RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux bos01-ppc64el-001 4.4.0-51-generic #72-Ubuntu SMP Thu Nov 24 18:27:59 UTC 2016 ppc64le Buildd toolchain package versions: launchpad-buildd_140 python-lpbuildd_140 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 dpkg-dev_1.18.4ubuntu1.1 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.6. Syncing the system clock with the buildd NTP service... 2 Dec 17:18:46 ntpdate[1666]: adjust time server 10.211.37.1 offset 0.000575 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-11407674', '/home/buildd/filecache-default/13c837fa8f013503c65d7b6fd85343da86753929'] Unpacking chroot for build PACKAGEBUILD-11407674 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-11407674'] Mounting chroot for build PACKAGEBUILD-11407674 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-11407674', 'deb http://ftpmaster.internal/ubuntu zesty main universe', 'deb http://ftpmaster.internal/ubuntu zesty-security main universe', 'deb http://ftpmaster.internal/ubuntu zesty-updates main universe', 'deb http://ftpmaster.internal/ubuntu zesty-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-11407674 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-11407674', 'ppc64el'] Updating debian chroot for build PACKAGEBUILD-11407674 Get:1 http://ftpmaster.internal/ubuntu zesty InRelease [253 kB] Get:2 http://ftpmaster.internal/ubuntu zesty-security InRelease [102 kB] Get:3 http://ftpmaster.internal/ubuntu zesty-updates InRelease [102 kB] Get:4 http://ftpmaster.internal/ubuntu zesty-proposed InRelease [102 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main ppc64el Packages [1178 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main Translation-en [584 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/universe ppc64el Packages [7657 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/universe Translation-en [4597 kB] Get:9 http://ftpmaster.internal/ubuntu zesty-proposed/main ppc64el Packages [84.2 kB] Get:10 http://ftpmaster.internal/ubuntu zesty-proposed/main Translation-en [42.0 kB] Get:11 http://ftpmaster.internal/ubuntu zesty-proposed/universe ppc64el Packages [505 kB] Get:12 http://ftpmaster.internal/ubuntu zesty-proposed/universe Translation-en [258 kB] Fetched 15.5 MB in 3s (3936 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: libperl5.22 perl-modules-5.22 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.24 perl-modules-5.24 The following packages will be upgraded: adduser apt apt-transport-https base-files base-passwd bash binutils bsdutils ca-certificates cpp cpp-6 debianutils diffutils dmsetup findutils g++ g++-6 gcc gcc-6 gcc-6-base grep init init-system-helpers libapparmor1 libapt-pkg5.0 libasan3 libasn1-8-heimdal libassuan0 libatomic1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libcurl3-gnutls libdevmapper1.02.1 libfdisk1 libgcc-6-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libitm1 libk5crypto3 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libksba8 libldap-2.4-2 liblzma5 libmount1 libnettle6 libnpth0 libpng16-16 libroken18-heimdal libsasl2-2 libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsmartcols1 libsqlite3-0 libssl1.0.0 libstdc++-6-dev libstdc++6 libsystemd0 libubsan0 libudev1 libustr-1.0-1 libuuid1 libwind0-heimdal linux-libc-dev mount multiarch-support openssl perl perl-base pinentry-curses pkg-create-dbgsym systemd systemd-sysv tar tzdata ubuntu-keyring util-linux xz-utils 97 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 51.8 MB of archives. After this operation, 43.9 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu zesty/main ppc64el base-files ppc64el 9.6ubuntu7 [56.6 kB] Get:2 http://ftpmaster.internal/ubuntu zesty/main ppc64el debianutils ppc64el 4.8.1 [86.0 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main ppc64el bash ppc64el 4.4-2ubuntu1 [644 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/main ppc64el bsdutils ppc64el 1:2.29-1ubuntu2 [54.9 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main ppc64el diffutils ppc64el 1:3.5-1 [171 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main ppc64el findutils ppc64el 4.6.0+git+20161106-1 [289 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/main ppc64el grep ppc64el 2.26-1 [145 kB] Get:8 http://ftpmaster.internal/ubuntu zesty-proposed/main ppc64el libc6-dev ppc64el 2.24-7ubuntu1 [2273 kB] Get:9 http://ftpmaster.internal/ubuntu zesty-proposed/main ppc64el libc-dev-bin ppc64el 2.24-7ubuntu1 [64.3 kB] Get:10 http://ftpmaster.internal/ubuntu zesty-proposed/main ppc64el linux-libc-dev ppc64el 4.9.0-3.4 [852 kB] Get:11 http://ftpmaster.internal/ubuntu zesty/main ppc64el libgomp1 ppc64el 6.2.1-5ubuntu1 [67.0 kB] Get:12 http://ftpmaster.internal/ubuntu zesty/main ppc64el libitm1 ppc64el 6.2.1-5ubuntu1 [28.2 kB] Get:13 http://ftpmaster.internal/ubuntu zesty/main ppc64el gcc-6-base ppc64el 6.2.1-5ubuntu1 [16.8 kB] Get:14 http://ftpmaster.internal/ubuntu zesty/main ppc64el libgcc1 ppc64el 1:6.2.1-5ubuntu1 [27.3 kB] Get:15 http://ftpmaster.internal/ubuntu zesty/main ppc64el libcc1-0 ppc64el 6.2.1-5ubuntu1 [30.6 kB] Get:16 http://ftpmaster.internal/ubuntu zesty/main ppc64el binutils ppc64el 2.27.51.20161201-1ubuntu1 [2321 kB] Get:17 http://ftpmaster.internal/ubuntu zesty/main ppc64el libatomic1 ppc64el 6.2.1-5ubuntu1 [8272 B] Get:18 http://ftpmaster.internal/ubuntu zesty/main ppc64el libasan3 ppc64el 6.2.1-5ubuntu1 [280 kB] Get:19 http://ftpmaster.internal/ubuntu zesty/main ppc64el libubsan0 ppc64el 6.2.1-5ubuntu1 [104 kB] Get:20 http://ftpmaster.internal/ubuntu zesty/main ppc64el g++-6 ppc64el 6.2.1-5ubuntu1 [6432 kB] Get:21 http://ftpmaster.internal/ubuntu zesty/main ppc64el libstdc++-6-dev ppc64el 6.2.1-5ubuntu1 [1453 kB] Get:22 http://ftpmaster.internal/ubuntu zesty/main ppc64el libgcc-6-dev ppc64el 6.2.1-5ubuntu1 [656 kB] Get:23 http://ftpmaster.internal/ubuntu zesty/main ppc64el gcc-6 ppc64el 6.2.1-5ubuntu1 [6197 kB] Get:24 http://ftpmaster.internal/ubuntu zesty/main ppc64el cpp-6 ppc64el 6.2.1-5ubuntu1 [5671 kB] Get:25 http://ftpmaster.internal/ubuntu zesty/main ppc64el libstdc++6 ppc64el 6.2.1-5ubuntu1 [418 kB] Get:26 http://ftpmaster.internal/ubuntu zesty-proposed/main ppc64el libc6 ppc64el 2.24-7ubuntu1 [2453 kB] Get:27 http://ftpmaster.internal/ubuntu zesty/main ppc64el libuuid1 ppc64el 2.29-1ubuntu2 [15.1 kB] Get:28 http://ftpmaster.internal/ubuntu zesty/main ppc64el libblkid1 ppc64el 2.29-1ubuntu2 [102 kB] Get:29 http://ftpmaster.internal/ubuntu zesty/main ppc64el libfdisk1 ppc64el 2.29-1ubuntu2 [132 kB] Get:30 http://ftpmaster.internal/ubuntu zesty/main ppc64el libselinux1 ppc64el 2.6-3 [67.3 kB] Get:31 http://ftpmaster.internal/ubuntu zesty/main ppc64el util-linux ppc64el 2.29-1ubuntu2 [881 kB] Get:32 http://ftpmaster.internal/ubuntu zesty/main ppc64el mount ppc64el 2.29-1ubuntu2 [126 kB] Get:33 http://ftpmaster.internal/ubuntu zesty/main ppc64el perl-modules-5.24 all 5.24.1~rc4-1 [2663 kB] Get:34 http://ftpmaster.internal/ubuntu zesty/main ppc64el libperl5.24 ppc64el 5.24.1~rc4-1 [3310 kB] Get:35 http://ftpmaster.internal/ubuntu zesty/main ppc64el perl ppc64el 5.24.1~rc4-1 [219 kB] Get:36 http://ftpmaster.internal/ubuntu zesty/main ppc64el perl-base ppc64el 5.24.1~rc4-1 [1228 kB] Get:37 http://ftpmaster.internal/ubuntu zesty/main ppc64el tar ppc64el 1.29b-1.1 [241 kB] Get:38 http://ftpmaster.internal/ubuntu zesty/main ppc64el base-passwd ppc64el 3.5.41 [49.4 kB] Get:39 http://ftpmaster.internal/ubuntu zesty/main ppc64el init-system-helpers all 1.46 [37.3 kB] Get:40 http://ftpmaster.internal/ubuntu zesty-proposed/main ppc64el libc-bin ppc64el 2.24-7ubuntu1 [575 kB] Get:41 http://ftpmaster.internal/ubuntu zesty/main ppc64el liblzma5 ppc64el 5.2.2-1.2 [101 kB] Get:42 http://ftpmaster.internal/ubuntu zesty-proposed/main ppc64el libapt-pkg5.0 ppc64el 1.4~beta1 [813 kB] Get:43 http://ftpmaster.internal/ubuntu zesty/main ppc64el adduser all 3.113+nmu3ubuntu5 [161 kB] Get:44 http://ftpmaster.internal/ubuntu zesty/main ppc64el ubuntu-keyring all 2016.10.27 [16.6 kB] Get:45 http://ftpmaster.internal/ubuntu zesty-proposed/main ppc64el apt ppc64el 1.4~beta1 [1105 kB] Get:46 http://ftpmaster.internal/ubuntu zesty/main ppc64el libapparmor1 ppc64el 2.10.95-4ubuntu5.2 [30.0 kB] Get:47 http://ftpmaster.internal/ubuntu zesty/main ppc64el libgpg-error0 ppc64el 1.25-1 [36.6 kB] Get:48 http://ftpmaster.internal/ubuntu zesty/main ppc64el libgcrypt20 ppc64el 1.7.3-2 [417 kB] Get:49 http://ftpmaster.internal/ubuntu zesty/main ppc64el libmount1 ppc64el 2.29-1ubuntu2 [107 kB] Get:50 http://ftpmaster.internal/ubuntu zesty/main ppc64el systemd ppc64el 232-7 [2174 kB] Get:51 http://ftpmaster.internal/ubuntu zesty/main ppc64el libsystemd0 ppc64el 232-7 [205 kB] Get:52 http://ftpmaster.internal/ubuntu zesty/main ppc64el init ppc64el 1.46 [5320 B] Get:53 http://ftpmaster.internal/ubuntu zesty/main ppc64el systemd-sysv ppc64el 232-7 [13.9 kB] Get:54 http://ftpmaster.internal/ubuntu zesty/main ppc64el libsepol1 ppc64el 2.6-1 [205 kB] Get:55 http://ftpmaster.internal/ubuntu zesty/main ppc64el libustr-1.0-1 ppc64el 1.0.4-6 [55.2 kB] Get:56 http://ftpmaster.internal/ubuntu zesty/main ppc64el libsemanage-common all 2.6-1 [6832 B] Get:57 http://ftpmaster.internal/ubuntu zesty/main ppc64el libsemanage1 ppc64el 2.6-1 [75.4 kB] Get:58 http://ftpmaster.internal/ubuntu zesty/main ppc64el libsmartcols1 ppc64el 2.29-1ubuntu2 [64.2 kB] Get:59 http://ftpmaster.internal/ubuntu zesty/main ppc64el libudev1 ppc64el 232-7 [54.5 kB] Get:60 http://ftpmaster.internal/ubuntu zesty-proposed/main ppc64el multiarch-support ppc64el 2.24-7ubuntu1 [6826 B] Get:61 http://ftpmaster.internal/ubuntu zesty/main ppc64el tzdata all 2016j-2 [204 kB] Get:62 http://ftpmaster.internal/ubuntu zesty/main ppc64el libdevmapper1.02.1 ppc64el 2:1.02.136-1ubuntu1 [128 kB] Get:63 http://ftpmaster.internal/ubuntu zesty/main ppc64el dmsetup ppc64el 2:1.02.136-1ubuntu1 [69.8 kB] Get:64 http://ftpmaster.internal/ubuntu zesty/main ppc64el libroken18-heimdal ppc64el 1.7~git20160703+dfsg-1ubuntu1 [39.0 kB] Get:65 http://ftpmaster.internal/ubuntu zesty/main ppc64el libasn1-8-heimdal ppc64el 1.7~git20160703+dfsg-1ubuntu1 [137 kB] Get:66 http://ftpmaster.internal/ubuntu zesty/main ppc64el libassuan0 ppc64el 2.4.3-2 [31.5 kB] Get:67 http://ftpmaster.internal/ubuntu zesty/main ppc64el libhogweed4 ppc64el 3.3-1 [133 kB] Get:68 http://ftpmaster.internal/ubuntu zesty/main ppc64el libnettle6 ppc64el 3.3-1 [121 kB] Get:69 http://ftpmaster.internal/ubuntu zesty/main ppc64el libgnutls30 ppc64el 3.5.6-4ubuntu2 [527 kB] Get:70 http://ftpmaster.internal/ubuntu zesty/main ppc64el libheimbase1-heimdal ppc64el 1.7~git20160703+dfsg-1ubuntu1 [28.7 kB] Get:71 http://ftpmaster.internal/ubuntu zesty/main ppc64el libhcrypto4-heimdal ppc64el 1.7~git20160703+dfsg-1ubuntu1 [95.1 kB] Get:72 http://ftpmaster.internal/ubuntu zesty/main ppc64el libwind0-heimdal ppc64el 1.7~git20160703+dfsg-1ubuntu1 [47.8 kB] Get:73 http://ftpmaster.internal/ubuntu zesty/main ppc64el libhx509-5-heimdal ppc64el 1.7~git20160703+dfsg-1ubuntu1 [101 kB] Get:74 http://ftpmaster.internal/ubuntu zesty-proposed/main ppc64el libsqlite3-0 ppc64el 3.15.2-1 [437 kB] Get:75 http://ftpmaster.internal/ubuntu zesty/main ppc64el libkrb5-26-heimdal ppc64el 1.7~git20160703+dfsg-1ubuntu1 [189 kB] Get:76 http://ftpmaster.internal/ubuntu zesty/main ppc64el libheimntlm0-heimdal ppc64el 1.7~git20160703+dfsg-1ubuntu1 [15.6 kB] Get:77 http://ftpmaster.internal/ubuntu zesty/main ppc64el libgssapi3-heimdal ppc64el 1.7~git20160703+dfsg-1ubuntu1 [86.1 kB] Get:78 http://ftpmaster.internal/ubuntu zesty/main ppc64el libksba8 ppc64el 1.3.5-2 [90.7 kB] Get:79 http://ftpmaster.internal/ubuntu zesty/main ppc64el libsasl2-modules-db ppc64el 2.1.27~72-g88d82a3+dfsg-1 [14.7 kB] Get:80 http://ftpmaster.internal/ubuntu zesty/main ppc64el libsasl2-2 ppc64el 2.1.27~72-g88d82a3+dfsg-1 [47.6 kB] Get:81 http://ftpmaster.internal/ubuntu zesty/main ppc64el libldap-2.4-2 ppc64el 2.4.42+dfsg-2ubuntu5 [151 kB] Get:82 http://ftpmaster.internal/ubuntu zesty/main ppc64el libnpth0 ppc64el 1.3-1 [8046 B] Get:83 http://ftpmaster.internal/ubuntu zesty/main ppc64el libslang2 ppc64el 2.3.1-5ubuntu1 [383 kB] Get:84 http://ftpmaster.internal/ubuntu zesty/main ppc64el libssl1.0.0 ppc64el 1.0.2g-1ubuntu10 [824 kB] Get:85 http://ftpmaster.internal/ubuntu zesty/main ppc64el pinentry-curses ppc64el 0.9.7-9 [31.4 kB] Get:86 http://ftpmaster.internal/ubuntu zesty/main ppc64el xz-utils ppc64el 5.2.2-1.2 [82.5 kB] Get:87 http://ftpmaster.internal/ubuntu zesty/main ppc64el libgssapi-krb5-2 ppc64el 1.15~beta1-1 [109 kB] Get:88 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ppc64el 4:6.2.1-1ubuntu1 [5184 B] Get:98 http://ftpmaster.internal/ubuntu zesty/main ppc64el g++ ppc64el 4:6.2.1-1ubuntu1 [1474 B] Get:99 http://ftpmaster.internal/ubuntu zesty/main ppc64el pkg-create-dbgsym all 0.73 [8952 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 51.8 MB in 1s (37.9 MB/s) (Reading database ... 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Unpacking ca-certificates (20161102) over (20160104ubuntu1) ... Preparing to unpack .../34-libpng16-16_1.6.26-2ubuntu1_ppc64el.deb ... Unpacking libpng16-16:ppc64el (1.6.26-2ubuntu1) over (1.6.25-1) ... Preparing to unpack .../35-cpp_4%3a6.2.1-1ubuntu1_ppc64el.deb ... Unpacking cpp (4:6.2.1-1ubuntu1) over (4:6.1.1-1ubuntu2) ... Preparing to unpack .../36-gcc_4%3a6.2.1-1ubuntu1_ppc64el.deb ... Removing old gcc doc directory. Unpacking gcc (4:6.2.1-1ubuntu1) over (4:6.1.1-1ubuntu2) ... Preparing to unpack .../37-g++_4%3a6.2.1-1ubuntu1_ppc64el.deb ... Unpacking g++ (4:6.2.1-1ubuntu1) over (4:6.1.1-1ubuntu2) ... Preparing to unpack .../38-pkg-create-dbgsym_0.73_all.deb ... Unpacking pkg-create-dbgsym (0.73) over (0.72) ... Setting up libnpth0:ppc64el (1.3-1) ... Setting up libgomp1:ppc64el (6.2.1-5ubuntu1) ... Setting up libatomic1:ppc64el (6.2.1-5ubuntu1) ... Setting up perl-modules-5.24 (5.24.1~rc4-1) ... Setting up libperl5.24:ppc64el (5.24.1~rc4-1) ... Setting up libnettle6:ppc64el (3.3-1) ... Setting up libcc1-0:ppc64el (6.2.1-5ubuntu1) ... Setting up libasan3:ppc64el (6.2.1-5ubuntu1) ... Setting up libssl1.0.0:ppc64el (1.0.2g-1ubuntu10) ... Setting up libpng16-16:ppc64el (1.6.26-2ubuntu1) ... Setting up tzdata (2016j-2) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Dec 2 17:19:13 UTC 2016. Universal Time is now: Fri Dec 2 17:19:13 UTC 2016. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (232-7) ... Setting up libubsan0:ppc64el (6.2.1-5ubuntu1) ... Setting up libsasl2-modules-db:ppc64el (2.1.27~72-g88d82a3+dfsg-1) ... Setting up linux-libc-dev:ppc64el (4.9.0-3.4) ... Setting up libsasl2-2:ppc64el (2.1.27~72-g88d82a3+dfsg-1) ... Setting up libroken18-heimdal:ppc64el (1.7~git20160703+dfsg-1ubuntu1) ... Setting up libksba8:ppc64el (1.3.5-2) ... Setting up libdevmapper1.02.1:ppc64el (2:1.02.136-1ubuntu1) ... Setting up libkrb5support0:ppc64el (1.15~beta1-1) ... Setting up libhogweed4:ppc64el (3.3-1) ... Setting up perl (5.24.1~rc4-1) ... Installing new version of config file /etc/perl/sitecustomize.pl ... Processing triggers for libc-bin (2.24-7ubuntu1) ... Setting up pkg-create-dbgsym (0.73) ... Setting up xz-utils (5.2.2-1.2) ... Setting up libheimbase1-heimdal:ppc64el (1.7~git20160703+dfsg-1ubuntu1) ... Setting up openssl (1.0.2g-1ubuntu10) ... Setting up libsqlite3-0:ppc64el (3.15.2-1) ... Setting up dmsetup (2:1.02.136-1ubuntu1) ... Setting up binutils (2.27.51.20161201-1ubuntu1) ... Setting up cpp-6 (6.2.1-5ubuntu1) ... Setting up libc-dev-bin (2.24-7ubuntu1) ... Setting up ca-certificates (20161102) ... Updating certificates in /etc/ssl/certs... 10 added, 10 removed; done. Setting up libc6-dev:ppc64el (2.24-7ubuntu1) ... Setting up libslang2:ppc64el (2.3.1-5ubuntu1) ... Setting up libassuan0:ppc64el (2.4.3-2) ... Setting up libitm1:ppc64el (6.2.1-5ubuntu1) ... Setting up cpp (4:6.2.1-1ubuntu1) ... Setting up libk5crypto3:ppc64el (1.15~beta1-1) ... Setting up libgcc-6-dev:ppc64el (6.2.1-5ubuntu1) ... Setting up libstdc++-6-dev:ppc64el (6.2.1-5ubuntu1) ... Setting up libwind0-heimdal:ppc64el (1.7~git20160703+dfsg-1ubuntu1) ... Setting up init (1.46) ... Setting up libasn1-8-heimdal:ppc64el (1.7~git20160703+dfsg-1ubuntu1) ... Setting up libhcrypto4-heimdal:ppc64el (1.7~git20160703+dfsg-1ubuntu1) ... Setting up libgnutls30:ppc64el (3.5.6-4ubuntu2) ... Setting up libhx509-5-heimdal:ppc64el (1.7~git20160703+dfsg-1ubuntu1) ... Setting up gcc-6 (6.2.1-5ubuntu1) ... Setting up g++-6 (6.2.1-5ubuntu1) ... Setting up pinentry-curses (0.9.7-9) ... Setting up libkrb5-3:ppc64el (1.15~beta1-1) ... Setting up libkrb5-26-heimdal:ppc64el (1.7~git20160703+dfsg-1ubuntu1) ... Setting up libheimntlm0-heimdal:ppc64el (1.7~git20160703+dfsg-1ubuntu1) ... Setting up gcc (4:6.2.1-1ubuntu1) ... Setting up libgssapi-krb5-2:ppc64el (1.15~beta1-1) ... Setting up g++ (4:6.2.1-1ubuntu1) ... Setting up libgssapi3-heimdal:ppc64el (1.7~git20160703+dfsg-1ubuntu1) ... Setting up libldap-2.4-2:ppc64el (2.4.42+dfsg-2ubuntu5) ... Setting up libcurl3-gnutls:ppc64el (7.51.0-1ubuntu1) ... Setting up apt-transport-https (1.4~beta1) ... Processing triggers for libc-bin (2.24-7ubuntu1) ... Processing triggers for ca-certificates (20161102) ... 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-11407674', 'ppc64el', 'zesty-proposed', '-c', 'chroot:autobuild', '--arch=ppc64el', '--dist=zesty-proposed', '--purge=never', '--nolog', 'subread_1.5.1+dfsg-4.dsc'] Initiating build PACKAGEBUILD-11407674 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-51-generic #72-Ubuntu SMP Thu Nov 24 18:27:59 UTC 2016 ppc64le sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos01-ppc64el-001.buildd +==============================================================================+ | subread 1.5.1+dfsg-4 (ppc64el) 02 Dec 2016 17:19 | +==============================================================================+ Package: subread Version: 1.5.1+dfsg-4 Source Version: 1.5.1+dfsg-4 Distribution: zesty-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el I: NOTICE: Log filtering will replace 'build/subread-XoqDBo/subread-1.5.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/subread-XoqDBo' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-11407674/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- subread_1.5.1+dfsg-4.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-mfRH00/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-mfRH00/apt_archive ./ InRelease Get:2 copy:/<>/resolver-mfRH00/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-mfRH00/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-mfRH00/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-mfRH00/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.22 perl-modules-5.22 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 772 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-mfRH00/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 772 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13977 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-7KRyh8/apt_archive/sbuild-build-depends-subread-dummy.deb'. Ign:1 copy:/<>/resolver-7KRyh8/apt_archive ./ InRelease Get:2 copy:/<>/resolver-7KRyh8/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-7KRyh8/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-7KRyh8/apt_archive ./ Sources [231 B] Get:5 copy:/<>/resolver-7KRyh8/apt_archive ./ Packages [552 B] Fetched 2902 B in 0s (0 B/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: libperl5.22 perl-modules-5.22 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 libunistring0 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 less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support Recommended packages: curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl 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 libunistring0 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, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 21.1 MB of archives. After this operation, 90.4 MB of additional disk space will be used. Get:1 copy:/<>/resolver-7KRyh8/apt_archive ./ sbuild-build-depends-subread-dummy 0.invalid.0 [794 B] Get:2 http://ftpmaster.internal/ubuntu zesty/main ppc64el liblocale-gettext-perl ppc64el 1.07-3build1 [16.8 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main ppc64el groff-base ppc64el 1.22.3-8 [1356 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/main ppc64el libbsd0 ppc64el 0.8.3-1 [48.2 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main ppc64el bsdmainutils ppc64el 9.0.12ubuntu1 [179 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main ppc64el libpipeline1 ppc64el 1.4.1-2 [24.1 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/main ppc64el man-db ppc64el 2.7.5-2 [851 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/main ppc64el libunistring0 ppc64el 0.9.3-5.2ubuntu1 [269 kB] Get:9 http://ftpmaster.internal/ubuntu zesty/main ppc64el libpython2.7-minimal ppc64el 2.7.12-7 [340 kB] Get:10 http://ftpmaster.internal/ubuntu zesty/main ppc64el python2.7-minimal ppc64el 2.7.12-7 [1345 kB] Get:11 http://ftpmaster.internal/ubuntu zesty/main ppc64el python-minimal ppc64el 2.7.11-2 [28.3 kB] Get:12 http://ftpmaster.internal/ubuntu zesty/main ppc64el mime-support all 3.60ubuntu1 [30.1 kB] Get:13 http://ftpmaster.internal/ubuntu zesty/main ppc64el libexpat1 ppc64el 2.2.0-1 [76.3 kB] Get:14 http://ftpmaster.internal/ubuntu zesty/main ppc64el libpython2.7-stdlib ppc64el 2.7.12-7 [1928 kB] Get:15 http://ftpmaster.internal/ubuntu zesty/main ppc64el python2.7 ppc64el 2.7.12-7 [228 kB] Get:16 http://ftpmaster.internal/ubuntu zesty/main ppc64el libpython-stdlib ppc64el 2.7.11-2 [7858 B] Get:17 http://ftpmaster.internal/ubuntu zesty/main ppc64el python ppc64el 2.7.11-2 [139 kB] Get:18 http://ftpmaster.internal/ubuntu zesty-proposed/main ppc64el libmagic-mgc ppc64el 1:5.29-1 [178 kB] Get:19 http://ftpmaster.internal/ubuntu zesty-proposed/main ppc64el libmagic1 ppc64el 1:5.29-1 [71.3 kB] Get:20 http://ftpmaster.internal/ubuntu zesty-proposed/main ppc64el file ppc64el 1:5.29-1 [22.5 kB] Get:21 http://ftpmaster.internal/ubuntu zesty/main ppc64el gettext-base ppc64el 0.19.8.1-1ubuntu2 [48.2 kB] Get:22 http://ftpmaster.internal/ubuntu zesty/main ppc64el libglib2.0-0 ppc64el 2.51.0-2 [1065 kB] Get:23 http://ftpmaster.internal/ubuntu zesty-proposed/main ppc64el libicu57 ppc64el 57.1-5 [7773 kB] Get:24 http://ftpmaster.internal/ubuntu zesty-proposed/main ppc64el libxml2 ppc64el 2.9.4+dfsg1-2.1 [609 kB] Get:25 http://ftpmaster.internal/ubuntu zesty/main ppc64el libsigsegv2 ppc64el 2.10-5 [14.2 kB] Get:26 http://ftpmaster.internal/ubuntu zesty/main ppc64el m4 ppc64el 1.4.17-5 [198 kB] Get:27 http://ftpmaster.internal/ubuntu zesty/main ppc64el autoconf all 2.69-10 [321 kB] Get:28 http://ftpmaster.internal/ubuntu zesty/main ppc64el autotools-dev all 20161112.1 [39.5 kB] Get:29 http://ftpmaster.internal/ubuntu zesty/main ppc64el automake all 1:1.15-5ubuntu1 [509 kB] Get:30 http://ftpmaster.internal/ubuntu zesty/main ppc64el autopoint all 0.19.8.1-1ubuntu2 [412 kB] Get:31 http://ftpmaster.internal/ubuntu zesty/main ppc64el bc ppc64el 1.06.95-9build2 [93.0 kB] Get:32 http://ftpmaster.internal/ubuntu zesty/main ppc64el libtool all 2.4.6-2 [194 kB] Get:33 http://ftpmaster.internal/ubuntu zesty/main ppc64el dh-autoreconf all 12 [15.8 kB] Get:34 http://ftpmaster.internal/ubuntu zesty/main ppc64el libarchive-zip-perl all 1.59-1 [84.0 kB] Get:35 http://ftpmaster.internal/ubuntu zesty/main ppc64el libfile-stripnondeterminism-perl all 0.028-1 [12.5 kB] Get:36 http://ftpmaster.internal/ubuntu zesty/main ppc64el libtimedate-perl all 2.3000-2 [37.5 kB] Get:37 http://ftpmaster.internal/ubuntu zesty/main ppc64el dh-strip-nondeterminism all 0.028-1 [4820 B] Get:38 http://ftpmaster.internal/ubuntu zesty/main ppc64el libcroco3 ppc64el 0.6.11-2 [74.4 kB] Get:39 http://ftpmaster.internal/ubuntu zesty/main ppc64el gettext ppc64el 0.19.8.1-1ubuntu2 [1114 kB] Get:40 http://ftpmaster.internal/ubuntu zesty/main ppc64el intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:41 http://ftpmaster.internal/ubuntu zesty/main ppc64el po-debconf all 1.0.20 [232 kB] Get:42 http://ftpmaster.internal/ubuntu zesty/main ppc64el debhelper all 10.2.2ubuntu1 [742 kB] Get:43 http://ftpmaster.internal/ubuntu zesty/universe ppc64el help2man ppc64el 1.47.4 [155 kB] Get:44 http://ftpmaster.internal/ubuntu zesty/main ppc64el zlib1g-dev ppc64el 1:1.2.8.dfsg-2ubuntu5 [168 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 21.1 MB in 0s (36.6 MB/s) Selecting previously unselected package liblocale-gettext-perl. 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Setting up libsigsegv2:ppc64el (2.10-5) ... Setting up groff-base (1.22.3-8) ... Setting up libglib2.0-0:ppc64el (2.51.0-2) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-1ubuntu2) ... Setting up libpipeline1:ppc64el (1.4.1-2) ... Setting up m4 (1.4.17-5) ... Setting up libicu57:ppc64el (57.1-5) ... Setting up libbsd0:ppc64el (0.8.3-1) ... Setting up libxml2:ppc64el (2.9.4+dfsg1-2.1) ... Setting up libmagic-mgc (1:5.29-1) ... Setting up libmagic1:ppc64el (1:5.29-1) ... Setting up libcroco3:ppc64el (0.6.11-2) ... Processing triggers for libc-bin (2.24-7ubuntu1) ... Setting up autotools-dev (20161112.1) ... Setting up libunistring0:ppc64el (0.9.3-5.2ubuntu1) ... Setting up liblocale-gettext-perl (1.07-3build1) ... Setting up bsdmainutils (9.0.12ubuntu1) ... 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 (2.7.12-7) ... Setting up autopoint (0.19.8.1-1ubuntu2) ... Setting up zlib1g-dev:ppc64el (1:1.2.8.dfsg-2ubuntu5) ... Setting up libfile-stripnondeterminism-perl (0.028-1) ... Setting up gettext (0.19.8.1-1ubuntu2) ... Setting up python2.7 (2.7.12-7) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.29-1) ... Setting up libpython-stdlib:ppc64el (2.7.11-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15-5ubuntu1) ... 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 (2.7.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python (2.7.11-2) ... Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (12) ... Setting up dh-strip-nondeterminism (0.028-1) ... Setting up debhelper (10.2.2ubuntu1) ... Setting up sbuild-build-depends-subread-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-7ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-51-generic ppc64el (ppc64le) Toolchain package versions: binutils_2.27.51.20161201-1ubuntu1 dpkg-dev_1.18.10ubuntu1 g++-6_6.2.1-5ubuntu1 gcc-6_6.2.1-5ubuntu1 libc6-dev_2.24-7ubuntu1 libstdc++-6-dev_6.2.1-5ubuntu1 libstdc++6_6.2.1-5ubuntu1 linux-libc-dev_4.9.0-3.4 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_1.20-1 apt_1.4~beta1 apt-transport-https_1.4~beta1 autoconf_2.69-10 automake_1:1.15-5ubuntu1 autopoint_0.19.8.1-1ubuntu2 autotools-dev_20161112.1 base-files_9.6ubuntu7 base-passwd_3.5.41 bash_4.4-2ubuntu1 bc_1.06.95-9build2 binutils_2.27.51.20161201-1ubuntu1 bsdmainutils_9.0.12ubuntu1 bsdutils_1:2.29-1ubuntu2 build-essential_12.1ubuntu2 bzip2_1.0.6-8build1 ca-certificates_20161102 coreutils_8.25-2ubuntu2 cpp_4:6.2.1-1ubuntu1 cpp-6_6.2.1-5ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.59ubuntu1 debhelper_10.2.2ubuntu1 debianutils_4.8.1 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dmsetup_2:1.02.136-1ubuntu1 dpkg_1.18.10ubuntu1 dpkg-dev_1.18.10ubuntu1 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-1ubuntu2 file_1:5.29-1 findutils_4.6.0+git+20161106-1 g++_4:6.2.1-1ubuntu1 g++-6_6.2.1-5ubuntu1 gcc_4:6.2.1-1ubuntu1 gcc-6_6.2.1-5ubuntu1 gcc-6-base_6.2.1-5ubuntu1 gettext_0.19.8.1-1ubuntu2 gettext-base_0.19.8.1-1ubuntu2 gnupg_2.1.15-1ubuntu6 gnupg-agent_2.1.15-1ubuntu6 gpgv_2.1.15-1ubuntu6 grep_2.26-1 groff-base_1.22.3-8 gzip_1.6-4ubuntu1 help2man_1.47.4 hostname_3.18 init_1.46 init-system-helpers_1.46 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapparmor1_2.10.95-4ubuntu5.2 libapt-pkg5.0_1.4~beta1 libarchive-zip-perl_1.59-1 libasan3_6.2.1-5ubuntu1 libasn1-8-heimdal_1.7~git20160703+dfsg-1ubuntu1 libassuan0_2.4.3-2 libatomic1_6.2.1-5ubuntu1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.6-1ubuntu1 libaudit1_1:2.6.6-1ubuntu1 libblkid1_2.29-1ubuntu2 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8build1 libc-bin_2.24-7ubuntu1 libc-dev-bin_2.24-7ubuntu1 libc6_2.24-7ubuntu1 libc6-dev_2.24-7ubuntu1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_6.2.1-5ubuntu1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.2-0ubuntu1 libcurl3-gnutls_7.51.0-1ubuntu1 libdb5.3_5.3.28-12 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.136-1ubuntu1 libdpkg-perl_1.18.10ubuntu1 libexpat1_2.2.0-1 libfakeroot_1.21-1ubuntu2 libfdisk1_2.29-1ubuntu2 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libgcc-6-dev_6.2.1-5ubuntu1 libgcc1_1:6.2.1-5ubuntu1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libglib2.0-0_2.51.0-2 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.6-4ubuntu2 libgomp1_6.2.1-5ubuntu1 libgpg-error0_1.25-1 libgssapi-krb5-2_1.15~beta1-1 libgssapi3-heimdal_1.7~git20160703+dfsg-1ubuntu1 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libpam-runtime_1.1.8-3.2ubuntu2 libpam0g_1.1.8-3.2ubuntu2 libpcre3_2:8.39-2 libperl5.22_5.22.2-3 libperl5.24_5.24.1~rc4-1 libpipeline1_1.4.1-2 libpng16-16_1.6.26-2ubuntu1 libprocps6_2:3.3.12-1ubuntu2 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.12-7 libpython2.7-stdlib_2.7.12-7 libreadline7_7.0-0ubuntu2 libroken18-heimdal_1.7~git20160703+dfsg-1ubuntu1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~72-g88d82a3+dfsg-1 libsasl2-modules-db_2.1.27~72-g88d82a3+dfsg-1 libseccomp2_2.3.1-2ubuntu2 libselinux1_2.6-3 libsemanage-common_2.6-1 libsemanage1_2.6-1 libsepol1_2.6-1 libsigsegv2_2.10-5 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.29-1ubuntu2 libsqlite3-0_3.15.2-1 libss2_1.43.3-1 libssl1.0.0_1.0.2g-1ubuntu10 libstdc++-6-dev_6.2.1-5ubuntu1 libstdc++6_6.2.1-5ubuntu1 libsystemd0_232-7 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libubsan0_6.2.1-5ubuntu1 libudev1_232-7 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1ubuntu2 libwind0-heimdal_1.7~git20160703+dfsg-1ubuntu1 libxml2_2.9.4+dfsg1-2.1 linux-libc-dev_4.9.0-3.4 lockfile-progs_0.1.17 login_1:4.2-3.2ubuntu1 lsb-base_9.20160110ubuntu5 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-2 mawk_1.3.3-17ubuntu2 mime-support_3.60ubuntu1 mount_2.29-1ubuntu2 multiarch-support_2.24-7ubuntu1 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu10 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu1 patch_2.7.5-1 perl_5.24.1~rc4-1 perl-base_5.24.1~rc4-1 perl-modules-5.22_5.22.2-3 perl-modules-5.24_5.24.1~rc4-1 pinentry-curses_0.9.7-9 pkg-create-dbgsym_0.73 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 python_2.7.11-2 python-minimal_2.7.11-2 python2.7_2.7.12-7 python2.7-minimal_2.7.12-7 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-subread-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 systemd_232-7 systemd-sysv_232-7 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tar_1.29b-1.1 tzdata_2016j-2 ubuntu-keyring_2016.10.27 util-linux_2.29-1ubuntu2 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2ubuntu5 zlib1g-dev_1:1.2.8.dfsg-2ubuntu5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Dec 2 07:47:25 2016 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./subread_1.5.1+dfsg-4.dsc dpkg-source: info: extracting subread in subread-1.5.1+dfsg dpkg-source: info: unpacking subread_1.5.1+dfsg.orig.tar.xz dpkg-source: info: unpacking subread_1.5.1+dfsg-4.debian.tar.xz 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-1.5.1+dfsg SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>/subread-1.5.1+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 1.5.1+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build subread-1.5.1+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-1.5.1+dfsg' cd src; make -f Makefile.Linux clean make[2]: Entering directory '/<>/subread-1.5.1+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-1.5.1+dfsg/src' dh_clean make[1]: Leaving directory '/<>/subread-1.5.1+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-1.5.1+dfsg' cd src; make -f Makefile.Linux make[2]: Entering directory '/<>/subread-1.5.1+dfsg/src' gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c core.c: In function ‘print_in_box’: core.c:158:7: 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:853:19: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types] gzFile * rawfp = gzopen(fname, "r"); ^~~~~~ core.c:864:25: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] char * bufr =gzgets(rawfp, linebuff, 3000); ^~~~~ In file included from subread.h:26:0, from core.c:43: /usr/include/zlib.h:1372:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’ ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len)); ^~~~~~ core.c:875:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] gzclose(rawfp); ^~~~~ In file included from subread.h:26:0, from core.c:43: /usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’ ZEXTERN int ZEXPORT gzclose OF((gzFile file)); ^~~~~~~ core.c: In function ‘calc_tlen’: core.c:1548:16: 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:2174:6: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] int ret; ^~~ core.c: In function ‘write_realignments_for_fragment’: core.c:2386:21: warning: variable ‘raw_r2’ set but not used [-Wunused-but-set-variable] mapping_result_t * raw_r2 = NULL; ^~~~~~ core.c:2383:21: 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:2452:6: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] int ret; ^~~ core.c: In function ‘do_voting’: core.c:3021:9: 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:2940:6: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] int ret, xk1; ^~~ core.c: In function ‘do_iteration_two’: core.c:2400:3: 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:2464:6: note: ‘read_len_1’ was declared here int read_len_1, read_len_2=0; ^~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c core-junction.c: In function ‘copy_vote_to_alignment_res’: core-junction.c:945:12: 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:1996:8: warning: variable ‘sp2s’ set but not used [-Wunused-but-set-variable] char sp2s[200]; ^~~~ core-junction.c: In function ‘finalise_explain_CIGAR’: core-junction.c:3119:10: warning: variable ‘is_front_search’ set but not used [-Wunused-but-set-variable] int is_front_search = 0; ^~~~~~~~~~~~~~~ core-junction.c:3255:94: 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; ^~~~~~~~~~~~~~~~~~~~~ core-junction.c:3235:28: warning: variable ‘isCigarOK’ set but not used [-Wunused-but-set-variable] int mismatch_bases = 0, isCigarOK = 0; ^~~~~~~~~ core-junction.c:3049:23: 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:5635:23: 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-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c core-indel.c: In function ‘find_new_indels’: core-indel.c:1589:9: warning: variable ‘best_j’ set but not used [-Wunused-but-set-variable] int best_j=0, best_score=-99999, is_ambiguous_indel= 0; ^~~~~~ core-indel.c: In function ‘full_indel_alignment’: core-indel.c:2936:41: warning: variable ‘best_right’ set but not used [-Wunused-but-set-variable] int best_edge_score = -1, best_left, best_right; ^~~~~~~~~~ core-indel.c:2936:30: 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:3035:24: 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:3313:3: 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:3314:3: 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:3315:3: 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:3392:3: 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:3393:3: 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:3394:3: 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:3756:3: 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:3757:3: 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:3758:3: 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-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c sambam-file.c: In function ‘PBam_get_next_zchunk’: sambam-file.c:352:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&ID1, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:353:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&ID2, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:354:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&CM, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:355:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&FLG, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:364:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&XLEN,1, 2, bam_fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:372:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&SI1, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:373:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&SI2, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:374:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&SLEN, 1, 2, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:378:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&BSIZE_MID, 1,2 , bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:390:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer, 1, CDATA_READING, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:394:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&real_len, 4, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c gene-algorithms.c: In function ‘show_cigar’: gene-algorithms.c:771:6: warning: variable ‘last_end’ set but not used [-Wunused-but-set-variable] int last_end=0, last_offset = 0, cursor = 0; ^~~~~~~~ gene-algorithms.c:770:9: 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:1183:28: 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:1732:6: 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:2373:7: 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-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c input-files.c: In function ‘SAM_pairer_get_next_read_BIN’: input-files.c:2754:11: 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:4297:23: 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:4755:9: warning: variable ‘ref_name’ set but not used [-Wunused-but-set-variable] char ref_name[MAX_CHROMOSOME_NAME_LEN]; ^~~~~~~~ input-files.c: In function ‘geinput_next_char’: input-files.c:523:5: 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:3406:2: 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:3613:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&rlen, 1, 2, fp); ^~~~~~~~~~~~~~~~~~~~~~ input-files.c:3625:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&rlen, 1, 2, fp); ^~~~~~~~~~~~~~~~~~~~~~ input-files.c: In function ‘SAM_pairer_osr_next_bin’: input-files.c:3635:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&rlen, 1, 2, fp); ^~~~~~~~~~~~~~~~~~~~~~ input-files.c:3639:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&rlen, 1, 2, fp); ^~~~~~~~~~~~~~~~~~~~~~ input-files.c:3642:2: 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:4273:4: 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:5067:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_name_len, 2,1 , bbfp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-files.c:5073:6: 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:5076:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_len,2,1,bbfp); ^~~~~~~~~~~~~~~~~~~~~~~~~ input-files.c:5082:6: 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:5135:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_name_len, 2,1 , bbfp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-files.c:5141:6: 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:5145:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_len, 2,1 , bbfp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-files.c:5148:6: 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-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c sorted-hashtable.c: In function ‘gehash_load_option’: sorted-hashtable.c:1264:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(magic_chars,1,8,fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sorted-hashtable.c:1269:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&option_key, 2, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ sorted-hashtable.c:1272:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&option_length, 2, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sorted-hashtable.c:1276:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(result ,option_length,1,fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sorted-hashtable.c: In function ‘gehash_load’: sorted-hashtable.c:1303:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(magic_chars,1,8,fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sorted-hashtable.c:1326:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&option_key, 2, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ sorted-hashtable.c:1329:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&option_length, 2, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sorted-hashtable.c:1332:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(the_table -> index_gap),2,1,fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sorted-hashtable.c:1334:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&(the_table -> padding),2,1,fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sorted-hashtable.c: In function ‘gehash_go_q_tolerable’: sorted-hashtable.c:513:22: warning: array subscript is above array bounds [-Warray-bounds] mutation_stack[j] = 0; ~~~~~~~~~~~~~~^~~ sorted-hashtable.c:530:22: warning: array subscript is above array bounds [-Warray-bounds] error_pos_stack[j] = error_pos_stack[i] + (j-i); ~~~~~~~~~~~~~~~^~~ sorted-hashtable.c: In function ‘gehash_go_q_CtoT’: sorted-hashtable.c:594:22: warning: array subscript is above array bounds [-Warray-bounds] mutation_stack[j] = 0; ~~~~~~~~~~~~~~^~~ sorted-hashtable.c:612:22: warning: array subscript is above array bounds [-Warray-bounds] error_pos_stack[j] = error_pos_stack[i] + (j-i); ~~~~~~~~~~~~~~~^~~ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c core-bigtable.c: In function ‘bigtable_readonly_result’: core-bigtable.c:70:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(write_ptr, loadjunc?sizeof(subjunc_result_t):sizeof(mapping_result_t), 1, global_context -> bigtable_cache_file_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ core-bigtable.c: In function ‘bigtable_retrieve_cache’: core-bigtable.c: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-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE readSummary.c: In function ‘calc_junctions_from_cigar’: readSummary.c:347:15: 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:1804:15: 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:1802:16: 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:1801:16: 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:1799:15: 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 ‘readSummary’: readSummary.c:4442:9: warning: variable ‘curchr_name’ set but not used [-Wunused-but-set-variable] char * curchr_name, * fasta_contigs_fname; ^~~~~~~~~~~ readSummary.c:4441:15: warning: variable ‘curpos’ set but not used [-Wunused-but-set-variable] long curchr, curpos; ^~~~~~ readSummary.c:4441:7: warning: variable ‘curchr’ set but not used [-Wunused-but-set-variable] long curchr, curpos; ^~~~~~ readSummary.c: In function ‘load_feature_info’: readSummary.c:927:3: 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:1555:3: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result] ftruncate(fileno(global_context -> SAM_output_fp), 0); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c: In function ‘calc_total_frag_len.part.2’: readSummary.c:1840:113: 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:1868:113: 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:1900:112: 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:1909:112: 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]; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ readSummary.c: In function ‘load_feature_info’: readSummary.c:865:10: warning: ‘token_temp’ may be used uninitialized in this function [-Wmaybe-uninitialized] char * token_temp, *chro_name; ^~~~~~~~~~ readSummary.c:929:10: warning: ‘token_temp’ may be used uninitialized in this function [-Wmaybe-uninitialized] char * token_temp; ^~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -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-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE SNPCalling.c: In function ‘read_tmp_block’: SNPCalling.c:275:4: 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:294:4: 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:295:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_len, sizeof(short), 1, tmp_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SNPCalling.c:296:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(read, sizeof(char), read_len, tmp_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SNPCalling.c:297:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(qual, sizeof(char), read_len, tmp_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE index-builder.c: In function ‘scan_gene_index’: index-builder.c:458:19: 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:1179:2: 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-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -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:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’ ZEXTERN int ZEXPORT gzclose OF((gzFile file)); ^~~~~~~ qualityScores.c: In function ‘rewind_qs_file’: qualityScores.c:275:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] gzclose(qs_context -> gzfq_reader); ^~~~~~~~~~ In file included from qualityScores.c:24:0: /usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’ ZEXTERN int ZEXPORT gzclose OF((gzFile file)); ^~~~~~~ qualityScores.c:282:29: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb"); ^ qualityScores.c: In function ‘start_qs_context’: qualityScores.c:313:29: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb"); ^ gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gcc -g -O3 -fdebug-prefix-map=/<>/subread-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE propmapped.c: In function ‘prop_PE’: propmapped.c:349:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_len,1,1,fp); ^~~~~~~~~~~~~~~~~~~~~~~ propmapped.c:352:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(read_name,read_len,1,fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ propmapped.c:356:6: 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-1.5.1+dfsg=. -fPIE -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=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o coverageCount coverage_calc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -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 ../bin/utilities ########################################################### # # # Installation complete. # # # # Generated executables were copied to directory ../bin/ # # # ########################################################### make[2]: Leaving directory '/<>/subread-1.5.1+dfsg/src' dh_auto_build -- CC=powerpc64le-linux-gnu-gcc make[1]: Leaving directory '/<>/subread-1.5.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/subread-1.5.1+dfsg' debian/tests/subread-tests /<>/subread-1.5.1+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 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.1 //=========================== 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=289.3k bps/s, total=0m || || 16%, 0 mins elapsed, rate=494.5k bps/s, total=0m || || 24%, 0 mins elapsed, rate=679.2k bps/s, total=0m || || 33%, 0 mins elapsed, rate=841.6k bps/s, total=0m || || 41%, 0 mins elapsed, rate=989.5k bps/s, total=0m || || 49%, 0 mins elapsed, rate=1123.4k bps/s, total=0m || || 58%, 0 mins elapsed, rate=1243.5k bps/s, total=0m || || 66%, 0 mins elapsed, rate=1352.0k bps/s, total=0m || || 74%, 0 mins elapsed, rate=1439.3k bps/s, total=0m || || 83%, 0 mins elapsed, rate=1528.8k bps/s, total=0m || || 91%, 0 mins elapsed, rate=1605.1k bps/s, total=0m || || 99%, 0 mins elapsed, rate=1677.5k bps/s, total=0m || || 52 uninformative subreads were found. || || These subreads were excluded from index building. || || Build the index... || || 8%, 0 mins elapsed, rate=730.9k bps/s, total=0m || || 16%, 0 mins elapsed, rate=760.9k bps/s, total=0m || || 24%, 0 mins elapsed, rate=778.7k bps/s, total=0m || || 33%, 0 mins elapsed, rate=837.4k bps/s, total=0m || || 41%, 0 mins elapsed, rate=907.6k bps/s, total=0m || || 49%, 0 mins elapsed, rate=989.9k bps/s, total=0m || || 58%, 0 mins elapsed, rate=1072.1k bps/s, total=0m || || 66%, 0 mins elapsed, rate=1155.2k bps/s, total=0m || || 74%, 0 mins elapsed, rate=1237.4k bps/s, total=0m || || 83%, 0 mins elapsed, rate=1310.0k bps/s, total=0m || || 91%, 0 mins elapsed, rate=1382.3k bps/s, total=0m || || 99%, 0 mins elapsed, rate=1451.1k 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/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.1 //========================== 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 : no || || || \\===================== http://subread.sourceforge.net/ ======================// //====================== Running (02-Dec-2016 17:20:24) ======================\\ || || || 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=29.4k reads per second || || 39% completed, 0.0 mins elapsed, rate=29.3k reads per second || || 46% completed, 0.0 mins elapsed, rate=29.3k reads per second || || 53% completed, 0.0 mins elapsed, rate=29.3k reads per second || || 60% completed, 0.0 mins elapsed, rate=29.3k reads per second || || 74% completed, 0.0 mins elapsed, rate=10.7k reads per second || || 83% completed, 0.0 mins elapsed, rate=11.1k reads per second || || 91% completed, 0.0 mins elapsed, rate=11.5k reads per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 19998 reads || || Mapped : 19997 reads (100.0%) || || Indels : 7 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.1 //========================== 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 (02-Dec-2016 17:20:26) ======================\\ || || || 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=29.5k reads per second || || 39% completed, 0.0 mins elapsed, rate=29.4k reads per second || || 46% completed, 0.0 mins elapsed, rate=29.4k reads per second || || 53% completed, 0.0 mins elapsed, rate=29.4k reads per second || || 60% completed, 0.0 mins elapsed, rate=29.4k reads per second || || 74% completed, 0.0 mins elapsed, rate=11.2k reads per second || || 83% completed, 0.0 mins elapsed, rate=11.7k reads per second || || 91% completed, 0.0 mins elapsed, rate=12.1k reads per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 19998 reads || || Mapped : 18758 reads (93.8%) || || Indels : 5 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.1 //========================== 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 : no || || || \\===================== http://subread.sourceforge.net/ ======================// //====================== Running (02-Dec-2016 17:20:29) ======================\\ || || || 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=14.4k fragments per second || || 39% completed, 0.0 mins elapsed, rate=14.4k fragments per second || || 46% completed, 0.0 mins elapsed, rate=14.4k fragments per second || || 53% completed, 0.0 mins elapsed, rate=14.4k fragments per second || || 60% completed, 0.0 mins elapsed, rate=14.4k fragments per second || || 74% completed, 0.0 mins elapsed, rate=7.9k fragments per second || || 83% completed, 0.0 mins elapsed, rate=8.0k fragments per second || || 91% completed, 0.0 mins elapsed, rate=8.1k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 19998 fragments || || Mapped : 19998 fragments (100.0%) || || Correctly paired : 19554 fragments || || Indels : 23 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.1 //========================== 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 (02-Dec-2016 17:20:32) ======================\\ || || || 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=14.3k fragments per second || || 39% completed, 0.0 mins elapsed, rate=14.3k fragments per second || || 46% completed, 0.0 mins elapsed, rate=14.3k fragments per second || || 53% completed, 0.0 mins elapsed, rate=14.2k fragments per second || || 60% completed, 0.0 mins elapsed, rate=14.2k fragments per second || || 74% completed, 0.0 mins elapsed, rate=7.8k fragments per second || || 83% completed, 0.0 mins elapsed, rate=7.9k fragments per second || || 91% completed, 0.0 mins elapsed, rate=8.0k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 19998 fragments || || Mapped : 19216 fragments (96.1%) || || Correctly paired : 18830 fragments || || Indels : 22 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.1 //========================== 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 : no || || || \\===================== http://subread.sourceforge.net/ ======================// //====================== Running (02-Dec-2016 17:20:36) ======================\\ || || || 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=14.7k fragments per second || || 39% completed, 0.0 mins elapsed, rate=14.7k fragments per second || || 46% completed, 0.0 mins elapsed, rate=14.7k fragments per second || || 53% completed, 0.0 mins elapsed, rate=14.8k fragments per second || || 60% completed, 0.0 mins elapsed, rate=14.7k fragments per second || || 74% completed, 0.0 mins elapsed, rate=7.9k fragments per second || || 83% completed, 0.0 mins elapsed, rate=8.0k fragments per second || || 91% completed, 0.0 mins elapsed, rate=8.1k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 20000 fragments || || Mapped : 19568 fragments (97.8%) || || Correctly paired : 14442 fragments || || Indels : 63 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.1 //========================== 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 : no || || Read group name : MyTestGroup || || || \\===================== http://subread.sourceforge.net/ ======================// //====================== Running (02-Dec-2016 17:20:39) ======================\\ || || || 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=23.8k fragments per second || || 40% completed, 0.0 mins elapsed, rate=23.9k fragments per second || || 48% completed, 0.0 mins elapsed, rate=24.1k fragments per second || || 53% completed, 0.0 mins elapsed, rate=24.1k fragments per second || || 59% completed, 0.0 mins elapsed, rate=24.2k fragments per second || || 67% completed, 0.0 mins elapsed, rate=24.4k fragments per second || || 75% completed, 0.0 mins elapsed, rate=10.4k fragments per second || || 83% completed, 0.0 mins elapsed, rate=11.0k fragments per second || || 92% completed, 0.0 mins elapsed, rate=11.5k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 20001 fragments || || Mapped : 19528 fragments (97.6%) || || Correctly paired : 14071 fragments || || Indels : 179 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.0 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// 800234850b92e12efa33175355898843 ../small1.00.b.array 3b39eb4b0aad6902d8a1be198cf2478d ../small1.00.b.tab ************************************************* *** SINGLE-END READS NO ERROR ****** ************************************************* unmatched= 532 ; matched= 19465 ; unmapped= 1 ; reads= 19998 ;NN= 0 accuracy= 0.973396009401 ; sensitivity= 0.999949994999 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= 563 ; matched= 39432 ; unmapped= 1 ; reads= 39996 ;NN= 0 accuracy= 0.985923240405 ; sensitivity= 0.9999749975 paired_match= 39414 ; paired= 0.999543517955 ************************************************* *** 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= 454 ; matched= 33883 ; unmapped= 5663 ; reads= 40000 ;NN= 0 accuracy= 0.986778111076 ; sensitivity= 0.858425 paired_match= 29154 ; paired= 0.860431484815 ************************************************* *** READS WITH SEQUENCING ERROR AND MUTATION *** *** SUBREAD IS RUN WITH LONG INDEL DETECTION *** ************************************************* unmatched= 499 ; matched= 33456 ; unmapped= 6045 ; reads= 40002 ;NN= 0 accuracy= 0.985304078928 ; sensitivity= 0.848832558372 paired_match= 28432 ; paired= 0.849832615973 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.1 //=========================== 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=688.6k bps/s, total=0m || || 16%, 0 mins elapsed, rate=1068.2k bps/s, total=0m || || 24%, 0 mins elapsed, rate=1404.2k bps/s, total=0m || || 33%, 0 mins elapsed, rate=1683.2k bps/s, total=0m || || 41%, 0 mins elapsed, rate=1937.6k bps/s, total=0m || || 49%, 0 mins elapsed, rate=2164.1k bps/s, total=0m || || 58%, 0 mins elapsed, rate=2370.8k bps/s, total=0m || || 66%, 0 mins elapsed, rate=2563.6k bps/s, total=0m || || 74%, 0 mins elapsed, rate=2736.7k bps/s, total=0m || || 83%, 0 mins elapsed, rate=2893.0k bps/s, total=0m || || 91%, 0 mins elapsed, rate=3044.8k bps/s, total=0m || || 99%, 0 mins elapsed, rate=3184.1k bps/s, total=0m || || 2 uninformative subreads were found. || || These subreads were excluded from index building. || || Build the index... || || 8%, 0 mins elapsed, rate=1666.3k bps/s, total=0m || || 16%, 0 mins elapsed, rate=1649.8k bps/s, total=0m || || 24%, 0 mins elapsed, rate=1677.5k bps/s, total=0m || || 33%, 0 mins elapsed, rate=1709.1k bps/s, total=0m || || 41%, 0 mins elapsed, rate=1735.8k bps/s, total=0m || || 49%, 0 mins elapsed, rate=1760.2k bps/s, total=0m || || 58%, 0 mins elapsed, rate=1800.1k bps/s, total=0m || || 66%, 0 mins elapsed, rate=1836.2k bps/s, total=0m || || 74%, 0 mins elapsed, rate=1856.1k bps/s, total=0m || || 83%, 0 mins elapsed, rate=1776.5k bps/s, total=0m || || 91%, 0 mins elapsed, rate=1749.0k bps/s, total=0m || || 99%, 0 mins elapsed, rate=1706.2k 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/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.1 //============================= 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 : no || || || \\===================== http://subread.sourceforge.net/ ======================// //====================== Running (02-Dec-2016 17:20:43) ======================\\ || || || 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=9.6k fragments per second || || 48% completed, 0.0 mins elapsed, rate=9.7k fragments per second || || 54% completed, 0.0 mins elapsed, rate=9.7k fragments per second || || 61% completed, 0.0 mins elapsed, rate=9.7k fragments per second || || 77% completed, 0.0 mins elapsed, rate=4.6k fragments per second || || 87% completed, 0.0 mins elapsed, rate=4.8k fragments per second || || 97% completed, 0.1 mins elapsed, rate=5.1k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 16052 fragments || || Mapped : 15914 fragments (99.1%) || || Correctly paired : 14370 fragments || || Junctions : 425 || || Indels : 187 || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.1 //============================= 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 : no || || || \\===================== http://subread.sourceforge.net/ ======================// //====================== Running (02-Dec-2016 17:20:47) ======================\\ || || || 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=5.2k fragments per second || || 48% completed, 0.0 mins elapsed, rate=5.2k fragments per second || || 54% completed, 0.1 mins elapsed, rate=5.2k fragments per second || || 61% completed, 0.1 mins elapsed, rate=5.2k fragments per second || || 77% completed, 0.1 mins elapsed, rate=3.2k fragments per second || || 87% completed, 0.1 mins elapsed, rate=3.3k fragments per second || || 97% completed, 0.1 mins elapsed, rate=3.4k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 16052 fragments || || Mapped : 15907 fragments (99.1%) || || Correctly paired : 14274 fragments || || Junctions : 455 || || Fusions : 99 || || Indels : 188 || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ================================================================================ FeatureCounts Basic Test http://subread.sourceforge.net/ ================================================================================ ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.1 //========================== 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 || || Overlapping bases : 0.0% || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file data/test-minimum.GTF ... || || Features : 23 || || Meta-features : 7 || || Chromosomes/contigs : 3 || || || || Process SAM file data/test-minimum.sam... || || Paired-end reads are included. || || Assign reads to features... || || Total reads : 998 || || Successfully assigned reads : 389 (39.0%) || || Running time : 0.00 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================// ================================================================================ 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 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.1 //============================= 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 (02-Dec-2016 17:20:54) ======================\\ || || || Split BAM file into ./temp-snps-012068-FA163EE6E811-* ... || || 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-1.5.1+dfsg' 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-1.5.1+dfsg' find /<>/subread-1.5.1+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \; mkdir -p /<>/subread-1.5.1+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-1.5.1+dfsg/bin/subread-align | debian/filter.pl > /<>/subread-1.5.1+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-1.5.1+dfsg/bin/subread-buildindex | debian/filter.pl > /<>/subread-1.5.1+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-1.5.1+dfsg/bin/subjunc | debian/filter.pl > /<>/subread-1.5.1+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-1.5.1+dfsg/bin/featureCounts | debian/filter.pl > /<>/subread-1.5.1+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-1.5.1+dfsg/bin/exactSNP | debian/filter.pl > /<>/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/exactSNP.1; help2man --no-info --help-option="''" --no-discard-stderr --name='detect short and long indels' \ /<>/subread-1.5.1+dfsg/bin/subindel | debian/filter.pl > /<>/subread-1.5.1+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-1.5.1+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /<>/subread-1.5.1+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-1.5.1+dfsg/bin/utilities/coverageCount | debian/filter.pl > /<>/subread-1.5.1+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-1.5.1+dfsg/bin/utilities/propmapped | debian/filter.pl > /<>/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/propmapped.1; for i in removeDup repair qualityScores ; do \ help2man --no-info --help-option="''" --no-discard-stderr --name='a component of subread suite' /<>/subread-1.5.1+dfsg/bin/utilities/$i | debian/filter.pl > /<>/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/$i.1; \ done dh_auto_install make[1]: Leaving directory '/<>/subread-1.5.1+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_strip -a -O--parallel dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform ppc64el: subread dh_strip debug symbol extraction: packages to act on: subread dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol dh_makeshlibs -a -O--parallel dh_shlibdeps -a -O--parallel dh_installdeb -a -O--parallel dh_gencontrol -a -O--parallel dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform ppc64el: subread dh_gencontrol debug symbol wrapper: packages to act on: subread dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package subread (pkgdir debian/subread, ddeb package dir debian/subread-dbgsym) dh_gencontrol debug symbol wrapper: building subread-dbgsym_1.5.1+dfsg-4_ppc64el.ddeb dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_1.5.1+dfsg-4_ppc64el.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile subread-dbgsym_1.5.1+dfsg-4_ppc64el.ddeb science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a -O--parallel dh_builddeb -a -O--parallel INFO: pkgstriptranslations version 131 pkgstriptranslations: processing subread (in debian/subread); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/subread/DEBIAN/control, package subread, directory debian/subread pkgstripfiles: Truncating usr/share/doc/subread/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package subread ... pkgstripfiles: No PNG files. dpkg-deb: building package 'subread' in '../subread_1.5.1+dfsg-4_ppc64el.deb'. dpkg-genchanges --build=any -mLaunchpad Build Daemon >../subread_1.5.1+dfsg-4_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build subread-1.5.1+dfsg dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20161202-1721 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ subread_1.5.1+dfsg-4_ppc64el.changes: ------------------------------------- Format: 1.8 Date: Fri, 02 Dec 2016 08:22:05 +0100 Source: subread Binary: subread subread-data Architecture: ppc64el Version: 1.5.1+dfsg-4 Distribution: zesty-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: subread - toolkit for processing next-gen sequencing data subread-data - data files for subread package Changes: subread (1.5.1+dfsg-4) unstable; urgency=medium . * Fix watch file * debhelper 10 * remove outdated information from README.source Checksums-Sha1: 67b24d8922ce6bbedf54e4e1e700cf7ead1bc434 2147630 subread-dbgsym_1.5.1+dfsg-4_ppc64el.ddeb 1806683a936716249a005b80b2fdfe6e649a8135 662484 subread_1.5.1+dfsg-4_ppc64el.deb Checksums-Sha256: e0620d3632bd8b5f00cbb38b2a63a67d0e05a213891166ef4068fbf8d13e0007 2147630 subread-dbgsym_1.5.1+dfsg-4_ppc64el.ddeb 35a641437434664eae5c92e7fe0bc6bccf2bf68b0a8a3d2508b694a4e9bb45a3 662484 subread_1.5.1+dfsg-4_ppc64el.deb Files: 1023be9c96c297dbc9fa5e0ecc98119d 2147630 science extra subread-dbgsym_1.5.1+dfsg-4_ppc64el.ddeb f48ce212481671a806bd39db42fafff5 662484 science optional subread_1.5.1+dfsg-4_ppc64el.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ subread_1.5.1+dfsg-4_ppc64el.deb -------------------------------- new debian package, version 2.0. size 662484 bytes: control archive=1435 bytes. 704 bytes, 15 lines control 1819 bytes, 28 lines md5sums Package: subread Version: 1.5.1+dfsg-4 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 9552 Depends: libc6 (>= 2.17), zlib1g (>= 1:1.2.3.3) Section: science Priority: optional Homepage: http://sourceforge.net/projects/subread/ Description: toolkit for processing next-gen sequencing data Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments. drwxr-xr-x root/root 0 2016-12-02 07:22 ./ drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/ drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/bin/ -rwxr-xr-x root/root 854912 2016-12-02 07:22 ./usr/bin/exactSNP -rwxr-xr-x root/root 920992 2016-12-02 07:22 ./usr/bin/featureCounts -rwxr-xr-x root/root 789408 2016-12-02 07:22 ./usr/bin/subindel -rwxr-xr-x root/root 790944 2016-12-02 07:22 ./usr/bin/subjunc -rwxr-xr-x root/root 790816 2016-12-02 07:22 ./usr/bin/subread-align -rwxr-xr-x root/root 854848 2016-12-02 07:22 ./usr/bin/subread-buildindex drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/ drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/subread/ -rwxr-xr-x root/root 789408 2016-12-02 07:22 ./usr/lib/subread/coverageCount -rwxr-xr-x root/root 789408 2016-12-02 07:22 ./usr/lib/subread/propmapped -rwxr-xr-x root/root 789632 2016-12-02 07:22 ./usr/lib/subread/qualityScores -rwxr-xr-x root/root 789312 2016-12-02 07:22 ./usr/lib/subread/removeDup -rwxr-xr-x root/root 789312 2016-12-02 07:22 ./usr/lib/subread/repair -rwxr-xr-x root/root 789312 2016-12-02 07:22 ./usr/lib/subread/subread-fullscan drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/share/ drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/share/doc/subread/ -rw-r--r-- root/root 500 2016-12-02 07:22 ./usr/share/doc/subread/README.Debian -rw-r--r-- root/root 3670 2016-08-25 04:20 ./usr/share/doc/subread/README.txt -rw-r--r-- root/root 1053 2016-12-02 07:22 ./usr/share/doc/subread/changelog.Debian.gz -rw-r--r-- root/root 1138 2016-12-02 07:22 ./usr/share/doc/subread/copyright drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/share/man/ drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/share/man/man1/ -rw-r--r-- root/root 594 2016-12-02 07:22 ./usr/share/man/man1/coverageCount.1.gz -rw-r--r-- root/root 1173 2016-12-02 07:22 ./usr/share/man/man1/exactSNP.1.gz -rw-r--r-- root/root 2726 2016-12-02 07:22 ./usr/share/man/man1/featureCounts.1.gz -rw-r--r-- root/root 461 2016-12-02 07:22 ./usr/share/man/man1/propmapped.1.gz -rw-r--r-- root/root 565 2016-12-02 07:22 ./usr/share/man/man1/qualityScores.1.gz -rw-r--r-- root/root 495 2016-12-02 07:22 ./usr/share/man/man1/removeDup.1.gz -rw-r--r-- root/root 477 2016-12-02 07:22 ./usr/share/man/man1/repair.1.gz -rw-r--r-- root/root 347 2016-12-02 07:22 ./usr/share/man/man1/subindel.1.gz -rw-r--r-- root/root 1528 2016-12-02 07:22 ./usr/share/man/man1/subjunc.1.gz -rw-r--r-- root/root 1617 2016-12-02 07:22 ./usr/share/man/man1/subread-align.1.gz -rw-r--r-- root/root 764 2016-12-02 07:22 ./usr/share/man/man1/subread-buildindex.1.gz -rw-r--r-- root/root 377 2016-12-02 07:22 ./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: 125548 Build-Time: 103 Distribution: zesty-proposed Host Architecture: ppc64el Install-Time: 11 Job: subread_1.5.1+dfsg-4.dsc Machine Architecture: ppc64el Package: subread Package-Time: 117 Source-Version: 1.5.1+dfsg-4 Space: 125548 Status: successful Version: 1.5.1+dfsg-4 -------------------------------------------------------------------------------- Finished at 20161202-1721 Build needed 00:01:57, 125548k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-11407674'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-11407674/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-11407674'] Unmounting chroot for build PACKAGEBUILD-11407674... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-11407674'] Removing build PACKAGEBUILD-11407674