftpmaster.internal/ubuntu/ xenial/main libuuid1 ppc64el 2.27.1-1ubuntu3 [15.0 kB] Get:37 http://ftpmaster.internal/ubuntu/ xenial/main libblkid1 ppc64el 2.27.1-1ubuntu3 [99.2 kB] Get:38 http://ftpmaster.internal/ubuntu/ xenial/main libfdisk1 ppc64el 2.27.1-1ubuntu3 [129 kB] Get:39 http://ftpmaster.internal/ubuntu/ xenial/main debconf all 1.5.58ubuntu1 [136 kB] Get:40 http://ftpmaster.internal/ubuntu/ xenial/main sysvinit-utils ppc64el 2.88dsf-59.2ubuntu3 [25.7 kB] Get:41 http://ftpmaster.internal/ubuntu/ xenial/main sysv-rc all 2.88dsf-59.2ubuntu3 [36.1 kB] Get:42 http://ftpmaster.internal/ubuntu/ xenial/main initscripts ppc64el 2.88dsf-59.2ubuntu3 [24.8 kB] Get:43 http://ftpmaster.internal/ubuntu/ xenial/main util-linux ppc64el 2.27.1-1ubuntu3 [803 kB] Get:44 http://ftpmaster.internal/ubuntu/ xenial/main libudev1 ppc64el 228-4ubuntu1 [55.2 kB] Get:45 http://ftpmaster.internal/ubuntu/ xenial/main udev ppc64el 228-4ubuntu1 [971 kB] Get:46 http://ftpmaster.internal/ubuntu/ xenial/main libsystemd0 ppc64el 228-4ubuntu1 [197 kB] Get:47 http://ftpmaster.internal/ubuntu/ xenial/main systemd ppc64el 228-4ubuntu1 [3599 kB] Get:48 http://ftpmaster.internal/ubuntu/ xenial/main libpcre3 ppc64el 2:8.38-1ubuntu1 [220 kB] Get:49 http://ftpmaster.internal/ubuntu/ xenial/main libselinux1 ppc64el 2.4-3 [54.7 kB] Get:50 http://ftpmaster.internal/ubuntu/ xenial/main libtinfo5 ppc64el 6.0+20151024-2ubuntu1 [79.4 kB] Get:51 http://ftpmaster.internal/ubuntu/ xenial/main libncurses5 ppc64el 6.0+20151024-2ubuntu1 [97.2 kB] Get:52 http://ftpmaster.internal/ubuntu/ xenial/main libncursesw5 ppc64el 6.0+20151024-2ubuntu1 [111 kB] Get:53 http://ftpmaster.internal/ubuntu/ xenial/main libprocps4 ppc64el 2:3.3.10-4ubuntu2 [32.2 kB] Get:54 http://ftpmaster.internal/ubuntu/ xenial/main procps ppc64el 2:3.3.10-4ubuntu2 [221 kB] Get:55 http://ftpmaster.internal/ubuntu/ xenial/main libapparmor1 ppc64el 2.10-0ubuntu10 [28.5 kB] Get:56 http://ftpmaster.internal/ubuntu/ xenial/main libaudit-common all 1:2.4.5-1ubuntu1 [3880 B] Get:57 http://ftpmaster.internal/ubuntu/ xenial/main libaudit1 ppc64el 1:2.4.5-1ubuntu1 [38.8 kB] Get:58 http://ftpmaster.internal/ubuntu/ xenial/main libmount1 ppc64el 2.27.1-1ubuntu3 [104 kB] Get:59 http://ftpmaster.internal/ubuntu/ xenial/main libseccomp2 ppc64el 2.2.3-2ubuntu3 [42.1 kB] Get:60 http://ftpmaster.internal/ubuntu/ xenial/main libcap2-bin ppc64el 1:2.24-12 [20.1 kB] Get:61 http://ftpmaster.internal/ubuntu/ xenial/main lsb-base all 9.20160110 [13.5 kB] Get:62 http://ftpmaster.internal/ubuntu/ xenial/main mount ppc64el 2.27.1-1ubuntu3 [115 kB] Get:63 http://ftpmaster.internal/ubuntu/ xenial/main ncurses-bin ppc64el 6.0+20151024-2ubuntu1 [136 kB] Get:64 http://ftpmaster.internal/ubuntu/ xenial/main perl-modules-5.22 all 5.22.1-4 [2648 kB] Get:65 http://ftpmaster.internal/ubuntu/ xenial/main libperl5.22 ppc64el 5.22.1-4 [3192 kB] Get:66 http://ftpmaster.internal/ubuntu/ xenial/main perl ppc64el 5.22.1-4 [237 kB] Get:67 http://ftpmaster.internal/ubuntu/ xenial/main perl-base ppc64el 5.22.1-4 [1181 kB] Get:68 http://ftpmaster.internal/ubuntu/ xenial/main tar ppc64el 1.28-2.1 [222 kB] Get:69 http://ftpmaster.internal/ubuntu/ xenial/main libapt-pkg5.0 ppc64el 1.1.10 [723 kB] Get:70 http://ftpmaster.internal/ubuntu/ xenial/main apt ppc64el 1.1.10 [1000 kB] Get:71 http://ftpmaster.internal/ubuntu/ xenial/main gpgv ppc64el 1.4.19-6ubuntu1 [176 kB] Get:72 http://ftpmaster.internal/ubuntu/ xenial/main libusb-0.1-4 ppc64el 2:0.1.12-28 [15.9 kB] Get:73 http://ftpmaster.internal/ubuntu/ xenial/main gnupg ppc64el 1.4.19-6ubuntu1 [658 kB] Get:74 http://ftpmaster.internal/ubuntu/ xenial/main libdebconfclient0 ppc64el 0.198ubuntu1 [6282 B] Get:75 http://ftpmaster.internal/ubuntu/ xenial/main base-passwd ppc64el 3.5.39 [53.8 kB] Get:76 http://ftpmaster.internal/ubuntu/ xenial/main ncurses-base all 6.0+20151024-2ubuntu1 [17.1 kB] Get:77 http://ftpmaster.internal/ubuntu/ xenial/main systemd-sysv ppc64el 228-4ubuntu1 [15.5 kB] Get:78 http://ftpmaster.internal/ubuntu/ xenial/main libdbus-1-3 ppc64el 1.10.6-1ubuntu1 [156 kB] Get:79 http://ftpmaster.internal/ubuntu/ xenial/main libnih-dbus1 ppc64el 1.0.3-4.3ubuntu1 [13.2 kB] Get:80 http://ftpmaster.internal/ubuntu/ xenial/main libnih1 ppc64el 1.0.3-4.3ubuntu1 [44.9 kB] Get:81 http://ftpmaster.internal/ubuntu/ xenial/main libffi6 ppc64el 3.2.1-4 [19.8 kB] Get:82 http://ftpmaster.internal/ubuntu/ xenial/main libp11-kit0 ppc64el 0.23.2-3 [105 kB] Get:83 http://ftpmaster.internal/ubuntu/ xenial/main libtasn1-6 ppc64el 4.7-3 [42.9 kB] Get:84 http://ftpmaster.internal/ubuntu/ xenial/main libgnutls-deb0-28 ppc64el 3.3.18-1ubuntu1 [444 kB] Get:85 http://ftpmaster.internal/ubuntu/ xenial/main libldap-2.4-2 ppc64el 2.4.41+dfsg-1ubuntu3 [151 kB] Get:86 http://ftpmaster.internal/ubuntu/ xenial/main libcomerr2 ppc64el 1.42.13-1ubuntu1 [65.6 kB] Get:87 http://ftpmaster.internal/ubuntu/ xenial/main libdevmapper1.02.1 ppc64el 2:1.02.110-1ubuntu2 [134 kB] Get:88 http://ftpmaster.internal/ubuntu/ xenial/main libgpg-error0 ppc64el 1.21-1 [37.0 kB] Get:89 http://ftpmaster.internal/ubuntu/ xenial/main libgcrypt20 ppc64el 1.6.4-4 [355 kB] Get:90 http://ftpmaster.internal/ubuntu/ xenial/main libsepol1 ppc64el 2.4-2 [172 kB] Get:91 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage-common all 2.4-3 [6744 B] Get:92 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage1 ppc64el 2.4-3 [73.0 kB] Get:93 http://ftpmaster.internal/ubuntu/ xenial/main libss2 ppc64el 1.42.13-1ubuntu1 [69.6 kB] Get:94 http://ftpmaster.internal/ubuntu/ xenial/main multiarch-support ppc64el 2.21-0ubuntu5 [7186 B] Get:95 http://ftpmaster.internal/ubuntu/ xenial/main libpng12-0 ppc64el 1.2.54-1ubuntu1 [120 kB] Get:96 http://ftpmaster.internal/ubuntu/ xenial/main libsqlite3-0 ppc64el 3.10.1-1 [361 kB] Get:97 http://ftpmaster.internal/ubuntu/ xenial/main libssl1.0.0 ppc64el 1.0.2e-1ubuntu1 [830 kB] Get:98 http://ftpmaster.internal/ubuntu/ xenial/main dmsetup ppc64el 2:1.02.110-1ubuntu2 [56.8 kB] Get:99 http://ftpmaster.internal/ubuntu/ xenial/main libgssapi-krb5-2 ppc64el 1.13.2+dfsg-4 [109 kB] Get:100 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5-3 ppc64el 1.13.2+dfsg-4 [269 kB] Get:101 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5support0 ppc64el 1.13.2+dfsg-4 [29.7 kB] Get:102 http://ftpmaster.internal/ubuntu/ xenial/main libk5crypto3 ppc64el 1.13.2+dfsg-4 [98.3 kB] Get:103 http://ftpmaster.internal/ubuntu/ xenial/main libkeyutils1 ppc64el 1.5.9-8ubuntu1 [9812 B] Get:104 http://ftpmaster.internal/ubuntu/ xenial/main libidn11 ppc64el 1.32-3ubuntu1 [45.6 kB] Get:105 http://ftpmaster.internal/ubuntu/ xenial/main libcurl3-gnutls ppc64el 7.45.0-1ubuntu1 [175 kB] Get:106 http://ftpmaster.internal/ubuntu/ xenial/main apt-transport-https ppc64el 1.1.10 [30.0 kB] Get:107 http://ftpmaster.internal/ubuntu/ xenial/main openssl ppc64el 1.0.2e-1ubuntu1 [480 kB] Get:108 http://ftpmaster.internal/ubuntu/ xenial/main advancecomp ppc64el 1.20-1 [201 kB] Get:109 http://ftpmaster.internal/ubuntu/ xenial/main cpp ppc64el 4:5.2.1-16ubuntu2 [27.6 kB] Get:110 http://ftpmaster.internal/ubuntu/ xenial/main dpkg-dev all 1.18.4ubuntu1 [584 kB] Get:111 http://ftpmaster.internal/ubuntu/ xenial/main libdpkg-perl all 1.18.4ubuntu1 [195 kB] Get:112 http://ftpmaster.internal/ubuntu/ xenial-proposed/main make ppc64el 4.1-1 [150 kB] Get:113 http://ftpmaster.internal/ubuntu/ xenial/main gcc ppc64el 4:5.2.1-16ubuntu2 [5224 B] Get:114 http://ftpmaster.internal/ubuntu/ xenial/main g++ ppc64el 4:5.2.1-16ubuntu2 [1502 B] Get:115 http://ftpmaster.internal/ubuntu/ xenial/main pkg-create-dbgsym all 0.70 [9046 B] Get:116 http://ftpmaster.internal/ubuntu/ xenial/main pkgbinarymangler all 128 [42.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 129 MB in 4s (29.4 MB/s) (Reading database ... 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Updating /etc/profile to current default. Updating /etc/nsswitch.conf to current default. Updating /root/.profile to current default. (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 ... 11575 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.27.1-1ubuntu3_ppc64el.deb ... Unpacking bsdutils (1:2.27.1-1ubuntu3) over (1:2.26.2-6ubuntu3) ... Setting up bsdutils (1:2.27.1-1ubuntu3) ... (Reading database ... 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Preparing to unpack .../e2fslibs_1.42.13-1ubuntu1_ppc64el.deb ... Unpacking e2fslibs:ppc64el (1.42.13-1ubuntu1) over (1.42.12-1ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up e2fslibs:ppc64el (1.42.13-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 11551 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.42.13-1ubuntu1_ppc64el.deb ... Unpacking e2fsprogs (1.42.13-1ubuntu1) over (1.42.12-1ubuntu2) ... Setting up e2fsprogs (1.42.13-1ubuntu1) ... Installing new version of config file /etc/mke2fs.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 ... 11552 files and directories currently installed.) Preparing to unpack .../findutils_4.6.0-2_ppc64el.deb ... Unpacking findutils (4.6.0-2) over (4.4.2-9build1) ... Setting up findutils (4.6.0-2) ... (Reading database ... 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(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 ... 11560 files and directories currently installed.) Preparing to unpack .../systemd_228-4ubuntu1_ppc64el.deb ... Unpacking systemd (228-4ubuntu1) over (225-1ubuntu9) ... Setting up systemd (228-4ubuntu1) ... Installing new version of config file /etc/pam.d/systemd-user ... Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/system.conf ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. Removing obsolete conffile /etc/X11/xinit/xinitrc.d/50-systemd-user.sh ... (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 ... 11557 files and directories currently installed.) Preparing to unpack .../libpcre3_2%3a8.38-1ubuntu1_ppc64el.deb ... Unpacking libpcre3:ppc64el (2:8.38-1ubuntu1) over (2:8.35-7.1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libpcre3:ppc64el (2:8.38-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 11557 files and directories currently installed.) Preparing to unpack .../libselinux1_2.4-3_ppc64el.deb ... Unpacking libselinux1:ppc64el (2.4-3) over (2.3-2build1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libselinux1:ppc64el (2.4-3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 11557 files and directories currently installed.) Preparing to unpack .../libtinfo5_6.0+20151024-2ubuntu1_ppc64el.deb ... Unpacking libtinfo5:ppc64el (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libtinfo5:ppc64el (6.0+20151024-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 11557 files and directories currently installed.) Preparing to unpack .../libncurses5_6.0+20151024-2ubuntu1_ppc64el.deb ... Unpacking libncurses5:ppc64el (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libncurses5:ppc64el (6.0+20151024-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 11557 files and directories currently installed.) Preparing to unpack .../libncursesw5_6.0+20151024-2ubuntu1_ppc64el.deb ... Unpacking libncursesw5:ppc64el (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libncursesw5:ppc64el (6.0+20151024-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Selecting previously unselected package libprocps4:ppc64el. (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 ... 11557 files and directories currently installed.) Preparing to unpack .../libprocps4_2%3a3.3.10-4ubuntu2_ppc64el.deb ... Unpacking libprocps4:ppc64el (2:3.3.10-4ubuntu2) ... Preparing to unpack .../procps_2%3a3.3.10-4ubuntu2_ppc64el.deb ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of stop. Unpacking procps (2:3.3.10-4ubuntu2) over (1:3.3.9-1ubuntu8) ... Preparing to unpack .../libapparmor1_2.10-0ubuntu10_ppc64el.deb ... Unpacking libapparmor1:ppc64el (2.10-0ubuntu10) over (2.10-0ubuntu6) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libapparmor1:ppc64el (2.10-0ubuntu10) ... Processing triggers for systemd (228-4ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 11566 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a2.4.5-1ubuntu1_all.deb ... Unpacking libaudit-common (1:2.4.5-1ubuntu1) over (1:2.4.2-1ubuntu1) ... Setting up libaudit-common (1:2.4.5-1ubuntu1) ... (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 ... 11566 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a2.4.5-1ubuntu1_ppc64el.deb ... Unpacking libaudit1:ppc64el (1:2.4.5-1ubuntu1) over (1:2.4.2-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libaudit1:ppc64el (1:2.4.5-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 11566 files and directories currently installed.) Preparing to unpack .../libmount1_2.27.1-1ubuntu3_ppc64el.deb ... Unpacking libmount1:ppc64el (2.27.1-1ubuntu3) over (2.26.2-6ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libmount1:ppc64el (2.27.1-1ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 11566 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.2.3-2ubuntu3_ppc64el.deb ... Unpacking libseccomp2:ppc64el (2.2.3-2ubuntu3) over (2.2.3-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libseccomp2:ppc64el (2.2.3-2ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 11566 files and directories currently installed.) Preparing to unpack .../libcap2-bin_1%3a2.24-12_ppc64el.deb ... Unpacking libcap2-bin (1:2.24-12) over (1:2.24-9) ... Setting up libcap2-bin (1:2.24-12) ... (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 ... 11562 files and directories currently installed.) Removing perl-modules (5.20.2-6) ... Purging configuration files for perl-modules (5.20.2-6) ... (Reading database ... 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Unpacking libperl5.22:ppc64el (5.22.1-4) ... Preparing to unpack .../perl-base_5.22.1-4_ppc64el.deb ... Unpacking perl-base (5.22.1-4) over (5.20.2-6) ... Setting up perl-base (5.22.1-4) ... (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 ... 12138 files and directories currently installed.) Preparing to unpack .../tar_1.28-2.1_ppc64el.deb ... Unpacking tar (1.28-2.1) over (1.27.1-2) ... Setting up tar (1.28-2.1) ... (Reading database ... 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Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 12166 files and directories currently installed.) Preparing to unpack .../gpgv_1.4.19-6ubuntu1_ppc64el.deb ... Unpacking gpgv (1.4.19-6ubuntu1) over (1.4.18-7ubuntu1) ... Setting up gpgv (1.4.19-6ubuntu1) ... (Reading database ... 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Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 12165 files and directories currently installed.) Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.110-1ubuntu2_ppc64el.deb ... Unpacking libdevmapper1.02.1:ppc64el (2:1.02.110-1ubuntu2) over (2:1.02.99-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libdevmapper1.02.1:ppc64el (2:1.02.110-1ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 12165 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.21-1_ppc64el.deb ... Unpacking libgpg-error0:ppc64el (1.21-1) over (1.19-2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libgpg-error0:ppc64el (1.21-1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 12165 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.6.4-4_ppc64el.deb ... Unpacking libgcrypt20:ppc64el (1.6.4-4) over (1.6.3-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libgcrypt20:ppc64el (1.6.4-4) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 12165 files and directories currently installed.) Preparing to unpack .../libsepol1_2.4-2_ppc64el.deb ... Unpacking libsepol1:ppc64el (2.4-2) over (2.3-2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libsepol1:ppc64el (2.4-2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 12165 files and directories currently installed.) Preparing to unpack .../libss2_1.42.13-1ubuntu1_ppc64el.deb ... Unpacking libss2:ppc64el (1.42.13-1ubuntu1) over (1.42.12-1ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libss2:ppc64el (1.42.13-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 12165 files and directories currently installed.) Preparing to unpack .../multiarch-support_2.21-0ubuntu5_ppc64el.deb ... Unpacking multiarch-support (2.21-0ubuntu5) over (2.21-0ubuntu4) ... Setting up multiarch-support (2.21-0ubuntu5) ... (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 ... 12165 files and directories currently installed.) Preparing to unpack .../libpng12-0_1.2.54-1ubuntu1_ppc64el.deb ... Unpacking libpng12-0:ppc64el (1.2.54-1ubuntu1) over (1.2.51-0ubuntu3) ... Preparing to unpack .../libsqlite3-0_3.10.1-1_ppc64el.deb ... Unpacking libsqlite3-0:ppc64el (3.10.1-1) over (3.8.11.1-1) ... Preparing to unpack .../libssl1.0.0_1.0.2e-1ubuntu1_ppc64el.deb ... Unpacking libssl1.0.0:ppc64el (1.0.2e-1ubuntu1) over (1.0.2d-0ubuntu1) ... Preparing to unpack .../dmsetup_2%3a1.02.110-1ubuntu2_ppc64el.deb ... Unpacking dmsetup (2:1.02.110-1ubuntu2) over (2:1.02.99-1ubuntu1) ... Preparing to unpack .../libgssapi-krb5-2_1.13.2+dfsg-4_ppc64el.deb ... Unpacking libgssapi-krb5-2:ppc64el (1.13.2+dfsg-4) over (1.13.2+dfsg-2) ... Preparing to unpack .../libkrb5-3_1.13.2+dfsg-4_ppc64el.deb ... Unpacking libkrb5-3:ppc64el (1.13.2+dfsg-4) over (1.13.2+dfsg-2) ... Preparing to unpack .../libkrb5support0_1.13.2+dfsg-4_ppc64el.deb ... Unpacking libkrb5support0:ppc64el (1.13.2+dfsg-4) over (1.13.2+dfsg-2) ... Preparing to unpack .../libk5crypto3_1.13.2+dfsg-4_ppc64el.deb ... Unpacking libk5crypto3:ppc64el (1.13.2+dfsg-4) over (1.13.2+dfsg-2) ... Preparing to unpack .../libkeyutils1_1.5.9-8ubuntu1_ppc64el.deb ... Unpacking libkeyutils1:ppc64el (1.5.9-8ubuntu1) over (1.5.9-5ubuntu1) ... Preparing to unpack .../libidn11_1.32-3ubuntu1_ppc64el.deb ... 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Preparing to unpack .../make_4.1-1_ppc64el.deb ... Unpacking make (4.1-1) over (4.0-8.2) ... Preparing to unpack .../gcc_4%3a5.2.1-16ubuntu2_ppc64el.deb ... Removing old gcc doc directory. Unpacking gcc (4:5.2.1-16ubuntu2) over (4:5.2.1-3ubuntu1) ... Preparing to unpack .../g++_4%3a5.2.1-16ubuntu2_ppc64el.deb ... Unpacking g++ (4:5.2.1-16ubuntu2) over (4:5.2.1-3ubuntu1) ... Preparing to unpack .../pkg-create-dbgsym_0.70_all.deb ... Unpacking pkg-create-dbgsym (0.70) over (0.69) ... Preparing to unpack .../pkgbinarymangler_128_all.deb ... Unpacking pkgbinarymangler (128) over (122) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libc-dev-bin (2.21-0ubuntu5) ... Setting up linux-libc-dev:ppc64el (4.3.0-6.17) ... Setting up libc6-dev:ppc64el (2.21-0ubuntu5) ... Setting up libgomp1:ppc64el (5.3.1-6ubuntu1) ... Setting up libitm1:ppc64el (5.3.1-6ubuntu1) ... Setting up libatomic1:ppc64el (5.3.1-6ubuntu1) ... Setting up libasan2:ppc64el (5.3.1-6ubuntu1) ... Setting up libubsan0:ppc64el (5.3.1-6ubuntu1) ... Setting up libgmp10:ppc64el (2:6.1.0+dfsg-2) ... Setting up libisl15:ppc64el (0.15-3) ... Setting up libmpfr4:ppc64el (3.1.3-2) ... Setting up cpp-5 (5.3.1-6ubuntu1) ... Setting up libcc1-0:ppc64el (5.3.1-6ubuntu1) ... Setting up binutils (2.25.90.20160101-1ubuntu2) ... Setting up libgcc-5-dev:ppc64el (5.3.1-6ubuntu1) ... Setting up gcc-5 (5.3.1-6ubuntu1) ... Setting up libstdc++-5-dev:ppc64el (5.3.1-6ubuntu1) ... Setting up g++-5 (5.3.1-6ubuntu1) ... Setting up libprocps4:ppc64el (2:3.3.10-4ubuntu2) ... Setting up procps (2:3.3.10-4ubuntu2) ... 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 udev (228-4ubuntu1) ... Installing new version of config file /etc/init.d/udev ... addgroup: The group `input' already exists as a system group. Exiting. virtio network devices detected, disabling predictable interface names in /etc/systemd/network/50-virtio-kernel-names.link Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Removing obsolete conffile /etc/init.d/lvm2 ... Setting up perl-modules-5.22 (5.22.1-4) ... Setting up libperl5.22:ppc64el (5.22.1-4) ... Setting up perl (5.22.1-4) ... Setting up apt (1.1.10) ... Installing new version of config file /etc/apt/apt.conf.d/01-vendor-ubuntu ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt ... Installing new version of config file /etc/kernel/postinst.d/apt-auto-removal ... usermod: no changes Setting up libdbus-1-3:ppc64el (1.10.6-1ubuntu1) ... Setting up libnih1:ppc64el (1.0.3-4.3ubuntu1) ... Setting up libnih-dbus1:ppc64el (1.0.3-4.3ubuntu1) ... Setting up libffi6:ppc64el (3.2.1-4) ... Setting up libp11-kit0:ppc64el (0.23.2-3) ... Setting up libtasn1-6:ppc64el (4.7-3) ... Setting up libgnutls-deb0-28:ppc64el (3.3.18-1ubuntu1) ... Setting up libldap-2.4-2:ppc64el (2.4.41+dfsg-1ubuntu3) ... Setting up libpng12-0:ppc64el (1.2.54-1ubuntu1) ... Setting up libsqlite3-0:ppc64el (3.10.1-1) ... Setting up libssl1.0.0:ppc64el (1.0.2e-1ubuntu1) ... Setting up dmsetup (2:1.02.110-1ubuntu2) ... Setting up libkrb5support0:ppc64el (1.13.2+dfsg-4) ... Setting up libk5crypto3:ppc64el (1.13.2+dfsg-4) ... Setting up libkeyutils1:ppc64el (1.5.9-8ubuntu1) ... Setting up libkrb5-3:ppc64el (1.13.2+dfsg-4) ... Setting up libgssapi-krb5-2:ppc64el (1.13.2+dfsg-4) ... Setting up libidn11:ppc64el (1.32-3ubuntu1) ... Setting up libcurl3-gnutls:ppc64el (7.45.0-1ubuntu1) ... Setting up apt-transport-https (1.1.10) ... Setting up openssl (1.0.2e-1ubuntu1) ... Setting up advancecomp (1.20-1) ... Setting up cpp (4:5.2.1-16ubuntu2) ... Setting up libdpkg-perl (1.18.4ubuntu1) ... Setting up make (4.1-1) ... Setting up dpkg-dev (1.18.4ubuntu1) ... Setting up gcc (4:5.2.1-16ubuntu2) ... Setting up g++ (4:5.2.1-16ubuntu2) ... Setting up pkg-create-dbgsym (0.70) ... Setting up pkgbinarymangler (128) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Processing triggers for systemd (228-4ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-8865980', 'ppc64el', 'xenial-proposed', '-c', 'chroot:autobuild', '--arch=ppc64el', '--dist=xenial-proposed', '--purge=never', '--nolog', 'subread_1.5.0-p1+dfsg-2.dsc'] Initiating build PACKAGEBUILD-8865980 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.2.0-23-generic #28-Ubuntu SMP Sun Dec 27 17:46:45 UTC 2015 ppc64le sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bos01-ppc64el-012.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ subread 1.5.0-p1+dfsg-2 (ppc64el) 18 Jan 2016 17:10 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: subread Version: 1.5.0-p1+dfsg-2 Source Version: 1.5.0-p1+dfsg-2 Distribution: xenial-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el I: NOTICE: Log filtering will replace 'build/subread-URP5yC/subread-1.5.0-p1+dfsg' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/subread-URP5yC' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-8865980/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── subread_1.5.0-p1+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 '/«BUILDDIR»/resolver-yP5ReC/apt_archive/sbuild-build-depends-core-dummy.deb'. Get:1 file:/«BUILDDIR»/resolver-yP5ReC/apt_archive ./ InRelease Ign:1 file:/«BUILDDIR»/resolver-yP5ReC/apt_archive ./ InRelease Get:2 file:/«BUILDDIR»/resolver-yP5ReC/apt_archive ./ Release [2119 B] Get:2 file:/«BUILDDIR»/resolver-yP5ReC/apt_archive ./ Release [2119 B] Get:3 file:/«BUILDDIR»/resolver-yP5ReC/apt_archive ./ Release.gpg Ign:3 file:/«BUILDDIR»/resolver-yP5ReC/apt_archive ./ Release.gpg Get:4 file:/«BUILDDIR»/resolver-yP5ReC/apt_archive ./ Sources [208 B] Get:5 file:/«BUILDDIR»/resolver-yP5ReC/apt_archive ./ Packages [529 B] Ign:4 file:/«BUILDDIR»/resolver-yP5ReC/apt_archive ./ Sources Get:4 file:/«BUILDDIR»/resolver-yP5ReC/apt_archive ./ Sources [208 B] Ign:5 file:/«BUILDDIR»/resolver-yP5ReC/apt_archive ./ Packages Get:5 file:/«BUILDDIR»/resolver-yP5ReC/apt_archive ./ Packages [529 B] Reading package lists... W: The repository 'file:/«BUILDDIR»/resolver-yP5ReC/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 libprocps3 udev Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/772 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Get:1 file:/«BUILDDIR»/resolver-yP5ReC/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B] debconf: delaying package configuration, since apt-utils is not installed 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 ... 12161 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), help2man, zlib1g-dev Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), help2man, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-subread-dummy' in '/«BUILDDIR»/resolver-olSWnj/apt_archive/sbuild-build-depends-subread-dummy.deb'. Get:1 file:/«BUILDDIR»/resolver-olSWnj/apt_archive ./ InRelease Ign:1 file:/«BUILDDIR»/resolver-olSWnj/apt_archive ./ InRelease Get:2 file:/«BUILDDIR»/resolver-olSWnj/apt_archive ./ Release [2119 B] Get:2 file:/«BUILDDIR»/resolver-olSWnj/apt_archive ./ Release [2119 B] Get:3 file:/«BUILDDIR»/resolver-olSWnj/apt_archive ./ Release.gpg Ign:3 file:/«BUILDDIR»/resolver-olSWnj/apt_archive ./ Release.gpg Get:4 file:/«BUILDDIR»/resolver-olSWnj/apt_archive ./ Sources [432 B] Get:5 file:/«BUILDDIR»/resolver-olSWnj/apt_archive ./ Packages [695 B] Ign:4 file:/«BUILDDIR»/resolver-olSWnj/apt_archive ./ Sources Get:4 file:/«BUILDDIR»/resolver-olSWnj/apt_archive ./ Sources [432 B] Ign:5 file:/«BUILDDIR»/resolver-olSWnj/apt_archive ./ Packages Get:5 file:/«BUILDDIR»/resolver-olSWnj/apt_archive ./ Packages [695 B] Reading package lists... W: The repository 'file:/«BUILDDIR»/resolver-olSWnj/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install subread build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 libprocps3 udev Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: bsdmainutils debhelper dh-strip-nondeterminism file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasprintf0v5 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu55 liblocale-gettext-perl libmagic1 libpipeline1 libtimedate-perl libunistring0 libxml2 man-db po-debconf zlib1g-dev Suggested packages: wamerican | wordlist whois vacation dh-make gettext-doc autopoint groff less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xdg-user-dirs xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper dh-strip-nondeterminism file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasprintf0v5 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu55 liblocale-gettext-perl libmagic1 libpipeline1 libtimedate-perl libunistring0 libxml2 man-db po-debconf sbuild-build-depends-subread-dummy zlib1g-dev 0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded. Need to get 15.0 MB/15.0 MB of archives. After this operation, 62.4 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-subread-dummy Authentication warning overridden. Get:1 file:/«BUILDDIR»/resolver-olSWnj/apt_archive ./ sbuild-build-depends-subread-dummy 0.invalid.0 [940 B] Get:2 http://ftpmaster.internal/ubuntu xenial/main ppc64el liblocale-gettext-perl ppc64el 1.07-1build1 [17.2 kB] Get:3 http://ftpmaster.internal/ubuntu xenial/main ppc64el groff-base ppc64el 1.22.3-5 [1365 kB] Get:4 http://ftpmaster.internal/ubuntu xenial/main ppc64el bsdmainutils ppc64el 9.0.6ubuntu1 [175 kB] Get:5 http://ftpmaster.internal/ubuntu xenial/main ppc64el libpipeline1 ppc64el 1.4.1-2 [24.1 kB] Get:6 http://ftpmaster.internal/ubuntu xenial/main ppc64el man-db ppc64el 2.7.5-1 [850 kB] Get:7 http://ftpmaster.internal/ubuntu xenial/main ppc64el libunistring0 ppc64el 0.9.3-5.2ubuntu1 [269 kB] Get:8 http://ftpmaster.internal/ubuntu xenial/main ppc64el libmagic1 ppc64el 1:5.25-2ubuntu1 [220 kB] Get:9 http://ftpmaster.internal/ubuntu xenial/main ppc64el file ppc64el 1:5.25-2ubuntu1 [21.7 kB] Get:10 http://ftpmaster.internal/ubuntu xenial/main ppc64el libasprintf0v5 ppc64el 0.19.6-1ubuntu1 [7112 B] Get:11 http://ftpmaster.internal/ubuntu xenial/main ppc64el gettext-base ppc64el 0.19.6-1ubuntu1 [47.5 kB] Get:12 http://ftpmaster.internal/ubuntu xenial/main ppc64el libglib2.0-0 ppc64el 2.47.4-1 [1040 kB] Get:13 http://ftpmaster.internal/ubuntu xenial/main ppc64el libicu55 ppc64el 55.1-6ubuntu1 [7740 kB] Get:14 http://ftpmaster.internal/ubuntu xenial-proposed/main ppc64el libxml2 ppc64el 2.9.2+zdfsg1-4ubuntu3 [610 kB] Get:15 http://ftpmaster.internal/ubuntu xenial/main ppc64el libcroco3 ppc64el 0.6.11-1 [75.6 kB] Get:16 http://ftpmaster.internal/ubuntu xenial/main ppc64el gettext ppc64el 0.19.6-1ubuntu1 [1097 kB] Get:17 http://ftpmaster.internal/ubuntu xenial/main ppc64el intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:18 http://ftpmaster.internal/ubuntu xenial/main ppc64el po-debconf all 1.0.19 [234 kB] Get:19 http://ftpmaster.internal/ubuntu xenial/main ppc64el libarchive-zip-perl all 1.56-2 [84.1 kB] Get:20 http://ftpmaster.internal/ubuntu xenial/main ppc64el libfile-stripnondeterminism-perl all 0.014-1 [10.1 kB] Get:21 http://ftpmaster.internal/ubuntu xenial/main ppc64el libtimedate-perl all 2.3000-2 [37.5 kB] Get:22 http://ftpmaster.internal/ubuntu xenial/main ppc64el dh-strip-nondeterminism all 0.014-1 [5596 B] Get:23 http://ftpmaster.internal/ubuntu xenial/main ppc64el debhelper all 9.20151225ubuntu1 [744 kB] Get:24 http://ftpmaster.internal/ubuntu xenial/main ppc64el help2man ppc64el 1.47.3 [111 kB] Get:25 http://ftpmaster.internal/ubuntu xenial/main ppc64el zlib1g-dev ppc64el 1:1.2.8.dfsg-2ubuntu4 [168 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 15.0 MB in 0s (39.1 MB/s) Selecting previously unselected package liblocale-gettext-perl. (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 ... 12161 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-1build1_ppc64el.deb ... Unpacking liblocale-gettext-perl (1.07-1build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.3-5_ppc64el.deb ... Unpacking groff-base (1.22.3-5) ... Selecting previously unselected package bsdmainutils. 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Setting up liblocale-gettext-perl (1.07-1build1) ... Setting up groff-base (1.22.3-5) ... Setting up bsdmainutils (9.0.6ubuntu1) ... 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:ppc64el (1.4.1-2) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libunistring0:ppc64el (0.9.3-5.2ubuntu1) ... Setting up libmagic1:ppc64el (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up libasprintf0v5:ppc64el (0.19.6-1ubuntu1) ... Setting up gettext-base (0.19.6-1ubuntu1) ... Setting up libglib2.0-0:ppc64el (2.47.4-1) ... No schema files found: doing nothing. Setting up libicu55:ppc64el (55.1-6ubuntu1) ... Setting up libxml2:ppc64el (2.9.2+zdfsg1-4ubuntu3) ... Setting up libcroco3:ppc64el (0.6.11-1) ... Setting up gettext (0.19.6-1ubuntu1) ... 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Processing triggers for libc-bin (2.21-0ubuntu5) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 4.2.0-23-generic ppc64el (ppc64le) Toolchain package versions: binutils_2.25.90.20160101-1ubuntu2 dpkg-dev_1.18.4ubuntu1 g++-5_5.3.1-6ubuntu1 gcc-5_5.3.1-6ubuntu1 libc6-dev_2.21-0ubuntu5 libstdc++-5-dev_5.3.1-6ubuntu1 libstdc++6_5.3.1-6ubuntu1 linux-libc-dev_4.3.0-6.17 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.1.10 apt-transport-https_1.1.10 base-files_9.4ubuntu3 base-passwd_3.5.39 bash_4.3-14ubuntu1 binutils_2.25.90.20160101-1ubuntu2 bsdmainutils_9.0.6ubuntu1 bsdutils_1:2.27.1-1ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8 ca-certificates_20150426ubuntu1 coreutils_8.23-4ubuntu2 cpp_4:5.2.1-16ubuntu2 cpp-5_5.3.1-6ubuntu1 dash_0.5.7-4ubuntu2 debconf_1.5.58ubuntu1 debhelper_9.20151225ubuntu1 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-3 dmsetup_2:1.02.110-1ubuntu2 dpkg_1.18.4ubuntu1 dpkg-dev_1.18.4ubuntu1 e2fslibs_1.42.13-1ubuntu1 e2fsprogs_1.42.13-1ubuntu1 fakeroot_1.20.2-1ubuntu1 file_1:5.25-2ubuntu1 findutils_4.6.0-2 g++_4:5.2.1-16ubuntu2 g++-5_5.3.1-6ubuntu1 gcc_4:5.2.1-16ubuntu2 gcc-5_5.3.1-6ubuntu1 gcc-5-base_5.3.1-6ubuntu1 gettext_0.19.6-1ubuntu1 gettext-base_0.19.6-1ubuntu1 gnupg_1.4.19-6ubuntu1 gpgv_1.4.19-6ubuntu1 grep_2.22-1 groff-base_1.22.3-5 gzip_1.6-4ubuntu1 help2man_1.47.3 hostname_3.16ubuntu2 init_1.24ubuntu2 initscripts_2.88dsf-59.2ubuntu3 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-2 libapparmor1_2.10-0ubuntu10 libapt-pkg4.16_1.0.10.2ubuntu1 libapt-pkg5.0_1.1.10 libarchive-zip-perl_1.56-2 libasan2_5.3.1-6ubuntu1 libasn1-8-heimdal_1.6~rc2+dfsg-10ubuntu1 libasprintf0v5_0.19.6-1ubuntu1 libatomic1_5.3.1-6ubuntu1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1ubuntu1 libaudit1_1:2.4.5-1ubuntu1 libblkid1_2.27.1-1ubuntu3 libbz2-1.0_1.0.6-8 libc-bin_2.21-0ubuntu5 libc-dev-bin_2.21-0ubuntu5 libc6_2.21-0ubuntu5 libc6-dev_2.21-0ubuntu5 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-6ubuntu1 libcomerr2_1.42.13-1ubuntu1 libcroco3_0.6.11-1 libcryptsetup4_2:1.6.6-5ubuntu2 libcurl3-gnutls_7.45.0-1ubuntu1 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1ubuntu1 libdebconfclient0_0.198ubuntu1 libdevmapper1.02.1_2:1.02.110-1ubuntu2 libdpkg-perl_1.18.4ubuntu1 libfakeroot_1.20.2-1ubuntu1 libfdisk1_2.27.1-1ubuntu3 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.014-1 libgcc-5-dev_5.3.1-6ubuntu1 libgcc1_1:5.3.1-6ubuntu1 libgcrypt20_1.6.4-4 libgdbm3_1.8.3-13.1 libglib2.0-0_2.47.4-1 libgmp10_2:6.1.0+dfsg-2 libgnutls-deb0-28_3.3.18-1ubuntu1 libgomp1_5.3.1-6ubuntu1 libgpg-error0_1.21-1 libgssapi-krb5-2_1.13.2+dfsg-4 libgssapi3-heimdal_1.6~rc2+dfsg-10ubuntu1 libhcrypto4-heimdal_1.6~rc2+dfsg-10ubuntu1 libheimbase1-heimdal_1.6~rc2+dfsg-10ubuntu1 libheimntlm0-heimdal_1.6~rc2+dfsg-10ubuntu1 libhogweed4_3.1.1-4 libhx509-5-heimdal_1.6~rc2+dfsg-10ubuntu1 libicu55_55.1-6ubuntu1 libidn11_1.32-3ubuntu1 libisl13_0.14-2 libisl15_0.15-3 libitm1_5.3.1-6ubuntu1 libk5crypto3_1.13.2+dfsg-4 libkeyutils1_1.5.9-8ubuntu1 libkmod2_21-1ubuntu1 libkrb5-26-heimdal_1.6~rc2+dfsg-10ubuntu1 libkrb5-3_1.13.2+dfsg-4 libkrb5support0_1.13.2+dfsg-4 libldap-2.4-2_2.4.41+dfsg-1ubuntu3 liblocale-gettext-perl_1.07-1build1 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblzma5_5.1.1alpha+20120614-2ubuntu2 libmagic1_1:5.25-2ubuntu1 libmount1_2.27.1-1ubuntu3 libmpc3_1.0.3-1 libmpfr4_3.1.3-2 libncurses5_6.0+20151024-2ubuntu1 libncursesw5_6.0+20151024-2ubuntu1 libnettle6_3.1.1-4 libnih-dbus1_1.0.3-4.3ubuntu1 libnih1_1.0.3-4.3ubuntu1 libp11-kit0_0.23.2-3 libpam-modules_1.1.8-3.1ubuntu3 libpam-modules-bin_1.1.8-3.1ubuntu3 libpam-runtime_1.1.8-3.1ubuntu3 libpam0g_1.1.8-3.1ubuntu3 libpcre3_2:8.38-1ubuntu1 libperl5.22_5.22.1-4 libpipeline1_1.4.1-2 libpng12-0_1.2.54-1ubuntu1 libprocps3_1:3.3.9-1ubuntu8 libprocps4_2:3.3.10-4ubuntu2 libreadline6_6.3-8ubuntu1 libroken18-heimdal_1.6~rc2+dfsg-10ubuntu1 librtmp1_2.4+20150115.gita107cef-1build1 libsasl2-2_2.1.26.dfsg1-14 libsasl2-modules-db_2.1.26.dfsg1-14 libseccomp2_2.2.3-2ubuntu3 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libslang2_2.3.0-2ubuntu1 libsmartcols1_2.27.1-1ubuntu3 libsqlite3-0_3.10.1-1 libss2_1.42.13-1ubuntu1 libssl1.0.0_1.0.2e-1ubuntu1 libstdc++-5-dev_5.3.1-6ubuntu1 libstdc++6_5.3.1-6ubuntu1 libsystemd0_228-4ubuntu1 libtasn1-6_4.7-3 libtimedate-perl_2.3000-2 libtinfo5_6.0+20151024-2ubuntu1 libubsan0_5.3.1-6ubuntu1 libudev1_228-4ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1ubuntu3 libwind0-heimdal_1.6~rc2+dfsg-10ubuntu1 libxml2_2.9.2+zdfsg1-4ubuntu3 linux-libc-dev_4.3.0-6.17 lockfile-progs_0.1.17 login_1:4.1.5.1-1.1ubuntu7 lsb-base_9.20160110 make_4.1-1 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mount_2.27.1-1ubuntu3 multiarch-support_2.21-0ubuntu5 ncurses-base_6.0+20151024-2ubuntu1 ncurses-bin_6.0+20151024-2ubuntu1 openssl_1.0.2e-1ubuntu1 optipng_0.7.5-1 passwd_1:4.1.5.1-1.1ubuntu7 patch_2.7.5-1 perl_5.22.1-4 perl-base_5.22.1-4 perl-modules-5.22_5.22.1-4 pkg-create-dbgsym_0.70 pkgbinarymangler_128 po-debconf_1.0.19 policyrcd-script-zg2_0.1-2 procps_2:3.3.10-4ubuntu2 readline-common_6.3-8ubuntu1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-subread-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 systemd_228-4ubuntu1 systemd-sysv_228-4ubuntu1 sysv-rc_2.88dsf-59.2ubuntu3 sysvinit-utils_2.88dsf-59.2ubuntu3 tar_1.28-2.1 tzdata_2015g-1 ubuntu-keyring_2012.05.19 udev_228-4ubuntu1 util-linux_2.27.1-1ubuntu3 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu4 zlib1g-dev_1:1.2.8.dfsg-2ubuntu4 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: Signature made Mon Jan 18 12:26:14 2016 UTC using RSA key ID 1B5228B0 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./subread_1.5.0-p1+dfsg-2.dsc dpkg-source: info: extracting subread in subread-1.5.0-p1+dfsg dpkg-source: info: unpacking subread_1.5.0-p1+dfsg.orig.tar.gz dpkg-source: info: unpacking subread_1.5.0-p1+dfsg-2.debian.tar.xz dpkg-source: info: applying syntax_err.patch dpkg-source: info: applying arch_specific_flags.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C 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=/«BUILDDIR»/subread-1.5.0-p1+dfsg SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«BUILDDIR»/subread-1.5.0-p1+dfsg' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ───────────────── dpkg-buildpackage: source package subread dpkg-buildpackage: source version 1.5.0-p1+dfsg-2 dpkg-buildpackage: source distribution unstable dpkg-source --before-build subread-1.5.0-p1+dfsg dpkg-buildpackage: host architecture ppc64el fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean debian/rules override_dh_clean make[1]: Entering directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg' cd src; make -f Makefile.Linux clean make[2]: Entering directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg/src' rm -f core featureCounts exactSNP removeDup subread-buildindex core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o make[2]: Leaving directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg/src' dh_clean make[1]: Leaving directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg' debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg' cd src; make -f Makefile.Linux make[2]: Entering directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg/src' gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c core.c: In function 'print_in_box': core.c:139:7: warning: variable 'is_R_linebreak' set but not used [-Wunused-but-set-variable] char is_R_linebreak=0, * content, *out_line_buff; ^ core.c: In function 'convert_GZ_to_FQ': core.c:834:19: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types] gzFile * rawfp = gzopen(fname, "r"); ^ core.c:845:25: warning: passing argument 1 of 'gzgets' from incompatible pointer type [-Wincompatible-pointer-types] char * bufr =gzgets(rawfp, linebuff, 3000); ^ In file included from subread.h:26:0, from core.c:43: /usr/include/zlib.h:1372:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **' ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len)); ^ core.c:856:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] gzclose(rawfp); ^ In file included from subread.h:26:0, from core.c:43: /usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **' ZEXTERN int ZEXPORT gzclose OF((gzFile file)); ^ core.c: In function 'calc_tlen': core.c:1451:16: warning: variable 'section_start' set but not used [-Wunused-but-set-variable] unsigned int section_start = smaller_head_pos, section_end = 0; ^ core.c: In function 'do_iteration_one': core.c:2075:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable] int ret; ^ core.c: In function 'write_realignments_for_fragment': core.c:2286:21: warning: variable 'raw_r2' set but not used [-Wunused-but-set-variable] mapping_result_t * raw_r2 = NULL; ^ core.c:2283:21: warning: variable 'raw_r1' set but not used [-Wunused-but-set-variable] mapping_result_t * raw_r1 = NULL; ^ core.c: In function 'do_iteration_two': core.c:2352:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable] int ret; ^ core.c: In function 'do_voting': core.c:2896:9: warning: variable 'allsubreads_for_each_gap' set but not used [-Wunused-but-set-variable] int allsubreads_for_each_gap [GENE_SLIDING_STEP], noninformative_subreads_for_each_gap[GENE_SLIDING_STEP]; ^ core.c:2815:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable] int ret, xk1; ^ core.c: In function 'do_iteration_two': core.c:2300:3: warning: 'read_len_1' may be used uninitialized in this function [-Wmaybe-uninitialized] write_single_fragment(global_context, thread_context, r1_output, res1, r2_output, res2, multi_mapping_number , this_multi_mapping_i , read_name_1, read_name_2, rlen1, rlen2, read_text_1, read_text_2, qual_text_1, qual_text_2, read_number, non_informative_subreads_r1, non_informative_subreads_r2, is_1_OK, is_2_OK); ^ core.c:2364:6: note: 'read_len_1' was declared here int read_len_1, read_len_2=0; ^ gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c core-junction.c: In function 'copy_vote_to_alignment_res': core-junction.c:1022:12: warning: variable 'current_piece_minor_score' set but not used [-Wunused-but-set-variable] int i,j, current_piece_minor_score = 0; ^ core-junction.c: In function 'finalise_explain_CIGAR': core-junction.c:2331:10: warning: variable 'is_front_search' set but not used [-Wunused-but-set-variable] int is_front_search = 0; ^ core-junction.c:2467:94: warning: variable 'total_coverage_length' set but not used [-Wunused-but-set-variable] int final_qual = 0, applied_mismatch = 0, non_clipped_length = 0, total_indel_length = 0, total_coverage_length = 0, final_MATCH = 0; ^ core-junction.c:2447:28: warning: variable 'isCigarOK' set but not used [-Wunused-but-set-variable] int mismatch_bases = 0, isCigarOK = 0; ^ core-junction.c:2266:23: warning: variable 'tmp_cigar_exonic' set but not used [-Wunused-but-set-variable] char tmp_cigar[120], tmp_cigar_exonic[120]; ^ core-junction.c: In function 'find_translocation_brk_PQR': core-junction.c:4883:23: warning: variable 'candBrkPlist' set but not used [-Wunused-but-set-variable] chromosome_event_t * candBrkPlist [_PQR_LIST_SIZE]; ^ gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c core-indel.c: In function 'find_new_indels': core-indel.c:1580:9: warning: variable 'best_j' set but not used [-Wunused-but-set-variable] int best_j=0, best_score=-99999, is_ambiguous_indel= 0; ^ core-indel.c: In function 'full_indel_alignment': core-indel.c:2927:41: warning: variable 'best_right' set but not used [-Wunused-but-set-variable] int best_edge_score = -1, best_left, best_right; ^ core-indel.c:2927:30: warning: variable 'best_left' set but not used [-Wunused-but-set-variable] int best_edge_score = -1, best_left, best_right; ^ core-indel.c: In function 'find_potential_ultralong_indels': core-indel.c:3026:24: warning: variable 'best_c2_location' set but not used [-Wunused-but-set-variable] int best_match = -1, best_c2_location = -1; ^ core-indel.c: In function 'finalise_pileup_file': core-indel.c:3304:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&read_len, sizeof(short), 1, tmp_fp); ^ core-indel.c:3305:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(read_text, sizeof(char), read_len, tmp_fp); ^ core-indel.c:3306:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(qual_text, sizeof(char), read_len, tmp_fp); ^ core-indel.c:3383:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&read_len, sizeof(short), 1, tmp_fp); ^ core-indel.c:3384:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(read_text, sizeof(char), read_len, tmp_fp); ^ core-indel.c:3385:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(qual_text, sizeof(char), read_len, tmp_fp); ^ core-indel.c: In function 'finalise_pileup_file_by_debrujin': core-indel.c:3747:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&read_len, sizeof(short), 1, tmp_fp); ^ core-indel.c:3748:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(read_text, sizeof(char), read_len, tmp_fp); ^ core-indel.c:3749:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(qual_text, sizeof(char), read_len, tmp_fp); ^ gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c sambam-file.c: In function 'PBam_get_next_zchunk': sambam-file.c:346:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&ID1, 1, 1, bam_fp); ^ sambam-file.c:347:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&ID2, 1, 1, bam_fp); ^ sambam-file.c:348:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&CM, 1, 1, bam_fp); ^ sambam-file.c:349:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&FLG, 1, 1, bam_fp); ^ sambam-file.c:358:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&XLEN,1, 2, bam_fp ); ^ sambam-file.c:366:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&SI1, 1, 1, bam_fp); ^ sambam-file.c:367:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&SI2, 1, 1, bam_fp); ^ sambam-file.c:368:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&SLEN, 1, 2, bam_fp); ^ sambam-file.c:372:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&BSIZE_MID, 1,2 , bam_fp); ^ sambam-file.c:384:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(buffer, 1, CDATA_READING, bam_fp); ^ sambam-file.c:388:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&real_len, 4, 1, bam_fp); ^ gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c gene-algorithms.c: In function 'show_cigar': gene-algorithms.c:757:6: warning: variable 'last_end' set but not used [-Wunused-but-set-variable] int last_end=0, last_offset = 0, cursor = 0; ^ gene-algorithms.c:756:9: warning: variable 'is_error' set but not used [-Wunused-but-set-variable] int i, is_error = 0; ^ gene-algorithms.c: In function 'match_chro_indel': gene-algorithms.c:1169:28: warning: variable 'last_section_indels' set but not used [-Wunused-but-set-variable] int last_section_end = 0, last_section_indels=0; ^ gene-algorithms.c: In function 'search_DP_branch': gene-algorithms.c:1718:6: warning: variable 'table_mask2_j_1' set but not used [-Wunused-but-set-variable] int table_mask2_j_1 = 0, table_mask2_i_1 = 0; ^ gene-algorithms.c: In function 'final_mapping_quality': gene-algorithms.c:2359:7: warning: variable 'is_match_begin' set but not used [-Wunused-but-set-variable] int is_match_begin = 0; ^ gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c input-files.c: In function 'SAM_pairer_read_SAM_MB': input-files.c:2531:12: warning: variable 'last' set but not used [-Wunused-but-set-variable] int nch, last=-1; ^ input-files.c: In function 'SAM_pairer_get_next_read_BIN': input-files.c:2709:11: warning: variable 'ref_name' set but not used [-Wunused-but-set-variable] char ref_name[MAX_CHROMOSOME_NAME_LEN]; ^ input-files.c: In function 'fix_write_block': input-files.c:4008:23: warning: variable 'retbam' set but not used [-Wunused-but-set-variable] int x1, bam_len = 0, retbam; ^ input-files.c: In function 'SAM_nosort_run_once': input-files.c:4458:9: warning: variable 'ref_name' set but not used [-Wunused-but-set-variable] char ref_name[MAX_CHROMOSOME_NAME_LEN]; ^ input-files.c: In function 'geinput_next_char': input-files.c:508:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(out_buf, 1999,input->input_fp); ^ input-files.c: In function 'SAM_pairer_writer_reset': input-files.c:3349:2: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result] ftruncate(fileno(bam_main -> bam_fp), 0); ^ input-files.c: In function 'SAM_pairer_osr_next_name': input-files.c:3558:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&rlen, 1, 2, fp); ^ input-files.c:3570:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&rlen, 1, 2, fp); ^ input-files.c: In function 'SAM_pairer_osr_next_bin': input-files.c:3580:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&rlen, 1, 2, fp); ^ input-files.c:3584:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&rlen, 1, 2, fp); ^ input-files.c:3587:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(bin, 1, rlen, fp); ^ input-files.c: In function 'fix_load_next_block': input-files.c:3984:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(bam_buf, 1, bsize - xlen - 19, in); ^ input-files.c: In function 'sort_SAM_finalise': input-files.c:4767:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&read_name_len, 2,1 , bbfp); ^ input-files.c:4773:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(read_name, 1, read_name_len, bbfp); ^ input-files.c:4776:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&read_len,2,1,bbfp); ^ input-files.c:4782:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(new_line_mem, 1, read_len, bbfp); ^ input-files.c:4835:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&read_name_len, 2,1 , bbfp); ^ input-files.c:4841:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(read_name_buf, 1, read_name_len, bbfp); ^ input-files.c:4845:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&read_len, 2,1 , bbfp); ^ input-files.c:4848:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(read_line_buf, 1, read_len, bbfp); ^ gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c sorted-hashtable.c: In function 'gehash_load_option': sorted-hashtable.c:1264:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(magic_chars,1,8,fp); ^ sorted-hashtable.c:1269:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&option_key, 2, 1, fp); ^ sorted-hashtable.c:1272:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&option_length, 2, 1, fp); ^ sorted-hashtable.c:1276:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(result ,option_length,1,fp); ^ sorted-hashtable.c: In function 'gehash_load': sorted-hashtable.c:1303:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(magic_chars,1,8,fp); ^ sorted-hashtable.c:1326:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&option_key, 2, 1, fp); ^ sorted-hashtable.c:1329:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&option_length, 2, 1, fp); ^ sorted-hashtable.c:1332:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(the_table -> index_gap),2,1,fp); ^ sorted-hashtable.c:1334:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(the_table -> padding),2,1,fp); ^ sorted-hashtable.c: In function 'gehash_go_q_tolerable': sorted-hashtable.c:513:22: warning: array subscript is above array bounds [-Warray-bounds] mutation_stack[j] = 0; ^ sorted-hashtable.c:530:22: warning: array subscript is above array bounds [-Warray-bounds] error_pos_stack[j] = error_pos_stack[i] + (j-i); ^ sorted-hashtable.c: In function 'gehash_go_q_CtoT': sorted-hashtable.c:594:22: warning: array subscript is above array bounds [-Warray-bounds] mutation_stack[j] = 0; ^ sorted-hashtable.c:612:22: warning: array subscript is above array bounds [-Warray-bounds] error_pos_stack[j] = error_pos_stack[i] + (j-i); ^ gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c core-bigtable.c: In function 'bigtable_readonly_result': core-bigtable.c:70:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(write_ptr, loadjunc?sizeof(subjunc_result_t):sizeof(mapping_result_t), 1, global_context -> bigtable_cache_file_fp); ^ core-bigtable.c: In function 'bigtable_retrieve_cache': core-bigtable.c:219:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread( current_cache -> big_margin_data , sizeof(short) * 3 * global_context -> config.big_margin_record_size , 1, global_context -> bigtable_cache_file_fp ); ^ core-bigtable.c:220:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread( current_cache -> alignment_res , sizeof(mapping_result_t) * global_context -> config.multi_best_reads , 1, global_context -> bigtable_cache_file_fp ); ^ core-bigtable.c:223:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread( current_cache -> subjunc_res , sizeof(subjunc_result_t) * global_context -> config.multi_best_reads , 1, global_context -> bigtable_cache_file_fp); ^ core-bigtable.c:229:5: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result] ftruncate(fileno(global_context -> bigtable_cache_file_fp), new_file_size); ^ gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm readSummary.c: In function 'calc_junctions_from_cigar': readSummary.c:341:15: warning: variable 'right_boundary' set but not used [-Wunused-but-set-variable] unsigned int right_boundary = 0; ^ readSummary.c: In function 'readSummary': readSummary.c:3899:9: warning: variable 'curchr_name' set but not used [-Wunused-but-set-variable] char * curchr_name, * fasta_contigs_fname; ^ readSummary.c:3898:15: warning: variable 'curpos' set but not used [-Wunused-but-set-variable] long curchr, curpos; ^ readSummary.c:3898:7: warning: variable 'curchr' set but not used [-Wunused-but-set-variable] long curchr, curpos; ^ readSummary.c: In function 'load_feature_info': readSummary.c:896:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(file_line, MAX_LINE_LENGTH, fp); ^ readSummary.c: In function 'process_pairer_reset': readSummary.c:1486:3: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result] ftruncate(fileno(global_context -> SAM_output_fp), 0); ^ readSummary.c: In function 'load_feature_info': readSummary.c:834:10: warning: 'token_temp' may be used uninitialized in this function [-Wmaybe-uninitialized] char * token_temp, *chro_name; ^ readSummary.c:898:10: warning: 'token_temp' may be used uninitialized in this function [-Wmaybe-uninitialized] char * token_temp; ^ gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm removeDupReads.c: In function 'parse_base_blocks': removeDupReads.c:87:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&read_record, sizeof(base_block_temp_read_t), 1, block_fp); ^ removeDupReads.c:96:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&read_record, sizeof(base_block_temp_read_t), 1, block_fp); ^ gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm SNPCalling.c: In function 'read_tmp_block': SNPCalling.c:256:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&SNP_rec, sizeof(SNP_rec),1 , tmp_fp); ^ SNPCalling.c:275:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&read_rec, sizeof(read_rec), 1, tmp_fp); ^ SNPCalling.c:276:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&read_len, sizeof(short), 1, tmp_fp); ^ SNPCalling.c:277:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(read, sizeof(char), read_len, tmp_fp); ^ SNPCalling.c:278:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(qual, sizeof(char), read_len, tmp_fp); ^ gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm index-builder.c: In function 'scan_gene_index': index-builder.c:456:19: warning: variable 'table_no' set but not used [-Wunused-but-set-variable] int file_number, table_no, i ,j; ^ index-builder.c: In function 'main': index-builder.c:1177:2: warning: ignoring return value of 'mkstemp', declared with attribute warn_unused_result [-Wunused-result] mkstemp(tmp_fa_file); ^ gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm qualityScores.c: In function 'finalise_qs_context': qualityScores.c:82:12: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] gzclose(qs_context -> gzfq_reader); ^ In file included from qualityScores.c:24:0: /usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **' ZEXTERN int ZEXPORT gzclose OF((gzFile file)); ^ qualityScores.c: In function 'rewind_qs_file': qualityScores.c:275:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] gzclose(qs_context -> gzfq_reader); ^ In file included from qualityScores.c:24:0: /usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **' ZEXTERN int ZEXPORT gzclose OF((gzFile file)); ^ qualityScores.c:282:29: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb"); ^ qualityScores.c: In function 'start_qs_context': qualityScores.c:313:29: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb"); ^ gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm propmapped.c: In function 'prop_PE': propmapped.c:346:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&read_len,1,1,fp); ^ propmapped.c:349:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(read_name,read_len,1,fp); ^ propmapped.c:353:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&flags,1, sizeof(short), fp); ^ gcc -fsigned-char -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o coverageCount coverage_calc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm mkdir -p ../bin/utilities mv subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/ mv repair coverageCount propmapped qualityScores removeDup subread-fullscan ../bin/utilities ########################################################### # # # Installation finished. # # # # Generated executables were copied to directory ../bin/ # # # ########################################################### make[2]: Leaving directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg/src' dh_auto_build make[1]: Leaving directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg' debian/tests/subread-tests /«BUILDDIR»/subread-1.5.0-p1+dfsg ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || P data/test-minimum.sam || || || || Output file : test-minimum.FC || || Annotations : data/test-minimum.GTF (GTF) || || || || Threads : 1 || || Level : meta-feature level || || Paired-end : no || || Strand specific : no || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Read orientations : fr || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file data/test-minimum.GTF ... || || Features : 23 || || Meta-features : 7 || || Chromosomes/contigs : 3 || || || || Process SAM file data/test-minimum.sam... || || Paired-end reads are included. || || Assign reads to features... || || Total reads : 998 || || Successfully assigned reads : 389 (39.0%) || || Running time : 0.00 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //=========================== indexBuilder setting ===========================\\ || || || Index name : tmp/small1 || || Index space : base-space || || Memory : 8000 Mbytes || || Repeat threshold : 100 repeats || || Distance to next subread : 3 || || || || Input files : 1 file in total || || o ../chr901.fa || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Check the integrity of provided reference sequences ... || || There were 4 notes for reference sequences. || || The notes can be found in the log file, 'tmp/small1.log'. || || Scan uninformative subreads in reference sequences ... || || 8%, 0 mins elapsed, rate=281.5k bps/s, total=0m || || 16%, 0 mins elapsed, rate=465.5k bps/s, total=0m || || 24%, 0 mins elapsed, rate=637.6k bps/s, total=0m || || 33%, 0 mins elapsed, rate=795.4k bps/s, total=0m || || 41%, 0 mins elapsed, rate=948.9k bps/s, total=0m || || 49%, 0 mins elapsed, rate=1093.9k bps/s, total=0m || || 58%, 0 mins elapsed, rate=1222.7k bps/s, total=0m || || 66%, 0 mins elapsed, rate=1354.7k bps/s, total=0m || || 74%, 0 mins elapsed, rate=1476.1k bps/s, total=0m || || 83%, 0 mins elapsed, rate=1590.0k bps/s, total=0m || || 91%, 0 mins elapsed, rate=1703.5k bps/s, total=0m || || 99%, 0 mins elapsed, rate=1804.7k bps/s, total=0m || || 2 uninformative subreads were found. || || These subreads were excluded from index building. || || Build the index... || || 8%, 0 mins elapsed, rate=1572.0k bps/s, total=0m || || 16%, 0 mins elapsed, rate=1377.1k bps/s, total=0m || || 24%, 0 mins elapsed, rate=1412.2k bps/s, total=0m || || 33%, 0 mins elapsed, rate=1252.9k bps/s, total=0m || || 41%, 0 mins elapsed, rate=1183.5k bps/s, total=0m || || 49%, 0 mins elapsed, rate=1079.7k bps/s, total=0m || || 58%, 0 mins elapsed, rate=1035.9k bps/s, total=0m || || 66%, 0 mins elapsed, rate=1031.8k bps/s, total=0m || || 74%, 0 mins elapsed, rate=1051.7k bps/s, total=0m || || 83%, 0 mins elapsed, rate=1058.7k bps/s, total=0m || || 91%, 0 mins elapsed, rate=1058.3k bps/s, total=0m || || 99%, 0 mins elapsed, rate=1045.8k bps/s, total=0m || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || || [ 20.0% finished ] || || [ 30.0% finished ] || || [ 40.0% finished ] || || [ 50.0% finished ] || || [ 60.0% finished ] || || [ 70.0% finished ] || || [ 80.0% finished ] || || [ 90.0% finished ] || || [ 100.0% finished ] || || || || Total running time: 0.0 minutes. || || Index tmp/small1 was successfully built! || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //============================= subjunc setting ==============================\\ || || || Function : Read alignment + Junction detection (RNA-Seq) || || Threads : 1 || || Input file 1 : data/junction-reads-A.fq || || Input file 2 : data/junction-reads-B.fq || || Output file : junctions.sam (SAM) || || Index name : tmp/small1 || || Phred offset : 33 || || || || All subreads : 14 || || Min read1 votes : 1 || || Min read2 votes : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || || || Allowed mismatch : 3 bases || || Max indels : 5 || || # of Best mapping : 1 || || Unique mapping : no || || Hamming distance : no || || Quality scores : no || || || \\===================== http://subread.sourceforge.net/ ======================// //====================== Running (18-Jan-2016 17:11:34) ======================\\ || || || The input file contains base space reads. || || The range of Phred scores observed in the data is [2,41] || || Load the 1-th index block... || || Map fragments... || || 41% completed, 0.0 mins elapsed, rate=7.8k fragments per second || || 48% completed, 0.0 mins elapsed, rate=7.8k fragments per second || || 54% completed, 0.0 mins elapsed, rate=7.9k fragments per second || || 61% completed, 0.0 mins elapsed, rate=7.9k fragments per second || || Finish the 16052 fragments... || || 77% completed, 0.1 mins elapsed, rate=4.0k fragments per second || || 87% completed, 0.1 mins elapsed, rate=4.2k fragments per second || || 97% completed, 0.1 mins elapsed, rate=4.5k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 16052 fragments || || Mapped : 15914 fragments (99.1%) || || Correctly paired : 14375 fragments || || Junctions : 407 || || Indels : 187 || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //============================= subjunc setting ==============================\\ || || || Function : Read alignment + Junction/Fusion detection (RNA-Seq) || || Threads : 1 || || Input file 1 : data/junction-reads-A.fq || || Input file 2 : data/junction-reads-B.fq || || Output file : junctionsNfusions.bam (BAM) || || Index name : tmp/small1 || || Phred offset : 33 || || || || All subreads : 14 || || Min read1 votes : 1 || || Min read2 votes : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || || || Allowed mismatch : 3 bases || || Max indels : 5 || || # of Best mapping : 1 || || Unique mapping : no || || Hamming distance : no || || Quality scores : no || || || \\===================== http://subread.sourceforge.net/ ======================// //====================== Running (18-Jan-2016 17:11:39) ======================\\ || || || The input file contains base space reads. || || The range of Phred scores observed in the data is [2,41] || || Load the 1-th index block... || || Map fragments... || || 41% completed, 0.0 mins elapsed, rate=8.1k fragments per second || || 48% completed, 0.0 mins elapsed, rate=8.1k fragments per second || || 54% completed, 0.0 mins elapsed, rate=8.1k fragments per second || || 61% completed, 0.0 mins elapsed, rate=8.1k fragments per second || || Finish the 16052 fragments... || || 77% completed, 0.1 mins elapsed, rate=3.9k fragments per second || || 87% completed, 0.1 mins elapsed, rate=3.9k fragments per second || || 97% completed, 0.1 mins elapsed, rate=4.0k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 16052 fragments || || Mapped : 15915 fragments (99.1%) || || Correctly paired : 14344 fragments || || Junctions : 402 || || Fusions : 92 || || Indels : 188 || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //=========================== indexBuilder setting ===========================\\ || || || Index name : tmp/small1 || || Index space : base-space || || Memory : 100 Mbytes || || Repeat threshold : 100 repeats || || Distance to next subread : 1 || || || || Input files : 1 file in total || || o ../chr901.fa || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Check the integrity of provided reference sequences ... || || There were 4 notes for reference sequences. || || The notes can be found in the log file, 'tmp/small1.log'. || || Scan uninformative subreads in reference sequences ... || || 8%, 0 mins elapsed, rate=344.3k bps/s, total=0m || || 16%, 0 mins elapsed, rate=570.7k bps/s, total=0m || || 24%, 0 mins elapsed, rate=766.7k bps/s, total=0m || || 33%, 0 mins elapsed, rate=933.5k bps/s, total=0m || || 41%, 0 mins elapsed, rate=1082.0k bps/s, total=0m || || 49%, 0 mins elapsed, rate=1210.4k bps/s, total=0m || || 58%, 0 mins elapsed, rate=1322.5k bps/s, total=0m || || 66%, 0 mins elapsed, rate=1421.2k bps/s, total=0m || || 74%, 0 mins elapsed, rate=1505.7k bps/s, total=0m || || 83%, 0 mins elapsed, rate=1578.0k bps/s, total=0m || || 91%, 0 mins elapsed, rate=1639.5k bps/s, total=0m || || 99%, 0 mins elapsed, rate=1697.5k bps/s, total=0m || || 52 uninformative subreads were found. || || These subreads were excluded from index building. || || Build the index... || || 8%, 0 mins elapsed, rate=443.2k bps/s, total=0m || || 16%, 0 mins elapsed, rate=509.6k bps/s, total=0m || || 24%, 0 mins elapsed, rate=602.3k bps/s, total=0m || || 33%, 0 mins elapsed, rate=677.4k bps/s, total=0m || || 41%, 0 mins elapsed, rate=746.6k bps/s, total=0m || || 49%, 0 mins elapsed, rate=808.9k bps/s, total=0m || || 58%, 0 mins elapsed, rate=852.7k bps/s, total=0m || || 66%, 0 mins elapsed, rate=909.3k bps/s, total=0m || || 74%, 0 mins elapsed, rate=965.1k bps/s, total=0m || || 83%, 0 mins elapsed, rate=1016.1k bps/s, total=0m || || 91%, 0 mins elapsed, rate=1068.2k bps/s, total=0m || || 99%, 0 mins elapsed, rate=1124.6k bps/s, total=0m || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || || [ 20.0% finished ] || || [ 30.0% finished ] || || [ 40.0% finished ] || || [ 50.0% finished ] || || [ 60.0% finished ] || || [ 70.0% finished ] || || [ 80.0% finished ] || || [ 90.0% finished ] || || [ 100.0% finished ] || || || || Total running time: 0.0 minutes. || || Index tmp/small1 was successfully built! || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Threads : 1 || || Input file : data/test-noerror-r1.fq || || Output file : tmp/test-tmp.sam1 (SAM) || || Index name : tmp/small1 || || Phred offset : 33 || || || || Min votes : 3 / 10 || || Allowed mismatch : 3 bases || || Max indels : 5 || || # of Best mapping : 1 || || Unique mapping : no || || Hamming distance : yes || || Quality scores : no || || || \\===================== http://subread.sourceforge.net/ ======================// //====================== Running (18-Jan-2016 17:11:46) ======================\\ || || || The input file contains base space reads. || || WARNING - The specified Phred score offset (33) seems incorrect. || || ASCII values of the quality scores of read bases included in || || the first 3000 reads were found to be within the range of || || [73,73]. || || || || Load the 1-th index block... || || Map reads... || || 33% completed, 0.0 mins elapsed, rate=26.6k reads per second || || 39% completed, 0.0 mins elapsed, rate=26.5k reads per second || || 46% completed, 0.0 mins elapsed, rate=26.5k reads per second || || 53% completed, 0.0 mins elapsed, rate=26.5k reads per second || || 60% completed, 0.0 mins elapsed, rate=25.4k reads per second || || Finish the 19998 reads... || || 74% completed, 0.0 mins elapsed, rate=9.5k reads per second || || 83% completed, 0.0 mins elapsed, rate=10.0k reads per second || || 91% completed, 0.0 mins elapsed, rate=10.4k reads per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 19998 reads || || Mapped : 19997 reads (100.0%) || || Indels : 7 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Threads : 1 || || Input file : data/test-noerror-r1.fq || || Output file : tmp/test-tmp.sam2 (SAM) || || Index name : tmp/small1 || || Phred offset : 33 || || || || Min votes : 3 / 10 || || Allowed mismatch : 3 bases || || Max indels : 5 || || # of Best mapping : 1 || || Unique mapping : yes || || Hamming distance : yes || || Quality scores : no || || || \\===================== http://subread.sourceforge.net/ ======================// //====================== Running (18-Jan-2016 17:11:49) ======================\\ || || || The input file contains base space reads. || || WARNING - The specified Phred score offset (33) seems incorrect. || || ASCII values of the quality scores of read bases included in || || the first 3000 reads were found to be within the range of || || [73,73]. || || || || Load the 1-th index block... || || Map reads... || || 33% completed, 0.0 mins elapsed, rate=28.7k reads per second || || 39% completed, 0.0 mins elapsed, rate=28.7k reads per second || || 46% completed, 0.0 mins elapsed, rate=28.6k reads per second || || 53% completed, 0.0 mins elapsed, rate=28.7k reads per second || || 60% completed, 0.0 mins elapsed, rate=28.6k reads per second || || Finish the 19998 reads... || || 74% completed, 0.0 mins elapsed, rate=10.2k reads per second || || 83% completed, 0.0 mins elapsed, rate=10.6k reads per second || || 91% completed, 0.0 mins elapsed, rate=11.0k reads per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 19998 reads || || Mapped : 18758 reads (93.8%) || || Indels : 5 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Threads : 1 || || Input file 1 : data/test-noerror-r1.fq || || Input file 2 : data/test-noerror-r2.fq || || Output file : tmp/test-tmp.sam3 (SAM) || || Index name : tmp/small1 || || Phred offset : 33 || || || || All subreads : 10 || || Min read1 votes : 3 || || Min read2 votes : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || || || Allowed mismatch : 3 bases || || Max indels : 5 || || # of Best mapping : 1 || || Unique mapping : no || || Hamming distance : yes || || Quality scores : no || || || \\===================== http://subread.sourceforge.net/ ======================// //====================== Running (18-Jan-2016 17:11:51) ======================\\ || || || The input file contains base space reads. || || WARNING - The specified Phred score offset (33) seems incorrect. || || ASCII values of the quality scores of read bases included in || || the first 3000 reads were found to be within the range of || || [73,73]. || || || || Load the 1-th index block... || || Map fragments... || || 33% completed, 0.0 mins elapsed, rate=14.3k fragments per second || || 39% completed, 0.0 mins elapsed, rate=14.0k fragments per second || || 46% completed, 0.0 mins elapsed, rate=13.9k fragments per second || || 53% completed, 0.0 mins elapsed, rate=13.8k fragments per second || || 60% completed, 0.0 mins elapsed, rate=13.7k fragments per second || || Finish the 19998 fragments... || || 74% completed, 0.0 mins elapsed, rate=7.2k fragments per second || || 83% completed, 0.0 mins elapsed, rate=7.4k fragments per second || || 91% completed, 0.0 mins elapsed, rate=7.5k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 19998 fragments || || Mapped : 19998 fragments (100.0%) || || Correctly paired : 19554 fragments || || Indels : 23 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Threads : 1 || || Input file 1 : data/test-noerror-r1.fq || || Input file 2 : data/test-noerror-r2.fq || || Output file : tmp/test-tmp.sam4 (SAM) || || Index name : tmp/small1 || || Phred offset : 33 || || || || All subreads : 10 || || Min read1 votes : 3 || || Min read2 votes : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || || || Allowed mismatch : 3 bases || || Max indels : 5 || || # of Best mapping : 1 || || Unique mapping : yes || || Hamming distance : yes || || Quality scores : yes || || || \\===================== http://subread.sourceforge.net/ ======================// //====================== Running (18-Jan-2016 17:11:54) ======================\\ || || || The input file contains base space reads. || || WARNING - The specified Phred score offset (33) seems incorrect. || || ASCII values of the quality scores of read bases included in || || the first 3000 reads were found to be within the range of || || [73,73]. || || || || Load the 1-th index block... || || Map fragments... || || 33% completed, 0.0 mins elapsed, rate=13.8k fragments per second || || 39% completed, 0.0 mins elapsed, rate=13.8k fragments per second || || 46% completed, 0.0 mins elapsed, rate=13.8k fragments per second || || 53% completed, 0.0 mins elapsed, rate=13.8k fragments per second || || 60% completed, 0.0 mins elapsed, rate=13.8k fragments per second || || Finish the 19998 fragments... || || 74% completed, 0.0 mins elapsed, rate=7.0k fragments per second || || 83% completed, 0.0 mins elapsed, rate=7.2k fragments per second || || 91% completed, 0.0 mins elapsed, rate=7.3k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 19998 fragments || || Mapped : 19216 fragments (96.1%) || || Correctly paired : 18830 fragments || || Indels : 22 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Threads : 1 || || Input file 1 : data/test-error-r1.fq || || Input file 2 : data/test-error-r2.fq || || Output file : tmp/test-tmp.sam5 (SAM) || || Index name : tmp/small1 || || Phred offset : 33 || || || || All subreads : 10 || || Min read1 votes : 3 || || Min read2 votes : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || || || Allowed mismatch : 3 bases || || Max indels : 5 || || # of Best mapping : 1 || || Unique mapping : no || || Hamming distance : yes || || Quality scores : no || || || \\===================== http://subread.sourceforge.net/ ======================// //====================== Running (18-Jan-2016 17:11:58) ======================\\ || || || The input file contains base space reads. || || WARNING - The specified Phred score offset (33) seems incorrect. || || ASCII values of the quality scores of read bases included in || || the first 3000 reads were found to be within the range of || || [50,50]. || || || || Load the 1-th index block... || || Map fragments... || || 33% completed, 0.0 mins elapsed, rate=14.2k fragments per second || || 39% completed, 0.0 mins elapsed, rate=14.1k fragments per second || || 46% completed, 0.0 mins elapsed, rate=14.1k fragments per second || || 53% completed, 0.0 mins elapsed, rate=14.1k fragments per second || || 60% completed, 0.0 mins elapsed, rate=14.0k fragments per second || || Finish the 20000 fragments... || || 74% completed, 0.0 mins elapsed, rate=7.2k fragments per second || || 83% completed, 0.0 mins elapsed, rate=7.3k fragments per second || || 91% completed, 0.0 mins elapsed, rate=7.4k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 20000 fragments || || Mapped : 19568 fragments (97.8%) || || Correctly paired : 14442 fragments || || Indels : 63 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Threads : 1 || || Input file 1 : data/test-err-mut-r1.fq.gz || || Input file 2 : data/test-err-mut-r2.fq.gz || || Output file : tmp/test-tmp.sam6 (SAM) || || Index name : tmp/small1 || || Phred offset : 33 || || || || All subreads : 10 || || Min read1 votes : 3 || || Min read2 votes : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || || || Allowed mismatch : 3 bases || || Max indels : 5 || || # of Best mapping : 1 || || Unique mapping : no || || Hamming distance : yes || || Quality scores : no || || Read group name : MyTestGroup || || || \\===================== http://subread.sourceforge.net/ ======================// //====================== Running (18-Jan-2016 17:12:01) ======================\\ || || || The input file contains base space reads. || || WARNING - The specified Phred score offset (33) seems incorrect. || || ASCII values of the quality scores of read bases included in || || the first 3000 reads were found to be within the range of || || [50,50]. || || || || Load the 1-th index block... || || Map fragments... || || 34% completed, 0.0 mins elapsed, rate=25.3k fragments per second || || 40% completed, 0.0 mins elapsed, rate=25.0k fragments per second || || 48% completed, 0.0 mins elapsed, rate=25.0k fragments per second || || 53% completed, 0.0 mins elapsed, rate=24.8k fragments per second || || 59% completed, 0.0 mins elapsed, rate=24.7k fragments per second || || 67% completed, 0.0 mins elapsed, rate=24.7k fragments per second || || Finish the 20001 fragments... || || 75% completed, 0.0 mins elapsed, rate=9.7k fragments per second || || 83% completed, 0.0 mins elapsed, rate=10.3k fragments per second || || 92% completed, 0.0 mins elapsed, rate=10.8k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 20001 fragments || || Mapped : 19528 fragments (97.6%) || || Correctly paired : 14071 fragments || || Indels : 179 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.0-p1 //============================= exactSNP setting =============================\\ || || || Input file : data/test-in.BAM (BAM) || || Output file : test-out.VCF || || Reference genome : ../chr901.fa || || || || Threads : 1 || || Min supporting reads : 1 || || Min pct. of supporting reads : 0.0% || || Min base quality score : 13 || || Number of trimmed bases : 3 || || || || Q value cutoff : 10E-12.0 || || P value upper bound : 0.00500 || || Flanking windows size : 5 || || || \\===================== http://subread.sourceforge.net/ ======================// //====================== Running (18-Jan-2016 17:12:04) ======================\\ || || || Split BAM file into ./temp-snps-004682-2BABAE95-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed reads : 50204 || || Reported SNPs : 415 || || Reported indels : 21 || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// make[1]: Leaving directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg' fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg' find /«BUILDDIR»/subread-1.5.0-p1+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \; mkdir -p /«BUILDDIR»/subread-1.5.0-p1+dfsg/debian/subread/usr/share/man/man1 help2man --no-info --help-option="''" --no-discard-stderr --name='an accurate and efficient aligner for mapping both genomic \ DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \ /«BUILDDIR»/subread-1.5.0-p1+dfsg/bin/subread-align | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+dfsg/debian/subread/usr/share/man/man1/subread-align.1; help2man --no-info --help-option="''" --no-discard-stderr --name='builds an base-space or color-space index using the reference sequences' \ /«BUILDDIR»/subread-1.5.0-p1+dfsg/bin/subread-buildindex | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+dfsg/debian/subread/usr/share/man/man1/subread-buildindex.1; help2man --no-info --help-option="''" --no-discard-stderr --name='an RNA-seq aligner suitable for all purposes of RNA-seq analyses' \ /«BUILDDIR»/subread-1.5.0-p1+dfsg/bin/subjunc | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+dfsg/debian/subread/usr/share/man/man1/subjunc.1; help2man --no-info --help-option="''" --no-discard-stderr --name='a highly efficient and accurate read summarization program' \ /«BUILDDIR»/subread-1.5.0-p1+dfsg/bin/featureCounts | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+dfsg/debian/subread/usr/share/man/man1/featureCounts.1; help2man --no-info --help-option="''" --no-discard-stderr --name='a SNP caller that discovers SNPs by testing signals against local background noises' \ /«BUILDDIR»/subread-1.5.0-p1+dfsg/bin/exactSNP | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+dfsg/debian/subread/usr/share/man/man1/exactSNP.1; help2man --no-info --help-option="''" --no-discard-stderr --name='detect short and long indels' \ /«BUILDDIR»/subread-1.5.0-p1+dfsg/bin/subindel | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+dfsg/debian/subread/usr/share/man/man1/subindel.1; help2man --no-info --help-option="''" --no-discard-stderr --name='scans the entire genome and reports all matches of a specified sequence' \ /«BUILDDIR»/subread-1.5.0-p1+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+dfsg/debian/subread/usr/share/man/man1/subread-fullscan.1; help2man --no-info --help-option="''" --no-discard-stderr --name='counting the coverage of mapped reads at each location on the entire reference genome' \ /«BUILDDIR»/subread-1.5.0-p1+dfsg/bin/utilities/coverageCount | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+dfsg/debian/subread/usr/share/man/man1/coverageCount.1; help2man --no-info --help-option="''" --no-discard-stderr --name='calculate the proportion of mapped reads/fragments' \ /«BUILDDIR»/subread-1.5.0-p1+dfsg/bin/utilities/propmapped | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+dfsg/debian/subread/usr/share/man/man1/propmapped.1; for i in removeDup repair qualityScores ; do \ help2man --no-info --help-option="''" --no-discard-stderr --name='a component of subread suite' /«BUILDDIR»/subread-1.5.0-p1+dfsg/bin/utilities/$i | debian/filter.pl > /«BUILDDIR»/subread-1.5.0-p1+dfsg/debian/subread/usr/share/man/man1/$i.1; \ done dh_auto_install make[1]: Leaving directory '/«BUILDDIR»/subread-1.5.0-p1+dfsg' 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 '/«BUILDDIR»/subread-1.5.0-p1+dfsg' dh_compress -X.pdf -Xtest.tar.xz make[1]: Leaving directory '/«BUILDDIR»/subread-1.5.0-p1+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 ppc64el: subread dh_strip debug symbol extraction: packages to act on: subread dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: -is is deprecated; it is without effect dpkg-gencontrol: warning: -ip is deprecated; it is without effect 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 ppc64el: subread dh_gencontrol debug symbol wrapper: packages to act on: subread dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package subread (pkgdir debian/subread, ddeb package dir debian/subread-dbgsym) dh_gencontrol debug symbol wrapper: building subread-dbgsym_1.5.0-p1+dfsg-2_ppc64el.ddeb dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_1.5.0-p1+dfsg-2_ppc64el.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile subread-dbgsym_1.5.0-p1+dfsg-2_ppc64el.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 128 pkgstriptranslations: processing subread (in debian/subread); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/subread/DEBIAN/control, package subread, directory debian/subread pkgstripfiles: Truncating usr/share/doc/subread/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package subread ... pkgstripfiles: No PNG files. dpkg-deb: building package 'subread' in '../subread_1.5.0-p1+dfsg-2_ppc64el.deb'. dpkg-genchanges -B -mLaunchpad Build Daemon >../subread_1.5.0-p1+dfsg-2_ppc64el.changes dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build subread-1.5.0-p1+dfsg dpkg-buildpackage: binary-only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20160118-1712 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ subread_1.5.0-p1+dfsg-2_ppc64el.changes: ──────────────────────────────────────── Format: 1.8 Date: Mon, 18 Jan 2016 12:03:41 +0100 Source: subread Binary: subread subread-data Architecture: ppc64el Version: 1.5.0-p1+dfsg-2 Distribution: xenial-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Alexandre Mestiashvili Description: subread - toolkit for processing next-gen sequencing data subread-data - data files for subread package Changes: subread (1.5.0-p1+dfsg-2) unstable; urgency=medium . * d/control: remove hurd-i386 and mipsel due to failing tests Checksums-Sha1: eed6aa39f6dfe26c77205107ee3fbd61e7b5488a 2105508 subread-dbgsym_1.5.0-p1+dfsg-2_ppc64el.ddeb e3a405d8616ff0a06ac8f6f2c12866b8f0a2af36 644440 subread_1.5.0-p1+dfsg-2_ppc64el.deb Checksums-Sha256: 689907bf3a9109210009d4fb8673858f198cb72395f9510d4c6bec6c1656d9f1 2105508 subread-dbgsym_1.5.0-p1+dfsg-2_ppc64el.ddeb 44f829076c2129ce3679e1826b5cfca455aba0eebe8b9c277754da10892318bc 644440 subread_1.5.0-p1+dfsg-2_ppc64el.deb Files: 11023b43d472919b1a048162a49f995a 2105508 science extra subread-dbgsym_1.5.0-p1+dfsg-2_ppc64el.ddeb 4e30d9ed3b5e07eb82668667c3b110c4 644440 science optional subread_1.5.0-p1+dfsg-2_ppc64el.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ subread_1.5.0-p1+dfsg-2_ppc64el.deb ─────────────────────────────────── new debian package, version 2.0. size 644440 bytes: control archive=1439 bytes. 707 bytes, 15 lines control 1819 bytes, 28 lines md5sums Package: subread Version: 1.5.0-p1+dfsg-2 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 9423 Depends: libc6 (>= 2.17), zlib1g (>= 1:1.2.3.3) Section: science Priority: optional Homepage: http://sourceforge.net/projects/subread/ Description: toolkit for processing next-gen sequencing data Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments. drwxr-xr-x root/root 0 2016-01-18 17:12 ./ drwxr-xr-x root/root 0 2016-01-18 17:12 ./usr/ drwxr-xr-x root/root 0 2016-01-18 17:12 ./usr/bin/ -rwxr-xr-x root/root 854912 2016-01-18 17:12 ./usr/bin/exactSNP -rwxr-xr-x root/root 855392 2016-01-18 17:12 ./usr/bin/featureCounts -rwxr-xr-x root/root 789408 2016-01-18 17:12 ./usr/bin/subindel -rwxr-xr-x root/root 790976 2016-01-18 17:12 ./usr/bin/subjunc -rwxr-xr-x root/root 790816 2016-01-18 17:12 ./usr/bin/subread-align -rwxr-xr-x root/root 789312 2016-01-18 17:12 ./usr/bin/subread-buildindex drwxr-xr-x root/root 0 2016-01-18 17:12 ./usr/lib/ drwxr-xr-x root/root 0 2016-01-18 17:12 ./usr/lib/subread/ -rwxr-xr-x root/root 789408 2016-01-18 17:12 ./usr/lib/subread/coverageCount -rwxr-xr-x root/root 789408 2016-01-18 17:12 ./usr/lib/subread/propmapped -rwxr-xr-x root/root 789632 2016-01-18 17:12 ./usr/lib/subread/qualityScores -rwxr-xr-x root/root 789312 2016-01-18 17:12 ./usr/lib/subread/removeDup -rwxr-xr-x root/root 789312 2016-01-18 17:12 ./usr/lib/subread/repair -rwxr-xr-x root/root 789312 2016-01-18 17:12 ./usr/lib/subread/subread-fullscan drwxr-xr-x root/root 0 2016-01-18 17:12 ./usr/share/ drwxr-xr-x root/root 0 2016-01-18 17:12 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-01-18 17:12 ./usr/share/doc/subread/ -rw-r--r-- root/root 500 2016-01-18 11:06 ./usr/share/doc/subread/README.Debian -rw-r--r-- root/root 3670 2015-12-18 03:05 ./usr/share/doc/subread/README.txt -rw-r--r-- root/root 1087 2016-01-18 17:12 ./usr/share/doc/subread/changelog.Debian.gz -rw-r--r-- root/root 1137 2016-01-18 11:06 ./usr/share/doc/subread/copyright drwxr-xr-x root/root 0 2016-01-18 17:12 ./usr/share/man/ drwxr-xr-x root/root 0 2016-01-18 17:12 ./usr/share/man/man1/ -rw-r--r-- root/root 600 2016-01-18 17:12 ./usr/share/man/man1/coverageCount.1.gz -rw-r--r-- root/root 1177 2016-01-18 17:12 ./usr/share/man/man1/exactSNP.1.gz -rw-r--r-- root/root 2234 2016-01-18 17:12 ./usr/share/man/man1/featureCounts.1.gz -rw-r--r-- root/root 463 2016-01-18 17:12 ./usr/share/man/man1/propmapped.1.gz -rw-r--r-- root/root 569 2016-01-18 17:12 ./usr/share/man/man1/qualityScores.1.gz -rw-r--r-- root/root 500 2016-01-18 17:12 ./usr/share/man/man1/removeDup.1.gz -rw-r--r-- root/root 481 2016-01-18 17:12 ./usr/share/man/man1/repair.1.gz -rw-r--r-- root/root 351 2016-01-18 17:12 ./usr/share/man/man1/subindel.1.gz -rw-r--r-- root/root 1531 2016-01-18 17:12 ./usr/share/man/man1/subjunc.1.gz -rw-r--r-- root/root 1621 2016-01-18 17:12 ./usr/share/man/man1/subread-align.1.gz -rw-r--r-- root/root 766 2016-01-18 17:12 ./usr/share/man/man1/subread-buildindex.1.gz -rw-r--r-- root/root 380 2016-01-18 17:12 ./usr/share/man/man1/subread-fullscan.1.gz ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: ppc64el Build-Space: 116444 Build-Time: 100 Distribution: xenial-proposed Host Architecture: ppc64el Install-Time: 9 Job: subread_1.5.0-p1+dfsg-2.dsc Machine Architecture: ppc64el Package: subread Package-Time: 111 Source-Version: 1.5.0-p1+dfsg-2 Space: 116444 Status: successful Version: 1.5.0-p1+dfsg-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20160118-1712 Build needed 00:01:51, 116444k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-8865980'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-8865980/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-8865980'] Unmounting chroot for build PACKAGEBUILD-8865980... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-8865980'] Removing build PACKAGEBUILD-8865980