RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux bos01-ppc64el-022 4.4.0-87-generic #110-Ubuntu SMP Tue Jul 18 12:53:44 UTC 2017 ppc64le Buildd toolchain package versions: launchpad-buildd_147 python-lpbuildd_147 sbuild_0.67.0-2ubuntu7 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.1 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.14. Syncing the system clock with the buildd NTP service... 28 Jul 23:06:17 ntpdate[1747]: adjust time server 10.211.37.1 offset 0.002021 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-13167929', '/home/buildd/filecache-default/6f2309b02db3cfdb85003f9659f6426e55596487'] Unpacking chroot for build PACKAGEBUILD-13167929 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-13167929'] Mounting chroot for build PACKAGEBUILD-13167929 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-13167929', 'deb http://ftpmaster.internal/ubuntu artful main universe', 'deb http://ftpmaster.internal/ubuntu artful-security main universe', 'deb http://ftpmaster.internal/ubuntu artful-updates main universe', 'deb http://ftpmaster.internal/ubuntu artful-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-13167929 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-13167929', 'ppc64el'] Updating debian chroot for build PACKAGEBUILD-13167929 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:3 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed InRelease [235 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main ppc64el Packages [1101 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main Translation-en [558 kB] Get:7 http://ftpmaster.internal/ubuntu artful/universe ppc64el Packages [7999 kB] Get:8 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4777 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el Packages [111 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main Translation-en [66.3 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/universe ppc64el Packages [346 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/universe Translation-en [221 kB] Fetched 15.8 MB in 5s (2752 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.24 perl-modules-5.24 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: gcc-7-base libperl5.26 perl-modules-5.26 The following packages will be upgraded: advancecomp apt apt-transport-https base-files bash binutils bsdutils ca-certificates cpp cpp-6 debconf debianutils dmsetup dpkg dpkg-dev findutils g++ g++-6 gcc gcc-6 gcc-6-base grep init init-system-helpers libapparmor1 libapt-pkg5.0 libasan3 libasn1-8-heimdal libatomic1 libaudit-common libaudit1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libdb5.3 libdevmapper1.02.1 libdpkg-perl libfdisk1 libgcc-6-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libip4tc0 libitm1 libk5crypto3 libkmod2 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma5 libmount1 libnpth0 libp11-kit0 libpcre3 libperl5.24 libpng16-16 libpsl5 libroken18-heimdal libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.0.0 libstdc++-6-dev libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 libusb-0.1-4 libuuid1 libwind0-heimdal linux-libc-dev login mount multiarch-support openssl passwd perl perl-base perl-modules-5.24 sensible-utils systemd systemd-sysv tar tzdata util-linux xz-utils 104 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 61.8 MB of archives. After this operation, 47.5 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu artful/main ppc64el debconf all 1.5.63 [136 kB] Get:2 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el perl ppc64el 5.26.0-4 [205 kB] Get:3 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el perl-modules-5.26 all 5.26.0-4 [2762 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main ppc64el libperl5.24 ppc64el 5.24.1-7ubuntu1 [3316 kB] Get:5 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libperl5.26 ppc64el 5.26.0-4 [3343 kB] Get:6 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el perl-base ppc64el 5.26.0-4 [1258 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main ppc64el perl-modules-5.24 all 5.24.1-7ubuntu1 [2664 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main ppc64el libc6-dev ppc64el 2.24-12ubuntu1 [2240 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main ppc64el libc-dev-bin ppc64el 2.24-12ubuntu1 [64.5 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el linux-libc-dev ppc64el 4.11.0-11.16 [920 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el gcc-7-base ppc64el 7.1.0-10ubuntu1 [18.6 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libgcc1 ppc64el 1:7.1.0-10ubuntu1 [29.7 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main ppc64el libc6 ppc64el 2.24-12ubuntu1 [2447 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main ppc64el libdb5.3 ppc64el 5.3.28-13 [628 kB] Get:15 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el init-system-helpers all 1.49 [37.0 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main ppc64el base-files ppc64el 9.6ubuntu101 [59.1 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main ppc64el sensible-utils all 0.0.9+nmu1 [10.2 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main ppc64el debianutils ppc64el 4.8.1.1 [85.9 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main ppc64el bash ppc64el 4.4-5ubuntu1 [644 kB] Get:20 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el bsdutils ppc64el 1:2.30.1-0ubuntu1 [58.1 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main ppc64el tar ppc64el 1.29b-2 [240 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main ppc64el dpkg ppc64el 1.18.24ubuntu1 [1122 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main ppc64el findutils ppc64el 4.6.0+git+20170606-3 [299 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main ppc64el grep ppc64el 3.1-2 [150 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main ppc64el login ppc64el 1:4.2-3.2ubuntu2 [301 kB] Get:26 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libuuid1 ppc64el 2.30.1-0ubuntu1 [14.9 kB] Get:27 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libblkid1 ppc64el 2.30.1-0ubuntu1 [110 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main ppc64el libpcre3 ppc64el 2:8.39-4 [222 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main ppc64el libselinux1 ppc64el 2.6-3build1 [67.0 kB] Get:30 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libmount1 ppc64el 2.30.1-0ubuntu1 [118 kB] Get:31 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libfdisk1 ppc64el 2.30.1-0ubuntu1 [143 kB] Get:32 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libsmartcols1 ppc64el 2.30.1-0ubuntu1 [73.8 kB] Get:33 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el util-linux ppc64el 2.30.1-0ubuntu1 [906 kB] Get:34 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el mount ppc64el 2.30.1-0ubuntu1 [124 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main ppc64el libc-bin ppc64el 2.24-12ubuntu1 [575 kB] Get:36 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el liblzma5 ppc64el 5.2.2-1.3 [101 kB] Get:37 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libstdc++6 ppc64el 7.1.0-10ubuntu1 [447 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main ppc64el libapt-pkg5.0 ppc64el 1.5~beta1 [827 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main ppc64el apt-transport-https ppc64el 1.5~beta1 [39.4 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main ppc64el libp11-kit0 ppc64el 0.23.7-3 [152 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main ppc64el libtasn1-6 ppc64el 4.12-2.1 [35.8 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main ppc64el libgnutls30 ppc64el 3.5.8-6ubuntu1 [576 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main ppc64el apt ppc64el 1.5~beta1 [1134 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main ppc64el libip4tc0 ppc64el 1.6.1-2ubuntu1 [20.4 kB] Get:45 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libapparmor1 ppc64el 2.11.0-2ubuntu10 [29.1 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main ppc64el libaudit-common all 1:2.7.7-1ubuntu1 [4118 B] Get:47 http://ftpmaster.internal/ubuntu artful/main ppc64el libcap-ng0 ppc64el 0.7.7-3build1 [11.1 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main ppc64el libaudit1 ppc64el 1:2.7.7-1ubuntu1 [40.3 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main ppc64el libgpg-error0 ppc64el 1.27-3 [38.5 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main ppc64el libgcrypt20 ppc64el 1.7.8-2 [415 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main ppc64el libkmod2 ppc64el 24-1ubuntu1 [36.4 kB] Get:52 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el systemd ppc64el 234-2ubuntu1 [2672 kB] Get:53 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libsystemd0 ppc64el 234-2ubuntu1 [207 kB] Get:54 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el init ppc64el 1.49 [6040 B] Get:55 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el systemd-sysv ppc64el 234-2ubuntu1 [13.8 kB] Get:56 http://ftpmaster.internal/ubuntu artful/main ppc64el libsemanage-common all 2.6-2build1 [6738 B] Get:57 http://ftpmaster.internal/ubuntu artful/main ppc64el libsemanage1 ppc64el 2.6-2build1 [75.7 kB] Get:58 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libudev1 ppc64el 234-2ubuntu1 [54.3 kB] Get:59 http://ftpmaster.internal/ubuntu artful/main ppc64el passwd ppc64el 1:4.2-3.2ubuntu2 [754 kB] Get:60 http://ftpmaster.internal/ubuntu artful/main ppc64el multiarch-support ppc64el 2.24-12ubuntu1 [6838 B] Get:61 http://ftpmaster.internal/ubuntu artful/main ppc64el libdevmapper1.02.1 ppc64el 2:1.02.137-2ubuntu2 [128 kB] Get:62 http://ftpmaster.internal/ubuntu artful/main ppc64el dmsetup ppc64el 2:1.02.137-2ubuntu2 [69.8 kB] Get:63 http://ftpmaster.internal/ubuntu artful/main ppc64el libroken18-heimdal ppc64el 7.4.0.dfsg.1-2 [39.1 kB] Get:64 http://ftpmaster.internal/ubuntu artful/main ppc64el libasn1-8-heimdal ppc64el 7.4.0.dfsg.1-2 [137 kB] Get:65 http://ftpmaster.internal/ubuntu artful/main ppc64el libheimbase1-heimdal ppc64el 7.4.0.dfsg.1-2 [28.5 kB] Get:66 http://ftpmaster.internal/ubuntu artful/main ppc64el libhcrypto4-heimdal ppc64el 7.4.0.dfsg.1-2 [94.2 kB] Get:67 http://ftpmaster.internal/ubuntu artful/main ppc64el libwind0-heimdal ppc64el 7.4.0.dfsg.1-2 [47.9 kB] Get:68 http://ftpmaster.internal/ubuntu artful/main ppc64el libhx509-5-heimdal ppc64el 7.4.0.dfsg.1-2 [101 kB] Get:69 http://ftpmaster.internal/ubuntu artful/main ppc64el libsqlite3-0 ppc64el 3.19.3-3 [444 kB] Get:70 http://ftpmaster.internal/ubuntu artful/main ppc64el libkrb5-26-heimdal ppc64el 7.4.0.dfsg.1-2 [194 kB] Get:71 http://ftpmaster.internal/ubuntu artful/main ppc64el libheimntlm0-heimdal ppc64el 7.4.0.dfsg.1-2 [15.6 kB] Get:72 http://ftpmaster.internal/ubuntu artful/main ppc64el libgssapi3-heimdal ppc64el 7.4.0.dfsg.1-2 [86.2 kB] Get:73 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libldap-2.4-2 ppc64el 2.4.45+dfsg-1ubuntu1 [144 kB] Get:74 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libldap-common all 2.4.45+dfsg-1ubuntu1 [16.6 kB] Get:75 http://ftpmaster.internal/ubuntu artful/main ppc64el libnpth0 ppc64el 1.5-2 [7560 B] Get:76 http://ftpmaster.internal/ubuntu artful/main ppc64el libssl1.0.0 ppc64el 1.0.2g-1ubuntu13 [822 kB] Get:77 http://ftpmaster.internal/ubuntu artful/main ppc64el tzdata all 2017b-2 [203 kB] Get:78 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el xz-utils ppc64el 5.2.2-1.3 [82.5 kB] Get:79 http://ftpmaster.internal/ubuntu artful/main ppc64el openssl ppc64el 1.0.2g-1ubuntu13 [483 kB] Get:80 http://ftpmaster.internal/ubuntu artful/main ppc64el ca-certificates all 20161130+nmu1 [186 kB] Get:81 http://ftpmaster.internal/ubuntu artful/main ppc64el libgssapi-krb5-2 ppc64el 1.15.1-2 [109 kB] Get:82 http://ftpmaster.internal/ubuntu artful/main ppc64el libkrb5-3 ppc64el 1.15.1-2 [269 kB] Get:83 http://ftpmaster.internal/ubuntu artful/main ppc64el libkrb5support0 ppc64el 1.15.1-2 [31.3 kB] Get:84 http://ftpmaster.internal/ubuntu artful/main ppc64el libk5crypto3 ppc64el 1.15.1-2 [99.7 kB] Get:85 http://ftpmaster.internal/ubuntu artful/main ppc64el libidn2-0 ppc64el 2.0.2-1 [93.2 kB] Get:86 http://ftpmaster.internal/ubuntu artful/main ppc64el libpng16-16 ppc64el 1.6.30-2 [192 kB] Get:87 http://ftpmaster.internal/ubuntu artful/main ppc64el libpsl5 ppc64el 0.17.0-5 [41.5 kB] Get:88 http://ftpmaster.internal/ubuntu artful/main ppc64el advancecomp ppc64el 2.0-1 [255 kB] Get:89 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el binutils ppc64el 2.29-1ubuntu1 [2376 kB] Get:90 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libgomp1 ppc64el 7.1.0-10ubuntu1 [69.3 kB] Get:91 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libitm1 ppc64el 7.1.0-10ubuntu1 [29.8 kB] Get:92 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libubsan0 ppc64el 7.1.0-10ubuntu1 [129 kB] Get:93 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libatomic1 ppc64el 7.1.0-10ubuntu1 [8478 B] Get:94 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libasan3 ppc64el 6.4.0-2ubuntu1 [279 kB] Get:95 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el g++-6 ppc64el 6.4.0-2ubuntu1 [6446 kB] Get:96 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libstdc++-6-dev ppc64el 6.4.0-2ubuntu1 [1442 kB] Get:97 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el gcc-6 ppc64el 6.4.0-2ubuntu1 [6269 kB] Get:98 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libgcc-6-dev ppc64el 6.4.0-2ubuntu1 [657 kB] Get:99 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el libcc1-0 ppc64el 7.1.0-10ubuntu1 [39.1 kB] Get:100 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el cpp-6 ppc64el 6.4.0-2ubuntu1 [5663 kB] Get:101 http://ftpmaster.internal/ubuntu artful-proposed/main ppc64el gcc-6-base ppc64el 6.4.0-2ubuntu1 [17.2 kB] Get:102 http://ftpmaster.internal/ubuntu artful/main ppc64el cpp ppc64el 4:6.3.0-2ubuntu2 [27.5 kB] Get:103 http://ftpmaster.internal/ubuntu artful/main ppc64el dpkg-dev all 1.18.24ubuntu1 [608 kB] Get:104 http://ftpmaster.internal/ubuntu artful/main ppc64el libdpkg-perl all 1.18.24ubuntu1 [209 kB] Get:105 http://ftpmaster.internal/ubuntu artful/main ppc64el gcc ppc64el 4:6.3.0-2ubuntu2 [5270 B] Get:106 http://ftpmaster.internal/ubuntu artful/main ppc64el g++ ppc64el 4:6.3.0-2ubuntu2 [1478 B] Get:107 http://ftpmaster.internal/ubuntu artful/main ppc64el libusb-0.1-4 ppc64el 2:0.1.12-31 [16.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 61.8 MB in 2s (24.0 MB/s) (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 ... 14161 files and directories currently installed.) Preparing to unpack .../apt_1.5~beta1_ppc64el.deb ... Unpacking apt (1.5~beta1) over (1.4.1ubuntu2) ... Setting up apt (1.5~beta1) ... (Reading database ... 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Unpacking libaudit-common (1:2.7.7-1ubuntu1) over (1:2.6.6-1ubuntu1) ... Setting up libaudit-common (1:2.7.7-1ubuntu1) ... (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 ... 14160 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.7.7-3build1_ppc64el.deb ... Unpacking libcap-ng0:ppc64el (0.7.7-3build1) over (0.7.7-3) ... Setting up libcap-ng0:ppc64el (0.7.7-3build1) ... (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 ... 14160 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a2.7.7-1ubuntu1_ppc64el.deb ... Unpacking libaudit1:ppc64el (1:2.7.7-1ubuntu1) over (1:2.6.6-1ubuntu1) ... Setting up libaudit1:ppc64el (1:2.7.7-1ubuntu1) ... (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 ... 14160 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.7.8-2_ppc64el.deb ... Unpacking libgcrypt20:ppc64el (1.7.8-2) over (1.7.6-1) ... Setting up libgcrypt20:ppc64el (1.7.8-2) ... (Reading database ... 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Unpacking systemd (234-2ubuntu1) over (232-21ubuntu3) ... dpkg: warning: unable to delete old directory '/etc/dbus-1/system.d': Directory not empty dpkg: warning: unable to delete old directory '/etc/dbus-1': Directory not empty Preparing to unpack .../libsystemd0_234-2ubuntu1_ppc64el.deb ... Unpacking libsystemd0:ppc64el (234-2ubuntu1) over (232-21ubuntu3) ... Setting up libsystemd0:ppc64el (234-2ubuntu1) ... (Reading database ... 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Installing new version of config file /etc/systemd/resolved.conf ... Created symlink /etc/systemd/system/dbus-org.freedesktop.resolve1.service -> /lib/systemd/system/systemd-resolved.service. Created symlink /etc/systemd/system/multi-user.target.wants/systemd-resolved.service -> /lib/systemd/system/systemd-resolved.service. addgroup: The group `systemd-journal' already exists as a system group. Exiting. Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.hostname1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.locale1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.login1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.network1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.resolve1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.systemd1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.timedate1.conf ... (Reading database ... (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 ... 14185 files and directories currently installed.) Preparing to unpack .../systemd-sysv_234-2ubuntu1_ppc64el.deb ... Unpacking systemd-sysv (234-2ubuntu1) over (232-21ubuntu3) ... Preparing to unpack .../libsemanage-common_2.6-2build1_all.deb ... Unpacking libsemanage-common (2.6-2build1) over (2.6-2) ... Setting up libsemanage-common (2.6-2build1) ... (Reading database ... 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Preparing to unpack .../37-gcc-6_6.4.0-2ubuntu1_ppc64el.deb ... Unpacking gcc-6 (6.4.0-2ubuntu1) over (6.3.0-14ubuntu3) ... Replacing files in old package cpp-6 (6.3.0-14ubuntu3) ... Preparing to unpack .../38-libgcc-6-dev_6.4.0-2ubuntu1_ppc64el.deb ... Unpacking libgcc-6-dev:ppc64el (6.4.0-2ubuntu1) over (6.3.0-14ubuntu3) ... Preparing to unpack .../39-libcc1-0_7.1.0-10ubuntu1_ppc64el.deb ... Unpacking libcc1-0:ppc64el (7.1.0-10ubuntu1) over (6.3.0-14ubuntu3) ... Preparing to unpack .../40-cpp-6_6.4.0-2ubuntu1_ppc64el.deb ... Unpacking cpp-6 (6.4.0-2ubuntu1) over (6.3.0-14ubuntu3) ... Preparing to unpack .../41-gcc-6-base_6.4.0-2ubuntu1_ppc64el.deb ... Unpacking gcc-6-base:ppc64el (6.4.0-2ubuntu1) over (6.3.0-14ubuntu3) ... Preparing to unpack .../42-cpp_4%3a6.3.0-2ubuntu2_ppc64el.deb ... Unpacking cpp (4:6.3.0-2ubuntu2) over (4:6.3.0-2ubuntu1) ... Preparing to unpack .../43-dpkg-dev_1.18.24ubuntu1_all.deb ... Unpacking dpkg-dev (1.18.24ubuntu1) over (1.18.23ubuntu4) ... Preparing to unpack .../44-libdpkg-perl_1.18.24ubuntu1_all.deb ... Unpacking libdpkg-perl (1.18.24ubuntu1) over (1.18.23ubuntu4) ... Preparing to unpack .../45-gcc_4%3a6.3.0-2ubuntu2_ppc64el.deb ... Removing old gcc doc directory. Unpacking gcc (4:6.3.0-2ubuntu2) over (4:6.3.0-2ubuntu1) ... Preparing to unpack .../46-g++_4%3a6.3.0-2ubuntu2_ppc64el.deb ... Unpacking g++ (4:6.3.0-2ubuntu2) over (4:6.3.0-2ubuntu1) ... Preparing to unpack .../47-libusb-0.1-4_2%3a0.1.12-31_ppc64el.deb ... Unpacking libusb-0.1-4:ppc64el (2:0.1.12-31) over (2:0.1.12-30) ... Setting up libnpth0:ppc64el (1.5-2) ... Setting up libgomp1:ppc64el (7.1.0-10ubuntu1) ... Setting up libatomic1:ppc64el (7.1.0-10ubuntu1) ... Setting up perl-modules-5.24 (5.24.1-7ubuntu1) ... Setting up libperl5.24:ppc64el (5.24.1-7ubuntu1) ... Setting up libcc1-0:ppc64el (7.1.0-10ubuntu1) ... Setting up apt-transport-https (1.5~beta1) ... Setting up libidn2-0:ppc64el (2.0.2-1) ... Setting up libssl1.0.0:ppc64el (1.0.2g-1ubuntu13) ... Setting up libpng16-16:ppc64el (1.6.30-2) ... Setting up libldap-common (2.4.45+dfsg-1ubuntu1) ... Setting up libpsl5:ppc64el (0.17.0-5) ... Setting up multiarch-support (2.24-12ubuntu1) ... Setting up tzdata (2017b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jul 28 23:06:46 UTC 2017. Universal Time is now: Fri Jul 28 23:06:46 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (234-2ubuntu1) ... Setting up libubsan0:ppc64el (7.1.0-10ubuntu1) ... Setting up gcc-6-base:ppc64el (6.4.0-2ubuntu1) ... Setting up linux-libc-dev:ppc64el (4.11.0-11.16) ... Setting up advancecomp (2.0-1) ... Setting up libroken18-heimdal:ppc64el (7.4.0.dfsg.1-2) ... Setting up libdevmapper1.02.1:ppc64el (2:1.02.137-2ubuntu2) ... Setting up perl-modules-5.26 (5.26.0-4) ... Setting up libkrb5support0:ppc64el (1.15.1-2) ... Processing triggers for libc-bin (2.24-12ubuntu1) ... Setting up libperl5.26:ppc64el (5.26.0-4) ... Setting up xz-utils (5.2.2-1.3) ... Setting up libheimbase1-heimdal:ppc64el (7.4.0.dfsg.1-2) ... Setting up openssl (1.0.2g-1ubuntu13) ... Setting up libsqlite3-0:ppc64el (3.19.3-3) ... Setting up dmsetup (2:1.02.137-2ubuntu2) ... Setting up binutils (2.29-1ubuntu1) ... Setting up cpp-6 (6.4.0-2ubuntu1) ... Setting up libc-dev-bin (2.24-12ubuntu1) ... Setting up ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 7 removed; done. Setting up libc6-dev:ppc64el (2.24-12ubuntu1) ... Setting up libusb-0.1-4:ppc64el (2:0.1.12-31) ... Setting up libitm1:ppc64el (7.1.0-10ubuntu1) ... Setting up cpp (4:6.3.0-2ubuntu2) ... Setting up libk5crypto3:ppc64el (1.15.1-2) ... Setting up libasan3:ppc64el (6.4.0-2ubuntu1) ... Setting up libgcc-6-dev:ppc64el (6.4.0-2ubuntu1) ... Setting up libstdc++-6-dev:ppc64el (6.4.0-2ubuntu1) ... Setting up libwind0-heimdal:ppc64el (7.4.0.dfsg.1-2) ... Setting up init (1.49) ... Setting up libasn1-8-heimdal:ppc64el (7.4.0.dfsg.1-2) ... Setting up libhcrypto4-heimdal:ppc64el (7.4.0.dfsg.1-2) ... Setting up libhx509-5-heimdal:ppc64el (7.4.0.dfsg.1-2) ... Setting up gcc-6 (6.4.0-2ubuntu1) ... Setting up g++-6 (6.4.0-2ubuntu1) ... Setting up perl (5.26.0-4) ... Removing obsolete conffile /etc/perl/sitecustomize.pl ... Setting up libkrb5-3:ppc64el (1.15.1-2) ... Setting up libkrb5-26-heimdal:ppc64el (7.4.0.dfsg.1-2) ... Setting up libheimntlm0-heimdal:ppc64el (7.4.0.dfsg.1-2) ... Setting up libdpkg-perl (1.18.24ubuntu1) ... Setting up gcc (4:6.3.0-2ubuntu2) ... Setting up libgssapi-krb5-2:ppc64el (1.15.1-2) ... Setting up dpkg-dev (1.18.24ubuntu1) ... Setting up g++ (4:6.3.0-2ubuntu2) ... Setting up libgssapi3-heimdal:ppc64el (7.4.0.dfsg.1-2) ... Setting up libldap-2.4-2:ppc64el (2.4.45+dfsg-1ubuntu1) ... Processing triggers for libc-bin (2.24-12ubuntu1) ... Processing triggers for ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-13167929', 'ppc64el', 'artful-proposed', '-c', 'chroot:autobuild', '--arch=ppc64el', '--dist=artful-proposed', '--purge=never', '--nolog', 'subread_1.5.3+dfsg-1.dsc'] Initiating build PACKAGEBUILD-13167929 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-87-generic #110-Ubuntu SMP Tue Jul 18 12:53:44 UTC 2017 ppc64le sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos01-ppc64el-022.buildd +==============================================================================+ | subread 1.5.3+dfsg-1 (ppc64el) 28 Jul 2017 23:06 | +==============================================================================+ Package: subread Version: 1.5.3+dfsg-1 Source Version: 1.5.3+dfsg-1 Distribution: artful-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el I: NOTICE: Log filtering will replace 'build/subread-j34LjG/subread-1.5.3+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/subread-j34LjG' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13167929/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- subread_1.5.3+dfsg-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-cTgq_C/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-cTgq_C/apt_archive ./ InRelease Get:2 copy:/<>/resolver-cTgq_C/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-cTgq_C/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-cTgq_C/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-cTgq_C/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (279 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.24 perl-modules-5.24 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 780 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-cTgq_C/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [780 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 780 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14178 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: bc, debhelper (>= 10), help2man, python, zlib1g-dev Filtered Build-Depends: bc, debhelper (>= 10), help2man, python, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-subread-dummy' in '/<>/resolver-Dj9reB/apt_archive/sbuild-build-depends-subread-dummy.deb'. Ign:1 copy:/<>/resolver-Dj9reB/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Dj9reB/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Dj9reB/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Dj9reB/apt_archive ./ Sources [231 B] Get:5 copy:/<>/resolver-Dj9reB/apt_archive ./ Packages [550 B] Fetched 2900 B in 0s (261 kB/s) Reading package lists... 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: libperl5.24 perl-modules-5.24 Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bc bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support Recommended packages: curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bc bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal sbuild-build-depends-subread-dummy zlib1g-dev 0 upgraded, 43 newly installed, 1 to remove and 0 not upgraded. Need to get 21.0 MB of archives. After this operation, 88.0 MB of additional disk space will be used. 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Setting up libpipeline1:ppc64el (1.4.2-1) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:ppc64el (57.1-6) ... Setting up libbsd0:ppc64el (0.8.6-1) ... Setting up libxml2:ppc64el (2.9.4+dfsg1-3build1) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libmagic1:ppc64el (1:5.30-1) ... Setting up libcroco3:ppc64el (0.6.12-1) ... Processing triggers for libc-bin (2.24-12ubuntu1) ... Setting up autotools-dev (20161112.1) ... Setting up liblocale-gettext-perl (1.07-3build2) ... Setting up bsdmainutils (9.0.12+nmu1ubuntu1) ... 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 bc (1.06.95-9build2) ... Setting up libpython2.7-stdlib:ppc64el (2.7.13-4) ... Setting up autopoint (0.19.8.1-2ubuntu1) ... Setting up zlib1g-dev:ppc64el (1:1.2.11.dfsg-0ubuntu1) ... Setting up libfile-stripnondeterminism-perl (0.038-1) ... Setting up gettext (0.19.8.1-2ubuntu1) ... Setting up python2.7 (2.7.13-4) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up libpython-stdlib:ppc64el (2.7.13-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15-6ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up help2man (1.47.4) ... Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python (2.7.13-2) ... Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.038-1) ... Setting up debhelper (10.6.4ubuntu1) ... Setting up sbuild-build-depends-subread-dummy (0.invalid.0) ... (Reading database ... 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Processing triggers for libc-bin (2.24-12ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-87-generic ppc64el (ppc64le) Toolchain package versions: binutils_2.29-1ubuntu1 dpkg-dev_1.18.24ubuntu1 g++-6_6.4.0-2ubuntu1 gcc-6_6.4.0-2ubuntu1 libc6-dev_2.24-12ubuntu1 libstdc++-6-dev_6.4.0-2ubuntu1 libstdc++6_7.1.0-10ubuntu1 linux-libc-dev_4.11.0-11.16 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_2.0-1 apt_1.5~beta1 apt-transport-https_1.5~beta1 autoconf_2.69-10 automake_1:1.15-6ubuntu1 autopoint_0.19.8.1-2ubuntu1 autotools-dev_20161112.1 base-files_9.6ubuntu101 base-passwd_3.5.43 bash_4.4-5ubuntu1 bc_1.06.95-9build2 binutils_2.29-1ubuntu1 bsdmainutils_9.0.12+nmu1ubuntu1 bsdutils_1:2.30.1-0ubuntu1 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 coreutils_8.26-3ubuntu3 cpp_4:6.3.0-2ubuntu2 cpp-6_6.4.0-2ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.63 debhelper_10.6.4ubuntu1 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2ubuntu2 dpkg_1.18.24ubuntu1 dpkg-dev_1.18.24ubuntu1 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-1ubuntu2 file_1:5.30-1 findutils_4.6.0+git+20170606-3 g++_4:6.3.0-2ubuntu2 g++-6_6.4.0-2ubuntu1 gcc_4:6.3.0-2ubuntu2 gcc-6_6.4.0-2ubuntu1 gcc-6-base_6.4.0-2ubuntu1 gcc-7-base_7.1.0-10ubuntu1 gettext_0.19.8.1-2ubuntu1 gettext-base_0.19.8.1-2ubuntu1 gnupg_2.1.15-1ubuntu7 gnupg-agent_2.1.15-1ubuntu7 gpgv_2.1.15-1ubuntu7 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5ubuntu1 help2man_1.47.4 hostname_3.18 init_1.49 init-system-helpers_1.49 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu10 libapt-pkg5.0_1.5~beta1 libarchive-zip-perl_1.59-1 libasan3_6.4.0-2ubuntu1 libasn1-8-heimdal_7.4.0.dfsg.1-2 libassuan0_2.4.3-2 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libperl5.26_5.26.0-4 libpipeline1_1.4.2-1 libpng16-16_1.6.30-2 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.17.0-5 libpython-stdlib_2.7.13-2 libpython2.7-minimal_2.7.13-4 libpython2.7-stdlib_2.7.13-4 libreadline7_7.0-0ubuntu2 libroken18-heimdal_7.4.0.dfsg.1-2 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-2ubuntu1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-2ubuntu1 libseccomp2_2.3.1-2.1ubuntu1 libselinux1_2.6-3build1 libsemanage-common_2.6-2build1 libsemanage1_2.6-2build1 libsepol1_2.6-2 libsigsegv2_2.11-1 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.30.1-0ubuntu1 libsqlite3-0_3.19.3-3 libss2_1.43.4-2 libssl1.0.0_1.0.2g-1ubuntu13 libstdc++-6-dev_6.4.0-2ubuntu1 libstdc++6_7.1.0-10ubuntu1 libsystemd0_234-2ubuntu1 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libubsan0_7.1.0-10ubuntu1 libudev1_234-2ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.30.1-0ubuntu1 libwind0-heimdal_7.4.0.dfsg.1-2 libxml2_2.9.4+dfsg1-3build1 linux-libc-dev_4.11.0-11.16 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu2 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17ubuntu2 mime-support_3.60ubuntu1 mount_2.30.1-0ubuntu1 multiarch-support_2.24-12ubuntu1 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu13 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu2 patch_2.7.5-1build1 perl_5.26.0-4 perl-base_5.26.0-4 perl-modules-5.24_5.24.1-7ubuntu1 perl-modules-5.26_5.26.0-4 pinentry-curses_1.0.0-2 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 python_2.7.13-2 python-minimal_2.7.13-2 python2.7_2.7.13-4 python2.7-minimal_2.7.13-4 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-subread-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9+nmu1 systemd_234-2ubuntu1 systemd-sysv_234-2ubuntu1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tar_1.29b-2 tzdata_2017b-2 ubuntu-keyring_2016.10.27 util-linux_2.30.1-0ubuntu1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu1 zlib1g-dev_1:1.2.11.dfsg-0ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Jul 28 14:26:47 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./subread_1.5.3+dfsg-1.dsc dpkg-source: info: extracting subread in subread-1.5.3+dfsg dpkg-source: info: unpacking subread_1.5.3+dfsg.orig.tar.xz dpkg-source: info: unpacking subread_1.5.3+dfsg-1.debian.tar.xz dpkg-source: info: applying typo.patch dpkg-source: info: applying fix_ftbfs_kfreebsd.patch dpkg-source: info: applying arch_specific_flags.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<>/subread-1.5.3+dfsg SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>/subread-1.5.3+dfsg' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package subread dpkg-buildpackage: info: source version 1.5.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build subread-1.5.3+dfsg dpkg-buildpackage: info: host architecture ppc64el fakeroot debian/rules clean dh clean --parallel dh_testdir dh_auto_clean dh_autoreconf_clean debian/rules override_dh_clean make[1]: Entering directory '/<>/subread-1.5.3+dfsg' cd src; make -f Makefile.Linux clean make[2]: Entering directory '/<>/subread-1.5.3+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 '/<>/subread-1.5.3+dfsg/src' dh_clean make[1]: Leaving directory '/<>/subread-1.5.3+dfsg' debian/rules build-arch dh build-arch --parallel dh_testdir -a -O--parallel dh_update_autotools_config -a -O--parallel dh_autoreconf -a -O--parallel dh_auto_configure -a -O--parallel debian/rules override_dh_auto_build make[1]: Entering directory '/<>/subread-1.5.3+dfsg' cd src; make -f Makefile.Linux make[2]: Entering directory '/<>/subread-1.5.3+dfsg/src' gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -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:159:7: 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:898:19: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types] gzFile * rawfp = gzopen(fname, "r"); ^~~~~~ core.c:909:25: 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:1491:24: 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:920:11: 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:1630:24: 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:1609:16: 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:2275:6: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] int ret; ^~~ core.c: In function ‘write_realignments_for_fragment’: core.c:2491:21: warning: variable ‘raw_r2’ set but not used [-Wunused-but-set-variable] mapping_result_t * raw_r2 = NULL; ^~~~~~ core.c:2488:21: 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:2585:6: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] int ret; ^~~ core.c: In function ‘do_voting’: core.c:3235:9: 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:3145:6: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] int ret, xk1; ^~~ core.c: In function ‘do_iteration_two’: core.c:2533:3: 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:2597:6: note: ‘read_len_1’ was declared here int read_len_1, read_len_2=0; ^~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -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:960:12: 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 ‘find_donor_receptor’: core-junction.c:2011:8: warning: variable ‘sp2s’ set but not used [-Wunused-but-set-variable] char sp2s[200]; ^~~~ core-junction.c: In function ‘final_CIGAR_quality’: core-junction.c:2848:13: warning: variable ‘debug_ptr’ set but not used [-Wunused-but-set-variable] char * debug_ptr = read_text; ^~~~~~~~~ core-junction.c:2880:13: warning: variable ‘debug_ptr’ set but not used [-Wunused-but-set-variable] char * debug_ptr = read_text + read_cursor; ^~~~~~~~~ core-junction.c: In function ‘finalise_explain_CIGAR’: core-junction.c:3234:94: 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, chromosomal_length = 0, full_section_clipped = 0; ^~~~~~~~~~~~~~~~~~~~~ core-junction.c:3212:28: warning: variable ‘isCigarOK’ set but not used [-Wunused-but-set-variable] int mismatch_bases = 0, isCigarOK = 0; ^~~~~~~~~ core-junction.c:3050:23: 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:5616:23: warning: variable ‘candBrkPlist’ set but not used [-Wunused-but-set-variable] chromosome_event_t * candBrkPlist [_PQR_LIST_SIZE]; ^~~~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -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:2051:9: 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 ‘print_indel_table’: core-indel.c:2255:24: warning: unused variable ‘event_body’ [-Wunused-variable] chromosome_event_t * event_body = indel_context -> event_space_dynamic +xk1; ^~~~~~~~~~ core-indel.c:2269:26: warning: unused variable ‘event_body’ [-Wunused-variable] chromosome_event_t * event_body = indel_context -> event_space_dynamic + (env_array[env_i]-1); ^~~~~~~~~~ core-indel.c:2265:17: warning: unused variable ‘entry_pos’ [-Wunused-variable] unsigned int entry_pos = cursor->key - NULL; ^~~~~~~~~ core-indel.c: In function ‘full_indel_alignment’: core-indel.c:3436:41: warning: variable ‘best_right’ set but not used [-Wunused-but-set-variable] int best_edge_score = -1, best_left, best_right; ^~~~~~~~~~ core-indel.c:3436:30: 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:3535:24: 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:3813:3: 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:3814:3: 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:3815:3: 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:3892:3: 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:3893:3: 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:3894:3: 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:4256:3: 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:4257:3: 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:4258:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(qual_text, sizeof(char), read_len, tmp_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -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:356:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&ID1, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:357:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&ID2, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:358:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&CM, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:359:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&FLG, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:368:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&XLEN,1, 2, bam_fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:376:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&SI1, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:377:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&SI2, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:383:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&BSIZE_MID, 1,2 , bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:395:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer, 1, CDATA_READING, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -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:774:6: warning: variable ‘last_end’ set but not used [-Wunused-but-set-variable] int last_end=0, last_offset = 0, cursor = 0; ^~~~~~~~ gene-algorithms.c:773:9: 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:1186:28: 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:1735:6: 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:2376:7: warning: variable ‘is_match_begin’ set but not used [-Wunused-but-set-variable] int is_match_begin = 0; ^~~~~~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -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_get_next_read_BIN’: input-files.c:2782:11: 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:4418:23: 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:4961:9: warning: variable ‘ref_name’ set but not used [-Wunused-but-set-variable] char ref_name[MAX_CHROMOSOME_NAME_LEN]; ^~~~~~~~ input-files.c: In function ‘SAM_pairer_long_cigar_run’: input-files.c:5206:20: warning: unused variable ‘is_longcigar’ [-Wunused-variable] int x1, nch = 0, is_longcigar = 0, binptr = 0; ^~~~~~~~~~~~ input-files.c:5201:7: warning: unused variable ‘out_bin_ptr’ [-Wunused-variable] int out_bin_ptr = 0; ^~~~~~~~~~~ input-files.c:5199:7: warning: unused variable ‘disk_is_full’ [-Wunused-variable] int disk_is_full = 0; ^~~~~~~~~~~~ input-files.c: In function ‘geinput_next_char’: input-files.c:532:5: 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:3512:2: 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:3722:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&rlen, 1, 2, fp); ^~~~~~~~~~~~~~~~~~~~~~ input-files.c:3734:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&rlen, 1, 4, fp); ^~~~~~~~~~~~~~~~~~~~~~ input-files.c: In function ‘SAM_pairer_osr_next_bin’: input-files.c:3743:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&rlen, 1, 2, fp); ^~~~~~~~~~~~~~~~~~~~~~ input-files.c:3747:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&rlen, 1, 4, fp); ^~~~~~~~~~~~~~~~~~~~~~ input-files.c:3749:2: 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:4397:4: 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:5422:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_name_len, 2,1 , bbfp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-files.c:5428:6: 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:5431:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_len,2,1,bbfp); ^~~~~~~~~~~~~~~~~~~~~~~~~ input-files.c:5437:6: 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:5490:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_name_len, 2,1 , bbfp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-files.c:5496:6: 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:5500:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_len, 2,1 , bbfp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-files.c:5503:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(read_line_buf, 1, read_len, bbfp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -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 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -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:227:7: 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:228:7: 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:231:9: 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:237:5: 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 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o txUnique tx-unique.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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE tx-unique.c: In function ‘txunique_parse_options’: tx-unique.c:391:6: warning: unused variable ‘sort_needed’ [-Wunused-variable] int sort_needed = 0; ^~~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE readSummary.c: In function ‘calc_junctions_from_cigar’: readSummary.c:377:15: warning: variable ‘right_boundary’ set but not used [-Wunused-but-set-variable] unsigned int right_boundary = 0; ^~~~~~~~~~~~~~ readSummary.c: In function ‘calc_total_frag_len’: readSummary.c:1801:15: warning: variable ‘merged_section_indel_positions’ set but not used [-Wunused-but-set-variable] unsigned int merged_section_indel_positions[ MAXIMUM_INSERTION_IN_SECTION * 3 ][ MAXIMUM_INSERTION_IN_SECTION ]; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:1799:16: warning: variable ‘merged_section_belong_R2’ set but not used [-Wunused-but-set-variable] unsigned char merged_section_belong_R2[ MAXIMUM_INSERTION_IN_SECTION * 3 ]; ^~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:1798:16: warning: variable ‘merged_section_belong_R1’ set but not used [-Wunused-but-set-variable] unsigned char merged_section_belong_R1[ MAXIMUM_INSERTION_IN_SECTION * 3 ]; ^~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:1796:15: warning: variable ‘merged_section_start_positions’ set but not used [-Wunused-but-set-variable] unsigned int merged_section_start_positions[ MAXIMUM_INSERTION_IN_SECTION * 3 ]; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c: In function ‘compress_read_detail_BAM’: readSummary.c:2401:8: warning: unused variable ‘write_ptr’ [-Wunused-variable] int write_ptr, bin_len = write_end - write_start; ^~~~~~~~~ readSummary.c: In function ‘fc_thread_start_threads’: readSummary.c:3865:23: warning: too many arguments for format [-Wformat-extra-args] sprintf(tmp_fname, "%s.featureCounts%s", global_context -> raw_input_file_name, global_context -> input_file_short_name, global_context -> is_read_details_out == FILE_TYPE_BAM?".bam":(global_context -> is_read_details_out == FILE_TYPE_SAM?".sam":"")); ^~~~~~~~~~~~~~~~~~~~ readSummary.c: In function ‘readSummary’: readSummary.c:5023:9: warning: variable ‘curchr_name’ set but not used [-Wunused-but-set-variable] char * curchr_name, * fasta_contigs_fname; ^~~~~~~~~~~ readSummary.c:5022:15: warning: variable ‘curpos’ set but not used [-Wunused-but-set-variable] long curchr, curpos; ^~~~~~ readSummary.c:5022:7: warning: variable ‘curchr’ set but not used [-Wunused-but-set-variable] long curchr, curpos; ^~~~~~ readSummary.c: In function ‘load_feature_info’: readSummary.c:953:3: 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:1619:3: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result] ftruncate(fileno(global_context -> read_details_out_FP), 0); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c: In function ‘calc_total_frag_len.part.2’: readSummary.c:1837:113: warning: array subscript is above array bounds [-Warray-bounds] CIGAR_intervals_R2[R2_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R2[R2_i].insertion_start_pos[insmov_i]; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ readSummary.c:1865:113: warning: array subscript is above array bounds [-Warray-bounds] CIGAR_intervals_R1[R1_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R1[R1_i].insertion_start_pos[insmov_i]; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ readSummary.c:1897:112: warning: array subscript is above array bounds [-Warray-bounds] CIGAR_intervals_R1[R1_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R1[R1_i].insertion_start_pos[insmov_i]; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ readSummary.c:1906:112: warning: array subscript is above array bounds [-Warray-bounds] CIGAR_intervals_R2[R2_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R2[R2_i].insertion_start_pos[insmov_i]; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE removeDupReads.c: In function ‘parse_base_blocks’: removeDupReads.c:88:5: 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:97:5: 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 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE SNPCalling.c: In function ‘read_tmp_block’: SNPCalling.c:276:4: 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:295:4: 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:296:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_len, sizeof(short), 1, tmp_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SNPCalling.c:297:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(read, sizeof(char), read_len, tmp_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE index-builder.c: In function ‘scan_gene_index’: index-builder.c:474:19: 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:1210:2: warning: ignoring return value of ‘mkstemp’, declared with attribute warn_unused_result [-Wunused-result] mkstemp(tmp_fa_file); ^~~~~~~~~~~~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE 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:1630:24: 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:1630:24: 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 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE propmapped.c: In function ‘prop_PE’: propmapped.c:368:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_len,1,1,fp); ^~~~~~~~~~~~~~~~~~~~~~~ propmapped.c:371:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(read_name,read_len,1,fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ propmapped.c:375:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&flags,1, sizeof(short), fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.3"\" -D_FILE_OFFSET_BITS=64 -ggdb -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 -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE mkdir -p ../bin/utilities mv subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/ mv repair coverageCount propmapped qualityScores removeDup subread-fullscan txUnique ../bin/utilities ########################################################### # # # Installation successfully complete. # # # # Generated executables were copied to directory ../bin/ # # # ########################################################### make[2]: Leaving directory '/<>/subread-1.5.3+dfsg/src' dh_auto_build -- CC=powerpc64le-linux-gnu-gcc make[1]: Leaving directory '/<>/subread-1.5.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/subread-1.5.3+dfsg' debian/tests/subread-tests /<>/subread-1.5.3+dfsg  ************************************************** ************************************************** *** *** *** This script will test the major functions *** *** in our package, including the index build- *** *** er, subread-align, subjunc, featureCounts *** *** and exactSNP. *** *** *** *** Test will start in seconds. *** *** *** ************************************************** ************************************************** 9876543210[0,0H ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.3 //=========================== indexBuilder setting ===========================\\ || || || Index name : ../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, '../small1.log'. || || Scan uninformative subreads in reference sequences ... || || 8%, 0 mins elapsed, rate=275.0k bps/s, total=0m || || 16%, 0 mins elapsed, rate=470.7k bps/s, total=0m || || 24%, 0 mins elapsed, rate=647.5k bps/s, total=0m || || 33%, 0 mins elapsed, rate=799.2k bps/s, total=0m || || 41%, 0 mins elapsed, rate=940.4k bps/s, total=0m || || 49%, 0 mins elapsed, rate=1063.6k bps/s, total=0m || || 58%, 0 mins elapsed, rate=1173.5k bps/s, total=0m || || 66%, 0 mins elapsed, rate=1272.0k bps/s, total=0m || || 74%, 0 mins elapsed, rate=1356.0k bps/s, total=0m || || 83%, 0 mins elapsed, rate=1436.5k bps/s, total=0m || || 91%, 0 mins elapsed, rate=1509.9k bps/s, total=0m || || 99%, 0 mins elapsed, rate=1572.0k bps/s, total=0m || || 52 uninformative subreads were found. || || These subreads were excluded from index building. || || Build the index... || || 8%, 0 mins elapsed, rate=718.2k bps/s, total=0m || || 16%, 0 mins elapsed, rate=727.7k bps/s, total=0m || || 24%, 0 mins elapsed, rate=728.7k bps/s, total=0m || || 33%, 0 mins elapsed, rate=778.7k bps/s, total=0m || || 41%, 0 mins elapsed, rate=839.9k bps/s, total=0m || || 49%, 0 mins elapsed, rate=904.0k bps/s, total=0m || || 58%, 0 mins elapsed, rate=967.2k bps/s, total=0m || || 66%, 0 mins elapsed, rate=1028.6k bps/s, total=0m || || 74%, 0 mins elapsed, rate=1088.3k bps/s, total=0m || || 83%, 0 mins elapsed, rate=1144.5k bps/s, total=0m || || 91%, 0 mins elapsed, rate=1202.7k bps/s, total=0m || || 99%, 0 mins elapsed, rate=1265.6k 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 ../small1 was successfully built! || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.3 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Input file : data/test-noerror-r1.fq || || Output file : result/test-tmp.sam (SAM) || || Index name : ../small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || Min votes : 3 / 10 || || Maximum allowed mismatches : 3 || || Maximum allowed indel bases : 5 || || # of best alignments reported : 1 || || Unique mapping : yes || || || \\===================== http://subread.sourceforge.net/ ======================// //================ Running (28-Jul-2017 23:07:53, pid=11555) =================\\ || || || 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... || || 33% completed, 0.0 mins elapsed, rate=28.3k reads per second || || 39% completed, 0.0 mins elapsed, rate=28.3k reads per second || || 46% completed, 0.0 mins elapsed, rate=28.3k reads per second || || 53% completed, 0.0 mins elapsed, rate=28.3k reads per second || || 60% completed, 0.0 mins elapsed, rate=28.3k reads per second || || 74% completed, 0.0 mins elapsed, rate=9.3k reads per second || || 83% completed, 0.0 mins elapsed, rate=9.8k reads per second || || 91% completed, 0.0 mins elapsed, rate=10.2k reads per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 19998 reads || || Mapped : 18758 reads (93.8%), wherein || || Uniquely mapped : 18758 || || Multi-mapping : 0 || || || || Not mapped : 1240 || || || || Indels : 5 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.3 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Input file : data/test-noerror-r1.fq || || Output file : result/test-tmp.sam (SAM) || || Index name : ../small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || Min votes : 3 / 10 || || Maximum allowed mismatches : 3 || || Maximum allowed indel bases : 5 || || # of best alignments reported : 1 || || Unique mapping : yes || || || \\===================== http://subread.sourceforge.net/ ======================// //================ Running (28-Jul-2017 23:07:56, pid=11558) =================\\ || || || 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... || || 33% completed, 0.0 mins elapsed, rate=30.2k reads per second || || 39% completed, 0.0 mins elapsed, rate=30.2k reads per second || || 46% completed, 0.0 mins elapsed, rate=30.1k reads per second || || 53% completed, 0.0 mins elapsed, rate=30.1k reads per second || || 60% completed, 0.0 mins elapsed, rate=30.2k reads per second || || 74% completed, 0.0 mins elapsed, rate=10.5k reads per second || || 83% completed, 0.0 mins elapsed, rate=10.9k reads per second || || 91% completed, 0.0 mins elapsed, rate=11.3k reads per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 19998 reads || || Mapped : 18758 reads (93.8%), wherein || || Uniquely mapped : 18758 || || Multi-mapping : 0 || || || || Not mapped : 1240 || || || || Indels : 5 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.3 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : data/test-noerror-r1.fq || || Input file 2 : data/test-noerror-r2.fq || || Output file : result/test-tmp.sam (SAM) || || Index name : ../small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Maximum allowed mismatches : 3 || || Maximum allowed indel bases : 5 || || # of best alignments reported : 1 || || Unique mapping : yes || || || \\===================== http://subread.sourceforge.net/ ======================// //================ Running (28-Jul-2017 23:07:59, pid=11561) =================\\ || || || 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... || || 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=14.1k fragments per second || || 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 : 19998 fragments || || Mapped : 19216 fragments (96.1%), wherein || || Uniquely mapped : 19216 || || Multi-mapping : 0 || || || || Not mapped : 782 || || || || Correctly paired : 18830 fragments || || Not mapped in pairs : 386 fragments, wherein || || Only one end mapped : 1 fragments || || Multi-chromosomes : 0 fragments || || Different strands : 0 fragments || || Not in PE distance : 385 fragments || || Abnormal order : 0 fragments || || || || Indels : 22 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.3 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : data/test-noerror-r1.fq || || Input file 2 : data/test-noerror-r2.fq || || Output file : result/test-tmp.sam (SAM) || || Index name : ../small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Maximum allowed mismatches : 3 || || Maximum allowed indel bases : 5 || || # of best alignments reported : 1 || || Unique mapping : yes || || || \\===================== http://subread.sourceforge.net/ ======================// //================ Running (28-Jul-2017 23:08:03, pid=11564) =================\\ || || || 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... || || 33% completed, 0.0 mins elapsed, rate=13.9k fragments per second || || 39% completed, 0.0 mins elapsed, rate=13.8k fragments per second || || 46% completed, 0.0 mins elapsed, rate=13.7k fragments per second || || 53% completed, 0.0 mins elapsed, rate=13.6k fragments per second || || 60% completed, 0.0 mins elapsed, rate=13.5k fragments per second || || 74% completed, 0.0 mins elapsed, rate=7.4k fragments per second || || 83% completed, 0.0 mins elapsed, rate=7.5k fragments per second || || 91% completed, 0.0 mins elapsed, rate=7.6k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 19998 fragments || || Mapped : 19216 fragments (96.1%), wherein || || Uniquely mapped : 19216 || || Multi-mapping : 0 || || || || Not mapped : 782 || || || || Correctly paired : 18830 fragments || || Not mapped in pairs : 386 fragments, wherein || || Only one end mapped : 1 fragments || || Multi-chromosomes : 0 fragments || || Different strands : 0 fragments || || Not in PE distance : 385 fragments || || Abnormal order : 0 fragments || || || || Indels : 22 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.3 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : data/test-error-r1.fq || || Input file 2 : data/test-error-r2.fq || || Output file : result/test-tmp.sam (SAM) || || Index name : ../small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Maximum allowed mismatches : 3 || || Maximum allowed indel bases : 5 || || # of best alignments reported : 1 || || Unique mapping : yes || || || \\===================== http://subread.sourceforge.net/ ======================// //================ Running (28-Jul-2017 23:08:06, pid=11567) =================\\ || || || 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... || || 33% completed, 0.0 mins elapsed, rate=13.6k fragments per second || || 39% completed, 0.0 mins elapsed, rate=13.6k fragments per second || || 46% completed, 0.0 mins elapsed, rate=13.5k fragments per second || || 53% completed, 0.0 mins elapsed, rate=13.5k fragments per second || || 60% completed, 0.0 mins elapsed, rate=13.4k fragments per second || || 74% completed, 0.0 mins elapsed, rate=6.8k fragments per second || || 83% completed, 0.0 mins elapsed, rate=7.0k fragments per second || || 91% completed, 0.0 mins elapsed, rate=7.1k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 20000 fragments || || Mapped : 18698 fragments (93.5%), wherein || || Uniquely mapped : 18698 || || Multi-mapping : 0 || || || || Not mapped : 1302 || || || || Correctly paired : 13915 fragments || || Not mapped in pairs : 4783 fragments, wherein || || Only one end mapped : 4506 fragments || || Multi-chromosomes : 0 fragments || || Different strands : 0 fragments || || Not in PE distance : 273 fragments || || Abnormal order : 4 fragments || || || || Indels : 53 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.3 //========================== subread-align setting ===========================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : data/test-err-mut-r1.fq.gz || || Input file 2 : data/test-err-mut-r2.fq.gz || || Output file : result/test-tmp.sam (SAM) || || Index name : ../small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Maximum allowed mismatches : 3 || || Maximum allowed indel bases : 5 || || # of best alignments reported : 1 || || Unique mapping : yes || || Read group name : MyTestGroup || || || \\===================== http://subread.sourceforge.net/ ======================// //================ Running (28-Jul-2017 23:08:10, pid=11570) =================\\ || || || 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... || || 34% completed, 0.0 mins elapsed, rate=27.6k fragments per second || || 40% completed, 0.0 mins elapsed, rate=27.4k fragments per second || || 48% completed, 0.0 mins elapsed, rate=27.5k fragments per second || || 53% completed, 0.0 mins elapsed, rate=27.5k fragments per second || || 59% completed, 0.0 mins elapsed, rate=27.4k fragments per second || || 67% completed, 0.0 mins elapsed, rate=27.5k fragments per second || || 75% completed, 0.0 mins elapsed, rate=10.0k fragments per second || || 83% completed, 0.0 mins elapsed, rate=10.6k fragments per second || || 92% completed, 0.0 mins elapsed, rate=11.1k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 20001 fragments || || Mapped : 18659 fragments (93.3%), wherein || || Uniquely mapped : 18659 || || Multi-mapping : 0 || || || || Not mapped : 1342 || || || || Correctly paired : 13557 fragments || || Not mapped in pairs : 5102 fragments, wherein || || Only one end mapped : 4788 fragments || || Multi-chromosomes : 0 fragments || || Different strands : 0 fragments || || Not in PE distance : 309 fragments || || Abnormal order : 5 fragments || || || || Indels : 172 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// 6fb1cd9408bc8a874e3f21f370dfdc66 ../small1.00.b.array 3b39eb4b0aad6902d8a1be198cf2478d ../small1.00.b.tab ************************************************* *** SINGLE-END READS NO ERROR ****** ************************************************* unmatched= 0 ; matched= 18758 ; unmapped= 1240 ; reads= 19998 ;NN= 0 accuracy= 1.0 ; sensitivity= 0.93799379938 paired_match= 0 ; paired= 0.0 ************************************************* *** SINGLE-END READS NO ERROR NO DUP ****** ************************************************* unmatched= 0 ; matched= 18758 ; unmapped= 1240 ; reads= 19998 ;NN= 0 accuracy= 1.0 ; sensitivity= 0.93799379938 paired_match= 0 ; paired= 0.0 ************************************************* *** READS WITH NO ERROR ****** ************************************************* unmatched= 0 ; matched= 38431 ; unmapped= 1565 ; reads= 39996 ;NN= 0 accuracy= 1.0 ; sensitivity= 0.960871087109 paired_match= 38430 ; paired= 0.99997397934 ************************************************* *** READS NO ERROR, NO DUPLICATED REPORT ****** ************************************************* unmatched= 0 ; matched= 38431 ; unmapped= 1565 ; reads= 39996 ;NN= 0 accuracy= 1.0 ; sensitivity= 0.960871087109 paired_match= 38430 ; paired= 0.99997397934 ************************************************* *** READS WITH ONLY SEQUENCING ERROR ****** ************************************************* unmatched= 10 ; matched= 32880 ; unmapped= 7110 ; reads= 40000 ;NN= 0 accuracy= 0.999695956218 ; sensitivity= 0.82225 paired_match= 28374 ; paired= 0.86295620438 ************************************************* *** READS WITH SEQUENCING ERROR AND MUTATION *** *** SUBREAD IS RUN WITH LONG INDEL DETECTION *** ************************************************* unmatched= 13 ; matched= 32515 ; unmapped= 7472 ; reads= 40002 ;NN= 0 accuracy= 0.999600344319 ; sensitivity= 0.813159342033 paired_match= 27730 ; paired= 0.852837152084 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.3 //=========================== indexBuilder setting ===========================\\ || || || Index name : ../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, '../small1.log'. || || Scan uninformative subreads in reference sequences ... || || 8%, 0 mins elapsed, rate=590.9k bps/s, total=0m || || 16%, 0 mins elapsed, rate=905.6k bps/s, total=0m || || 24%, 0 mins elapsed, rate=1195.9k bps/s, total=0m || || 33%, 0 mins elapsed, rate=1449.0k bps/s, total=0m || || 41%, 0 mins elapsed, rate=1673.0k bps/s, total=0m || || 49%, 0 mins elapsed, rate=1879.3k bps/s, total=0m || || 58%, 0 mins elapsed, rate=2060.8k bps/s, total=0m || || 66%, 0 mins elapsed, rate=2236.7k bps/s, total=0m || || 74%, 0 mins elapsed, rate=2388.1k bps/s, total=0m || || 83%, 0 mins elapsed, rate=2532.4k bps/s, total=0m || || 91%, 0 mins elapsed, rate=2664.2k bps/s, total=0m || || 99%, 0 mins elapsed, rate=2792.7k bps/s, total=0m || || 2 uninformative subreads were found. || || These subreads were excluded from index building. || || Build the index... || || 8%, 0 mins elapsed, rate=1343.8k bps/s, total=0m || || 16%, 0 mins elapsed, rate=1365.9k bps/s, total=0m || || 24%, 0 mins elapsed, rate=1396.4k bps/s, total=0m || || 33%, 0 mins elapsed, rate=1406.2k bps/s, total=0m || || 41%, 0 mins elapsed, rate=1461.7k bps/s, total=0m || || 49%, 0 mins elapsed, rate=1474.6k bps/s, total=0m || || 58%, 0 mins elapsed, rate=1503.1k bps/s, total=0m || || 66%, 0 mins elapsed, rate=1542.9k bps/s, total=0m || || 74%, 0 mins elapsed, rate=1565.5k bps/s, total=0m || || 83%, 0 mins elapsed, rate=1523.2k bps/s, total=0m || || 91%, 0 mins elapsed, rate=1504.9k bps/s, total=0m || || 99%, 0 mins elapsed, rate=1483.4k 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 ../small1 was successfully built! || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.3 //============================= subjunc setting ==============================\\ || || || Function : Read alignment + Junction detection (RNA-Seq) || || Input file 1 : data/junction-reads-A.fq || || Input file 2 : data/junction-reads-B.fq || || Output file : result/junctions.sam (SAM) || || Index name : ../small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || # of extracted subreads : 14 || || Min read1 vote : 1 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Maximum allowed mismatches : 3 || || Maximum allowed indel bases : 5 || || # of best alignments reported : 1 || || Unique mapping : yes || || || \\===================== http://subread.sourceforge.net/ ======================// //================ Running (28-Jul-2017 23:08:15, pid=11577) =================\\ || || || 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... || || 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 || || 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 : 15251 fragments (95.0%), wherein || || Uniquely mapped : 15251 || || Multi-mapping : 0 || || || || Not mapped : 801 || || || || Correctly paired : 13813 fragments || || Not mapped in pairs : 1438 fragments, wherein || || Only one end mapped : 967 fragments || || Multi-chromosomes : 0 fragments || || Different strands : 37 fragments || || Not in PE distance : 333 fragments || || Abnormal order : 101 fragments || || || || Junctions : 416 || || Indels : 182 || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.3 //============================= subjunc setting ==============================\\ || || || Function : Read alignment + Junction/Fusion detection (RNA-Seq) || || Input file 1 : data/junction-reads-A.fq || || Input file 2 : data/junction-reads-B.fq || || Output file : result/junctionsNfusions.bam (BAM) || || Index name : ../small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || # of extracted subreads : 28 || || Min read1 vote : 1 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Maximum allowed mismatches : 3 || || Maximum allowed indel bases : 5 || || # of best alignments reported : 1 || || Unique mapping : yes || || || \\===================== http://subread.sourceforge.net/ ======================// //================ Running (28-Jul-2017 23:08:20, pid=11578) =================\\ || || || 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... || || 41% completed, 0.0 mins elapsed, rate=4.9k fragments per second || || 48% completed, 0.1 mins elapsed, rate=4.9k fragments per second || || 54% completed, 0.1 mins elapsed, rate=4.9k fragments per second || || 61% completed, 0.1 mins elapsed, rate=4.9k fragments per second || || 77% completed, 0.1 mins elapsed, rate=3.0k fragments per second || || 87% completed, 0.1 mins elapsed, rate=3.2k fragments per second || || 97% completed, 0.1 mins elapsed, rate=3.4k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 16052 fragments || || Mapped : 15235 fragments (94.9%), wherein || || Uniquely mapped : 15235 || || Multi-mapping : 0 || || || || Not mapped : 817 || || || || Correctly paired : 13723 fragments || || Not mapped in pairs : 1512 fragments, wherein || || Only one end mapped : 1010 fragments || || Multi-chromosomes : 0 fragments || || Different strands : 35 fragments || || Not in PE distance : 367 fragments || || Abnormal order : 100 fragments || || || || Junctions : 434 || || Fusions : 92 || || Indels : 183 || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ================================================================================ FeatureCounts Basic Test http://subread.sourceforge.net/ ================================================================================ ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.3 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || P data/test-minimum.sam || || || || Output file : result/test-minimum.FC || || Summary : result/test-minimum.FC.summary || || Annotation : data/test-minimum.GTF (GTF) || || Dir for temp files : result || || || || Threads : 1 || || Level : meta-feature level || || Paired-end : no || || Strand specific : no || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\===================== 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. || || || || Summary of counting results can be found in file "result/test-minimum.FC" || || || \\===================== http://subread.sourceforge.net/ ======================// ================================================================================ Basic Test finished. The results are in result/test-minimum.FC ================================================================================ ================================================================================ FeatureCounts Chromosome Name Aliases Tests http://subread.sourceforge.net/ ================================================================================ Testing chromosome aliases ... [PASS] ================================================================================ FeatureCounts Chromosome Name Inference Tests http://subread.sourceforge.net/ ================================================================================ Testing automatic inference of chromosome names ... [PASS] ================================================================================ FeatureCounts Corner Case Tests http://subread.sourceforge.net/ ================================================================================ Testing indel reads ... [PASS] Testing junction reads ... [PASS] Testing paired-end reads (fragment counting) ... [PASS] Testing paired-end reads (fragment counting, both ends mapped) ... [PASS] Testing multi-overlapping reads ... [PASS] Testing feature-level summarization ... [PASS] Testing gene-level summarization ... [PASS] Testing multi-mapping reads ... [PASS] Testing multi-mapping reads (primary only) ... [PASS] Testing both ends mapped ... [PASS] Testing disallowing chimeric fragments ... [PASS] Testing Allowing multi-mapped reads ... [PASS] Testing not sorting input file ... [PASS] Testing minimum overlapping length ... [PASS] Testing minimum overlapping fraction ... [PASS] Testing Largest Overlapping ... [PASS] Testing paired-end distance ... [PASS] Testing Read to position (5' end) ... [PASS] Testing Read to position (3' end) ... [PASS] Testing Read extension to the 3' end ... [PASS] Testing Read extension to the 5' end ... [PASS] Testing Low maxOPs value ... [PASS] Testing minimum mapping quality ... [PASS] Testing Ignoring duplicated reads ... [PASS] Testing Fraction counting ... [PASS] Testing Advanced fractions ... [PASS] Testing Junction counting ... [PASS,PASS] Skipping Junction counting (with genome). Testing GTF format annotations ... [PASS] Testing SAF format annotations ... [PASS] Testing SAM format input ... [PASS] Testing BAM format input ... [PASS] Testing unstranded read summarization ... [PASS] Testing stranded read summarization ... [PASS] Testing reversely stranded read summarization ... [PASS] Testing Ignoring duplicate fragments ... [PASS] Testing Junction reads only ... [PASS] Testing Exonic reads only ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] ../../bin/exactSNP -g ../chr901.fa -o result/test-out.VCF -i data/test-in.BAM -b ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.3 //============================= exactSNP setting =============================\\ || || || Input file : data/test-in.BAM (BAM) || || Output file : result/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 (28-Jul-2017 23:08:27) ======================\\ || || || Split BAM file into result/temp-snps-012343-FA163ED18BBA-* ... || || 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/ ======================//  ************************************************** ************************************************** *** *** *** Test finished. *** *** *** *** Should there be any error, please visit *** *** http://subread.sourceforge.net/ for more *** *** information. *** *** *** ************************************************** **************************************************  make[1]: Leaving directory '/<>/subread-1.5.3+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --parallel dh_testroot -a -O--parallel dh_prep -a -O--parallel debian/rules override_dh_auto_install make[1]: Entering directory '/<>/subread-1.5.3+dfsg' find /<>/subread-1.5.3+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \; mkdir -p /<>/subread-1.5.3+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)' \ /<>/subread-1.5.3+dfsg/bin/subread-align | debian/filter.pl > /<>/subread-1.5.3+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' \ /<>/subread-1.5.3+dfsg/bin/subread-buildindex | debian/filter.pl > /<>/subread-1.5.3+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' \ /<>/subread-1.5.3+dfsg/bin/subjunc | debian/filter.pl > /<>/subread-1.5.3+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' \ /<>/subread-1.5.3+dfsg/bin/featureCounts | debian/filter.pl > /<>/subread-1.5.3+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' \ /<>/subread-1.5.3+dfsg/bin/exactSNP | debian/filter.pl > /<>/subread-1.5.3+dfsg/debian/subread/usr/share/man/man1/exactSNP.1; help2man --no-info --help-option="''" --no-discard-stderr --name='detect short and long indels' \ /<>/subread-1.5.3+dfsg/bin/subindel | debian/filter.pl > /<>/subread-1.5.3+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' \ /<>/subread-1.5.3+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /<>/subread-1.5.3+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' \ /<>/subread-1.5.3+dfsg/bin/utilities/coverageCount | debian/filter.pl > /<>/subread-1.5.3+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' \ /<>/subread-1.5.3+dfsg/bin/utilities/propmapped | debian/filter.pl > /<>/subread-1.5.3+dfsg/debian/subread/usr/share/man/man1/propmapped.1; help2man --no-info --help-option="''" --no-discard-stderr --name='retrieve Phred score for read bases' \ /<>/subread-1.5.3+dfsg/bin/utilities/qualityScores| debian/filter.pl > /<>/subread-1.5.3+dfsg/debian/subread/usr/share/man/man1/qualityScores.1; help2man --no-info --help-option="''" --no-discard-stderr --name='Find reads that are from the same pair in the input and then place them next \ to each other in the output. A dummy read is added for each singleton read that does not have a pair. \ The output file is compatible with featureCounts program' \ /<>/subread-1.5.3+dfsg/bin/utilities/repair| debian/filter.pl > /<>/subread-1.5.3+dfsg/debian/subread/usr/share/man/man1/repair.1; help2man --no-info --help-option="''" --no-discard-stderr --name='Remove duplicated reads' \ /<>/subread-1.5.3+dfsg/bin/utilities/removeDup| debian/filter.pl > /<>/subread-1.5.3+dfsg/debian/subread/usr/share/man/man1/removeDup.1; dh_auto_install make[1]: Leaving directory '/<>/subread-1.5.3+dfsg' dh_install -a -O--parallel dh_installdocs -a -O--parallel dh_installchangelogs -a -O--parallel dh_installman -a -O--parallel dh_perl -a -O--parallel dh_link -a -O--parallel dh_strip_nondeterminism -a -O--parallel dh_compress -a -O--parallel dh_fixperms -a -O--parallel dh_missing -a -O--parallel dh_strip -a -O--parallel dh_makeshlibs -a -O--parallel dh_shlibdeps -a -O--parallel dh_installdeb -a -O--parallel dh_gencontrol -a -O--parallel dh_md5sums -a -O--parallel dh_builddeb -a -O--parallel INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 pkgstriptranslations: processing subread (in debian/subread); do_strip: , oemstrip: pkgstriptranslations: processing subread-dbgsym (in debian/.debhelper/subread/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/subread/DEBIAN/control, package subread, directory debian/subread pkgstripfiles: processing control file: debian/.debhelper/subread/dbgsym-root/DEBIAN/control, package subread-dbgsym, directory debian/.debhelper/subread/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package subread-dbgsym ... pkgstripfiles: Truncating usr/share/doc/subread/changelog.Debian.gz to topmost ten records pkgstripfiles: No PNG files. dpkg-deb: building package 'subread-dbgsym' in 'debian/.debhelper/scratch-space/build-subread/subread-dbgsym_1.5.3+dfsg-1_ppc64el.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package subread ... pkgstripfiles: No PNG files. dpkg-deb: building package 'subread' in '../subread_1.5.3+dfsg-1_ppc64el.deb'. Renaming subread-dbgsym_1.5.3+dfsg-1_ppc64el.deb to subread-dbgsym_1.5.3+dfsg-1_ppc64el.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../subread_1.5.3+dfsg-1_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build subread-1.5.3+dfsg dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20170728-2308 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ subread_1.5.3+dfsg-1_ppc64el.changes: ------------------------------------- Format: 1.8 Date: Fri, 28 Jul 2017 16:09:49 +0200 Source: subread Binary: subread subread-data Architecture: ppc64el Version: 1.5.3+dfsg-1 Distribution: artful-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 (1.5.3+dfsg-1) unstable; urgency=medium . * Bump Standards-Version to 4.0.0 * New upstream version 1.5.3+dfsg * Refresh and update paches * Update man pages * Remove trailing whitespaces from changelog Checksums-Sha1: 2f529268a2b0e13e87e4204a6d500b0e6f7912ae 7117054 subread-dbgsym_1.5.3+dfsg-1_ppc64el.ddeb 349e4a1ac24393a8219405947960f3fc790e9660 5296 subread_1.5.3+dfsg-1_ppc64el.buildinfo 82c4838b20cd9c6d57d4abe89e5b3dbe752983ea 496326 subread_1.5.3+dfsg-1_ppc64el.deb Checksums-Sha256: 6d71e92a288b2ca6ee6d2c06b1330a900da5d5bfd644c1f50af7b8ece59af207 7117054 subread-dbgsym_1.5.3+dfsg-1_ppc64el.ddeb e8365777b1d480b78a28a08d366397cd07923ddb6d8f7c65e7752d811be5a3b8 5296 subread_1.5.3+dfsg-1_ppc64el.buildinfo ad5e4fc8723e2beefa35b6ac5e71329c0b03023e825c5fe51323963fc4e21869 496326 subread_1.5.3+dfsg-1_ppc64el.deb Files: ed5e571d623bd77278d0625cc39aa1b1 7117054 debug extra subread-dbgsym_1.5.3+dfsg-1_ppc64el.ddeb 87116fe86b8ce8db2f922f3ff44af5e0 5296 science optional subread_1.5.3+dfsg-1_ppc64el.buildinfo a13dfcb4c90671433e5ba445a9f14207 496326 science optional subread_1.5.3+dfsg-1_ppc64el.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ subread_1.5.3+dfsg-1_ppc64el.deb -------------------------------- new debian package, version 2.0. size 496326 bytes: control archive=1442 bytes. 704 bytes, 15 lines control 1819 bytes, 28 lines md5sums Package: subread Version: 1.5.3+dfsg-1 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 7827 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 2017-07-28 14:09 ./ drwxr-xr-x root/root 0 2017-07-28 14:09 ./usr/ drwxr-xr-x root/root 0 2017-07-28 14:09 ./usr/bin/ -rwxr-xr-x root/root 658232 2017-07-28 14:09 ./usr/bin/exactSNP -rwxr-xr-x root/root 724376 2017-07-28 14:09 ./usr/bin/featureCounts -rwxr-xr-x root/root 658264 2017-07-28 14:09 ./usr/bin/subindel -rwxr-xr-x root/root 659992 2017-07-28 14:09 ./usr/bin/subjunc -rwxr-xr-x root/root 659800 2017-07-28 14:09 ./usr/bin/subread-align -rwxr-xr-x root/root 658168 2017-07-28 14:09 ./usr/bin/subread-buildindex drwxr-xr-x root/root 0 2017-07-28 14:09 ./usr/lib/ drwxr-xr-x root/root 0 2017-07-28 14:09 ./usr/lib/subread/ -rwxr-xr-x root/root 658264 2017-07-28 14:09 ./usr/lib/subread/coverageCount -rwxr-xr-x root/root 658264 2017-07-28 14:09 ./usr/lib/subread/propmapped -rwxr-xr-x root/root 658488 2017-07-28 14:09 ./usr/lib/subread/qualityScores -rwxr-xr-x root/root 658168 2017-07-28 14:09 ./usr/lib/subread/removeDup -rwxr-xr-x root/root 658168 2017-07-28 14:09 ./usr/lib/subread/repair -rwxr-xr-x root/root 658168 2017-07-28 14:09 ./usr/lib/subread/subread-fullscan drwxr-xr-x root/root 0 2017-07-28 14:09 ./usr/share/ drwxr-xr-x root/root 0 2017-07-28 14:09 ./usr/share/doc/ drwxr-xr-x root/root 0 2017-07-28 14:09 ./usr/share/doc/subread/ -rw-r--r-- root/root 500 2017-07-28 14:09 ./usr/share/doc/subread/README.Debian -rw-r--r-- root/root 3850 2017-07-12 00:54 ./usr/share/doc/subread/README.txt -rw-r--r-- root/root 986 2017-07-28 14:09 ./usr/share/doc/subread/changelog.Debian.gz -rw-r--r-- root/root 1138 2017-07-28 14:09 ./usr/share/doc/subread/copyright drwxr-xr-x root/root 0 2017-07-28 14:09 ./usr/share/man/ drwxr-xr-x root/root 0 2017-07-28 14:09 ./usr/share/man/man1/ -rw-r--r-- root/root 594 2017-07-28 14:09 ./usr/share/man/man1/coverageCount.1.gz -rw-r--r-- root/root 1166 2017-07-28 14:09 ./usr/share/man/man1/exactSNP.1.gz -rw-r--r-- root/root 3212 2017-07-28 14:09 ./usr/share/man/man1/featureCounts.1.gz -rw-r--r-- root/root 473 2017-07-28 14:09 ./usr/share/man/man1/propmapped.1.gz -rw-r--r-- root/root 576 2017-07-28 14:09 ./usr/share/man/man1/qualityScores.1.gz -rw-r--r-- root/root 480 2017-07-28 14:09 ./usr/share/man/man1/removeDup.1.gz -rw-r--r-- root/root 602 2017-07-28 14:09 ./usr/share/man/man1/repair.1.gz -rw-r--r-- root/root 368 2017-07-28 14:09 ./usr/share/man/man1/subindel.1.gz -rw-r--r-- root/root 2100 2017-07-28 14:09 ./usr/share/man/man1/subjunc.1.gz -rw-r--r-- root/root 2180 2017-07-28 14:09 ./usr/share/man/man1/subread-align.1.gz -rw-r--r-- root/root 705 2017-07-28 14:09 ./usr/share/man/man1/subread-buildindex.1.gz -rw-r--r-- root/root 370 2017-07-28 14:09 ./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: 135488 Build-Time: 94 Distribution: artful-proposed Host Architecture: ppc64el Install-Time: 11 Job: subread_1.5.3+dfsg-1.dsc Machine Architecture: ppc64el Package: subread Package-Time: 108 Source-Version: 1.5.3+dfsg-1 Space: 135488 Status: successful Version: 1.5.3+dfsg-1 -------------------------------------------------------------------------------- Finished at 20170728-2308 Build needed 00:01:48, 135488k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-13167929'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-13167929/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-13167929'] Unmounting chroot for build PACKAGEBUILD-13167929... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-13167929'] Removing build PACKAGEBUILD-13167929