RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux bos01-arm64-031 4.4.0-75-generic #96-Ubuntu SMP Thu Apr 20 09:56:48 UTC 2017 aarch64 Buildd toolchain package versions: launchpad-buildd_142 python-lpbuildd_142 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_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.11. Syncing the system clock with the buildd NTP service... 30 Apr 03:47:02 ntpdate[1812]: adjust time server 10.211.37.1 offset -0.047244 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-12500012', '/home/buildd/filecache-default/42e17d2fa25e748a1aa6eaeef2fe6722beaed5a9'] Unpacking chroot for build PACKAGEBUILD-12500012 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-12500012'] Mounting chroot for build PACKAGEBUILD-12500012 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-12500012', 'deb http://ftpmaster.internal/ubuntu artful main universe', 'deb http://ftpmaster.internal/ubuntu artful-security main universe', 'deb http://ftpmaster.internal/ubuntu artful-updates main universe', 'deb http://ftpmaster.internal/ubuntu artful-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-12500012 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-12500012', 'armhf'] Updating debian chroot for build PACKAGEBUILD-12500012 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:3 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed InRelease [85.4 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main armhf Packages [1138 kB] Get:6 http://ftpmaster.internal/ubuntu artful/universe armhf Packages [7858 kB] Get:7 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4682 kB] Get:8 http://ftpmaster.internal/ubuntu artful-proposed/main armhf Packages [60.5 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main Translation-en [36.1 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/universe armhf Packages [243 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/universe Translation-en [183 kB] Fetched 14.7 MB in 5s (2794 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: advancecomp debianutils libapparmor1 libsystemd0 libudev1 libusb-0.1-4 systemd systemd-sysv 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2792 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu artful-proposed/main armhf debianutils armhf 4.8.1.1 [84.3 kB] Get:2 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libapparmor1 armhf 2.11.0-2ubuntu5 [26.3 kB] Get:3 http://ftpmaster.internal/ubuntu artful-proposed/main armhf systemd armhf 233-5ubuntu1 [2250 kB] Get:4 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libsystemd0 armhf 233-5ubuntu1 [191 kB] Get:5 http://ftpmaster.internal/ubuntu artful-proposed/main armhf systemd-sysv armhf 233-5ubuntu1 [13.7 kB] Get:6 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libudev1 armhf 233-5ubuntu1 [52.8 kB] Get:7 http://ftpmaster.internal/ubuntu artful-proposed/main armhf advancecomp armhf 1.23-1 [158 kB] Get:8 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libusb-0.1-4 armhf 2:0.1.12-31 [15.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2792 kB in 0s (24.5 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12213 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.1.1_armhf.deb ... Unpacking debianutils (4.8.1.1) over (4.8.1) ... Setting up debianutils (4.8.1.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12213 files and directories currently installed.) Preparing to unpack .../libapparmor1_2.11.0-2ubuntu5_armhf.deb ... Unpacking libapparmor1:armhf (2.11.0-2ubuntu5) over (2.11.0-2ubuntu4) ... Preparing to unpack .../systemd_233-5ubuntu1_armhf.deb ... Unpacking systemd (233-5ubuntu1) over (232-21ubuntu3) ... dpkg: warning: unable to delete old directory '/etc/dbus-1/system.d': Directory not empty dpkg: warning: unable to delete old directory '/etc/dbus-1': Directory not empty Preparing to unpack .../libsystemd0_233-5ubuntu1_armhf.deb ... Unpacking libsystemd0:armhf (233-5ubuntu1) over (232-21ubuntu3) ... Setting up libsystemd0:armhf (233-5ubuntu1) ... Setting up libapparmor1:armhf (2.11.0-2ubuntu5) ... Setting up systemd (233-5ubuntu1) ... Installing new version of config file /etc/systemd/resolved.conf ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.hostname1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.locale1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.login1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.network1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.resolve1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.systemd1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.timedate1.conf ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12239 files and directories currently installed.) Preparing to unpack .../systemd-sysv_233-5ubuntu1_armhf.deb ... Unpacking systemd-sysv (233-5ubuntu1) over (232-21ubuntu3) ... Preparing to unpack .../libudev1_233-5ubuntu1_armhf.deb ... Unpacking libudev1:armhf (233-5ubuntu1) over (232-21ubuntu3) ... Setting up libudev1:armhf (233-5ubuntu1) ... (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 ... 12239 files and directories currently installed.) Preparing to unpack .../advancecomp_1.23-1_armhf.deb ... Unpacking advancecomp (1.23-1) over (1.20-1) ... Preparing to unpack .../libusb-0.1-4_2%3a0.1.12-31_armhf.deb ... Unpacking libusb-0.1-4:armhf (2:0.1.12-31) over (2:0.1.12-30) ... Setting up systemd-sysv (233-5ubuntu1) ... Setting up advancecomp (1.23-1) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Setting up libusb-0.1-4:armhf (2:0.1.12-31) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-12500012', 'armhf', 'artful-proposed', '-c', 'chroot:autobuild', '--arch=armhf', '--dist=artful-proposed', '--purge=never', '--nolog', 'subread_1.5.2+dfsg-1.dsc'] Initiating build PACKAGEBUILD-12500012 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-75-generic #96-Ubuntu SMP Thu Apr 20 09:56:48 UTC 2017 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos01-arm64-031.buildd +==============================================================================+ | subread 1.5.2+dfsg-1 (armhf) 30 Apr 2017 03:47 | +==============================================================================+ Package: subread Version: 1.5.2+dfsg-1 Source Version: 1.5.2+dfsg-1 Distribution: artful-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/subread-PJNPdt/subread-1.5.2+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/subread-PJNPdt' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-12500012/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- subread_1.5.2+dfsg-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-2qPvH1/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-2qPvH1/apt_archive ./ InRelease Get:2 copy:/<>/resolver-2qPvH1/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-2qPvH1/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-2qPvH1/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-2qPvH1/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (148 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 778 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-2qPvH1/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [778 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 778 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (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 ... 12239 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.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-kU_e23/apt_archive/sbuild-build-depends-subread-dummy.deb'. Ign:1 copy:/<>/resolver-kU_e23/apt_archive ./ InRelease Get:2 copy:/<>/resolver-kU_e23/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-kU_e23/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-kU_e23/apt_archive ./ Sources [231 B] Get:5 copy:/<>/resolver-kU_e23/apt_archive ./ Packages [549 B] Fetched 2899 B in 0s (136 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install subread build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bc bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support Recommended packages: curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bc bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal sbuild-build-depends-subread-dummy zlib1g-dev 0 upgraded, 43 newly installed, 1 to remove and 0 not upgraded. Need to get 19.7 MB of archives. After this operation, 72.8 MB of additional disk space will be used. Get:1 copy:/<>/resolver-kU_e23/apt_archive ./ sbuild-build-depends-subread-dummy 0.invalid.0 [800 B] Get:2 http://ftpmaster.internal/ubuntu artful/main armhf liblocale-gettext-perl armhf 1.07-3build1 [16.4 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main armhf groff-base armhf 1.22.3-9 [1013 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main armhf libbsd0 armhf 0.8.3-1 [48.3 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main armhf bsdmainutils armhf 9.0.12ubuntu1 [169 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main armhf libpipeline1 armhf 1.4.1-2 [21.0 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main armhf man-db armhf 2.7.6.1-2 [873 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main armhf libpython2.7-minimal armhf 2.7.13-2 [338 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main armhf python2.7-minimal armhf 2.7.13-2 [1118 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main armhf python-minimal armhf 2.7.13-2 [28.2 kB] Get:11 http://ftpmaster.internal/ubuntu artful/main armhf mime-support all 3.60ubuntu1 [30.1 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main armhf libexpat1 armhf 2.2.0-2 [53.2 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main armhf libpython2.7-stdlib armhf 2.7.13-2 [1839 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main armhf python2.7 armhf 2.7.13-2 [229 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main armhf libpython-stdlib armhf 2.7.13-2 [7774 B] Get:16 http://ftpmaster.internal/ubuntu artful/main armhf python armhf 2.7.13-2 [139 kB] Get:17 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libmagic-mgc armhf 1:5.30-1 [181 kB] Get:18 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libmagic1 armhf 1:5.30-1 [63.0 kB] Get:19 http://ftpmaster.internal/ubuntu artful-proposed/main armhf file armhf 1:5.30-1 [21.5 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main armhf gettext-base armhf 0.19.8.1-2ubuntu1 [44.8 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main armhf libglib2.0-0 armhf 2.52.0-1 [1004 kB] Get:22 http://ftpmaster.internal/ubuntu artful-proposed/main armhf libicu57 armhf 57.1-6 [7442 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main armhf libxml2 armhf 2.9.4+dfsg1-2.2 [606 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main armhf libsigsegv2 armhf 2.10-5 [13.3 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main armhf m4 armhf 1.4.18-1 [181 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main armhf autoconf all 2.69-10 [321 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main armhf autotools-dev all 20161112.1 [39.5 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main armhf automake all 1:1.15-5ubuntu1 [509 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main armhf autopoint all 0.19.8.1-2ubuntu1 [411 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main armhf bc armhf 1.06.95-9build2 [76.4 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main armhf libtool all 2.4.6-2 [194 kB] Get:32 http://ftpmaster.internal/ubuntu artful-proposed/main armhf dh-autoreconf all 14 [15.5 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main armhf libarchive-zip-perl all 1.59-1 [84.0 kB] Get:34 http://ftpmaster.internal/ubuntu artful/main armhf libfile-stripnondeterminism-perl all 0.032-1 [12.9 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main armhf libtimedate-perl all 2.3000-2 [37.5 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main armhf dh-strip-nondeterminism all 0.032-1 [4894 B] Get:37 http://ftpmaster.internal/ubuntu artful/main armhf libcroco3 armhf 0.6.11-3 [69.6 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main armhf gettext armhf 0.19.8.1-2ubuntu1 [1018 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main armhf po-debconf all 1.0.20 [232 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main armhf debhelper all 10.2.5ubuntu2 [870 kB] Get:42 http://ftpmaster.internal/ubuntu artful/universe armhf help2man armhf 1.47.4 [155 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-0ubuntu1 [166 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.7 MB in 1s (12.2 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12239 files and directories currently installed.) Removing pkg-create-dbgsym (0.73) ... Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12230 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3build1_armhf.deb ... Unpacking liblocale-gettext-perl (1.07-3build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../01-groff-base_1.22.3-9_armhf.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package libbsd0:armhf. Preparing to unpack .../02-libbsd0_0.8.3-1_armhf.deb ... Unpacking libbsd0:armhf (0.8.3-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../03-bsdmainutils_9.0.12ubuntu1_armhf.deb ... Unpacking bsdmainutils (9.0.12ubuntu1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.4.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.7.6.1-2_armhf.deb ... Unpacking man-db (2.7.6.1-2) ... Selecting previously unselected package libpython2.7-minimal:armhf. Preparing to unpack .../06-libpython2.7-minimal_2.7.13-2_armhf.deb ... Unpacking libpython2.7-minimal:armhf (2.7.13-2) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.13-2_armhf.deb ... Unpacking python2.7-minimal (2.7.13-2) ... Selecting previously unselected package python-minimal. Preparing to unpack .../08-python-minimal_2.7.13-2_armhf.deb ... Unpacking python-minimal (2.7.13-2) ... Selecting previously unselected package mime-support. Preparing to unpack .../09-mime-support_3.60ubuntu1_all.deb ... Unpacking mime-support (3.60ubuntu1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../10-libexpat1_2.2.0-2_armhf.deb ... Unpacking libexpat1:armhf (2.2.0-2) ... Selecting previously unselected package libpython2.7-stdlib:armhf. Preparing to unpack .../11-libpython2.7-stdlib_2.7.13-2_armhf.deb ... Unpacking libpython2.7-stdlib:armhf (2.7.13-2) ... Selecting previously unselected package python2.7. Preparing to unpack .../12-python2.7_2.7.13-2_armhf.deb ... Unpacking python2.7 (2.7.13-2) ... Selecting previously unselected package libpython-stdlib:armhf. Preparing to unpack .../13-libpython-stdlib_2.7.13-2_armhf.deb ... Unpacking libpython-stdlib:armhf (2.7.13-2) ... Setting up libpython2.7-minimal:armhf (2.7.13-2) ... Setting up python2.7-minimal (2.7.13-2) ... Setting up python-minimal (2.7.13-2) ... Selecting previously unselected package python. (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 ... 13528 files and directories currently installed.) Preparing to unpack .../00-python_2.7.13-2_armhf.deb ... Unpacking python (2.7.13-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.30-1_armhf.deb ... Unpacking libmagic-mgc (1:5.30-1) ... 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Setting up libbsd0:armhf (0.8.3-1) ... Setting up libxml2:armhf (2.9.4+dfsg1-2.2) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libmagic1:armhf (1:5.30-1) ... Setting up libcroco3:armhf (0.6.11-3) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... Setting up autotools-dev (20161112.1) ... 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:armhf (2.7.13-2) ... Setting up autopoint (0.19.8.1-2ubuntu1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-0ubuntu1) ... Setting up libfile-stripnondeterminism-perl (0.032-1) ... Setting up gettext (0.19.8.1-2ubuntu1) ... Setting up python2.7 (2.7.13-2) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up libpython-stdlib:armhf (2.7.13-2) ... 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 (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python (2.7.13-2) ... Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (14) ... Setting up dh-strip-nondeterminism (0.032-1) ... Setting up debhelper (10.2.5ubuntu2) ... Setting up sbuild-build-depends-subread-dummy (0.invalid.0) ... (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 ... 15030 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-75-generic arm64 (armv7l) Toolchain package versions: binutils_2.28-4ubuntu1 dpkg-dev_1.18.23ubuntu4 g++-6_6.3.0-14ubuntu3 gcc-6_6.3.0-14ubuntu3 libc6-dev_2.24-9ubuntu2 libstdc++-6-dev_6.3.0-14ubuntu3 libstdc++6_6.3.0-14ubuntu3 linux-libc-dev_4.10.0-20.22 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_1.23-1 apt_1.4.1ubuntu2 apt-transport-https_1.4.1ubuntu2 autoconf_2.69-10 automake_1:1.15-5ubuntu1 autopoint_0.19.8.1-2ubuntu1 autotools-dev_20161112.1 base-files_9.6ubuntu99 base-passwd_3.5.43 bash_4.4-2ubuntu1 bc_1.06.95-9build2 binutils_2.28-4ubuntu1 bsdmainutils_9.0.12ubuntu1 bsdutils_1:2.29-1ubuntu2 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20161130 coreutils_8.26-3ubuntu3 cpp_4:6.3.0-2ubuntu1 cpp-6_6.3.0-14ubuntu3 dash_0.5.8-2.3ubuntu1 debconf_1.5.60ubuntu1 debhelper_10.2.5ubuntu2 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.032-1 diffutils_1:3.5-3 dmsetup_2:1.02.136-1ubuntu5 dpkg_1.18.23ubuntu4 dpkg-dev_1.18.23ubuntu4 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-1ubuntu2 file_1:5.30-1 findutils_4.6.0+git+20161106-2 g++_4:6.3.0-2ubuntu1 g++-6_6.3.0-14ubuntu3 gcc_4:6.3.0-2ubuntu1 gcc-6_6.3.0-14ubuntu3 gcc-6-base_6.3.0-14ubuntu3 gettext_0.19.8.1-2ubuntu1 gettext-base_0.19.8.1-2ubuntu1 gnupg_2.1.15-1ubuntu7 gnupg-agent_2.1.15-1ubuntu7 gpgv_2.1.15-1ubuntu7 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5ubuntu1 help2man_1.47.4 hostname_3.18 init_1.47 init-system-helpers_1.47 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu5 libapt-pkg5.0_1.4.1ubuntu2 libarchive-zip-perl_1.59-1 libasan3_6.3.0-14ubuntu3 libasn1-8-heimdal_7.1.0+dfsg-9ubuntu1 libassuan0_2.4.3-2 libatomic1_6.3.0-14ubuntu3 libattr1_1:2.4.47-2build1 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_1.0.6-8.1 libc-bin_2.24-9ubuntu2 libc-dev-bin_2.24-9ubuntu2 libc6_2.24-9ubuntu2 libc6-dev_2.24-9ubuntu2 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_6.3.0-14ubuntu3 libcomerr2_1.43.4-2 libcroco3_0.6.11-3 libcryptsetup4_2:1.7.2-0ubuntu1 libcurl3-gnutls_7.52.1-5ubuntu1 libdb5.3_5.3.28-12 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.136-1ubuntu5 libdpkg-perl_1.18.23ubuntu4 libexpat1_2.2.0-2 libfakeroot_1.21-1ubuntu2 libfdisk1_2.29-1ubuntu2 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.032-1 libgcc-6-dev_6.3.0-14ubuntu3 libgcc1_1:6.3.0-14ubuntu3 libgcrypt20_1.7.6-1 libgdbm3_1.8.3-14 libglib2.0-0_2.52.0-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.6-4ubuntu4 libgomp1_6.3.0-14ubuntu3 libgpg-error0_1.26-2 libgssapi-krb5-2_1.15-2 libgssapi3-heimdal_7.1.0+dfsg-9ubuntu1 libhcrypto4-heimdal_7.1.0+dfsg-9ubuntu1 libheimbase1-heimdal_7.1.0+dfsg-9ubuntu1 libheimntlm0-heimdal_7.1.0+dfsg-9ubuntu1 libhogweed4_3.3-1 libhx509-5-heimdal_7.1.0+dfsg-9ubuntu1 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_0.16-1 libip4tc0_1.6.0-3ubuntu2 libisl15_0.18-1 libk5crypto3_1.15-2 libkeyutils1_1.5.9-9ubuntu1 libkmod2_22-1.1ubuntu1 libkrb5-26-heimdal_7.1.0+dfsg-9ubuntu1 libkrb5-3_1.15-2 libkrb5support0_1.15-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.44+dfsg-4ubuntu1 libldap-common_2.4.44+dfsg-4ubuntu1 liblocale-gettext-perl_1.07-3build1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29-1ubuntu2 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-1 libnpth0_1.3-1 libp11-kit0_0.23.3-5 libpam-modules_1.1.8-3.2ubuntu3 libpam-modules-bin_1.1.8-3.2ubuntu3 libpam-runtime_1.1.8-3.2ubuntu3 libpam0g_1.1.8-3.2ubuntu3 libpcre3_2:8.39-3 libperl5.24_5.24.1-2ubuntu1 libpipeline1_1.4.1-2 libpng16-16_1.6.29-2 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.17.0-4 libpython-stdlib_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libreadline7_7.0-0ubuntu2 libroken18-heimdal_7.1.0+dfsg-9ubuntu1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-2ubuntu1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-2ubuntu1 libseccomp2_2.3.1-2.1ubuntu1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.10-5 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.29-1ubuntu2 libsqlite3-0_3.16.2-3 libss2_1.43.4-2 libssl1.0.0_1.0.2g-1ubuntu12 libstdc++-6-dev_6.3.0-14ubuntu3 libstdc++6_6.3.0-14ubuntu3 libsystemd0_233-5ubuntu1 libtasn1-6_4.10-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libubsan0_6.3.0-14ubuntu3 libudev1_233-5ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1ubuntu2 libwind0-heimdal_7.1.0+dfsg-9ubuntu1 libxml2_2.9.4+dfsg1-2.2 linux-libc-dev_4.10.0-20.22 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu1 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17ubuntu2 mime-support_3.60ubuntu1 mount_2.29-1ubuntu2 multiarch-support_2.24-9ubuntu2 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu12 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu1 patch_2.7.5-1build1 perl_5.24.1-2ubuntu1 perl-base_5.24.1-2ubuntu1 perl-modules-5.24_5.24.1-2ubuntu1 pinentry-curses_1.0.0-2 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 python_2.7.13-2 python-minimal_2.7.13-2 python2.7_2.7.13-2 python2.7-minimal_2.7.13-2 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-subread-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 systemd_233-5ubuntu1 systemd-sysv_233-5ubuntu1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tar_1.29b-1.1 tzdata_2017b-1 ubuntu-keyring_2016.10.27 util-linux_2.29-1ubuntu2 xz-utils_5.2.2-1.2 zlib1g_1:1.2.11.dfsg-0ubuntu1 zlib1g-dev_1:1.2.11.dfsg-0ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Mar 21 15:25:35 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./subread_1.5.2+dfsg-1.dsc dpkg-source: info: extracting subread in subread-1.5.2+dfsg dpkg-source: info: unpacking subread_1.5.2+dfsg.orig.tar.xz dpkg-source: info: unpacking subread_1.5.2+dfsg-1.debian.tar.xz dpkg-source: info: applying typo.patch dpkg-source: info: applying fix_ftbfs_kfreebsd.patch dpkg-source: info: applying arch_specific_flags.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<>/subread-1.5.2+dfsg SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>/subread-1.5.2+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 1.5.2+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build subread-1.5.2+dfsg dpkg-buildpackage: info: host architecture armhf 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-1.5.2+dfsg' cd src; make -f Makefile.Linux clean make[2]: Entering directory '/<>/subread-1.5.2+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-1.5.2+dfsg/src' dh_clean make[1]: Leaving directory '/<>/subread-1.5.2+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-1.5.2+dfsg' cd src; make -f Makefile.Linux make[2]: Entering directory '/<>/subread-1.5.2+dfsg/src' gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c core.c: In function ‘print_in_box’: core.c:159:7: warning: variable ‘is_R_linebreak’ set but not used [-Wunused-but-set-variable] char is_R_linebreak=0, * content, *out_line_buff; ^~~~~~~~~~~~~~ core.c: In function ‘convert_GZ_to_FQ’: core.c:884:19: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types] gzFile * rawfp = gzopen(fname, "r"); ^~~~~~ core.c:895:25: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types] char * bufr =gzgets(rawfp, linebuff, 3000); ^~~~~ In file included from subread.h:26:0, from core.c:43: /usr/include/zlib.h:1491:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’ ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len)); ^~~~~~ core.c:906:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] gzclose(rawfp); ^~~~~ In file included from subread.h:26:0, from core.c:43: /usr/include/zlib.h:1630:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’ ZEXTERN int ZEXPORT gzclose OF((gzFile file)); ^~~~~~~ core.c: In function ‘calc_tlen’: core.c:1579:16: 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:2245:6: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] int ret; ^~~ core.c: In function ‘write_realignments_for_fragment’: core.c:2460:21: warning: variable ‘raw_r2’ set but not used [-Wunused-but-set-variable] mapping_result_t * raw_r2 = NULL; ^~~~~~ core.c:2457:21: 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:2526:6: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] int ret; ^~~ core.c: In function ‘do_voting’: core.c:3176:9: 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:3086:6: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] int ret, xk1; ^~~ core.c: In function ‘run_maybe_threads’: core.c:3478:4: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for(current_thread_no = 0 ; current_thread_no < global_context->config.all_threads ; current_thread_no ++) ^~~ core.c:3480:5: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘for’ thread_contexts[current_thread_no].all_correct_PE_reads = 0; ^~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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:965:12: 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:2016:8: warning: variable ‘sp2s’ set but not used [-Wunused-but-set-variable] char sp2s[200]; ^~~~ core-junction.c: In function ‘final_CIGAR_quality’: core-junction.c:2847:13: warning: variable ‘debug_ptr’ set but not used [-Wunused-but-set-variable] char * debug_ptr = read_text; ^~~~~~~~~ core-junction.c:2879:13: warning: variable ‘debug_ptr’ set but not used [-Wunused-but-set-variable] char * debug_ptr = read_text + read_cursor; ^~~~~~~~~ core-junction.c: In function ‘finalise_explain_CIGAR’: core-junction.c:3233:94: warning: variable ‘total_coverage_length’ set but not used [-Wunused-but-set-variable] int final_qual = 0, applied_mismatch = 0, non_clipped_length = 0, total_indel_length = 0, total_coverage_length = 0, final_MATCH = 0, chromosomal_length = 0, full_section_clipped = 0; ^~~~~~~~~~~~~~~~~~~~~ core-junction.c:3211:28: 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:5615:23: warning: variable ‘candBrkPlist’ set but not used [-Wunused-but-set-variable] chromosome_event_t * candBrkPlist [_PQR_LIST_SIZE]; ^~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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:2072:9: 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:3457:41: warning: variable ‘best_right’ set but not used [-Wunused-but-set-variable] int best_edge_score = -1, best_left, best_right; ^~~~~~~~~~ core-indel.c:3457:30: 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:3556:24: 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:3834:3: 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:3835:3: 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:3836:3: 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:3913:3: 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:3914:3: 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:3915:3: 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:4277:3: 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:4278:3: 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:4279:3: 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 -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c sambam-file.c: In function ‘PBam_get_next_zchunk’: sambam-file.c:356:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&ID1, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:357:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&ID2, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:358:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&CM, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:359:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&FLG, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:368:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&XLEN,1, 2, bam_fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:376:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&SI1, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:377:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&SI2, 1, 1, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:383:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&BSIZE_MID, 1,2 , bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sambam-file.c:395:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer, 1, CDATA_READING, bam_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c gene-algorithms.c: In function ‘show_cigar’: gene-algorithms.c:774:6: warning: variable ‘last_end’ set but not used [-Wunused-but-set-variable] int last_end=0, last_offset = 0, cursor = 0; ^~~~~~~~ gene-algorithms.c:773:9: warning: variable ‘is_error’ set but not used [-Wunused-but-set-variable] int i, is_error = 0; ^~~~~~~~ gene-algorithms.c: In function ‘match_chro_indel’: gene-algorithms.c:1186:28: warning: variable ‘last_section_indels’ set but not used [-Wunused-but-set-variable] int last_section_end = 0, last_section_indels=0; ^~~~~~~~~~~~~~~~~~~ gene-algorithms.c: In function ‘search_DP_branch’: gene-algorithms.c:1735:6: warning: variable ‘table_mask2_j_1’ set but not used [-Wunused-but-set-variable] int table_mask2_j_1 = 0, table_mask2_i_1 = 0; ^~~~~~~~~~~~~~~ gene-algorithms.c: In function ‘final_mapping_quality’: gene-algorithms.c:2376:7: warning: variable ‘is_match_begin’ set but not used [-Wunused-but-set-variable] int is_match_begin = 0; ^~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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 ‘f_subr_open’: input-files.c:53:10: warning: implicit declaration of function ‘fopen64’ [-Wimplicit-function-declaration] return fopen64(fname, mode); ^~~~~~~ input-files.c:53:10: warning: return makes pointer from integer without a cast [-Wint-conversion] return fopen64(fname, mode); ^~~~~~~~~~~~~~~~~~~~ input-files.c: In function ‘SAM_pairer_get_next_read_BIN’: input-files.c:2772:11: 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:4327:23: 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:4819:9: 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:3424:2: 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:3631:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&rlen, 1, 2, fp); ^~~~~~~~~~~~~~~~~~~~~~ input-files.c:3643:3: 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:3653:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&rlen, 1, 2, fp); ^~~~~~~~~~~~~~~~~~~~~~ input-files.c:3657:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&rlen, 1, 2, fp); ^~~~~~~~~~~~~~~~~~~~~~ input-files.c:3660:2: 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:4306:4: 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:5145:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_name_len, 2,1 , bbfp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-files.c:5151:6: 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:5154:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_len,2,1,bbfp); ^~~~~~~~~~~~~~~~~~~~~~~~~ input-files.c:5160:6: 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:5213:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_name_len, 2,1 , bbfp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-files.c:5219:6: 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:5223:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_len, 2,1 , bbfp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-files.c:5226:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(read_line_buf, 1, read_len, bbfp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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 -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c long-hashtable.c: In function ‘lnhash_create’: long-hashtable.c:43:45: warning: large integer implicitly truncated to unsigned type [-Woverflow] the_table -> key_repeated_numbers = malloc(sizeof(short) * 0x100000000llu); ^~~~~~ gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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 -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -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:1798:15: 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:1796:16: 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:1795:16: 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:1793:15: 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:4479:9: warning: variable ‘curchr_name’ set but not used [-Wunused-but-set-variable] char * curchr_name, * fasta_contigs_fname; ^~~~~~~~~~~ readSummary.c:4478:15: warning: variable ‘curpos’ set but not used [-Wunused-but-set-variable] long curchr, curpos; ^~~~~~ readSummary.c:4478:7: warning: variable ‘curchr’ set but not used [-Wunused-but-set-variable] long curchr, curpos; ^~~~~~ readSummary.c: In function ‘load_feature_info’: readSummary.c:921:3: 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:1549:3: 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’: readSummary.c:1834:113: 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:1862:113: 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:1894:112: 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:1903:112: warning: array subscript is above array bounds [-Warray-bounds] CIGAR_intervals_R2[R2_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R2[R2_i].insertion_start_pos[insmov_i]; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -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 -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -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:276:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&SNP_rec, sizeof(SNP_rec),1 , tmp_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SNPCalling.c:295:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_rec, sizeof(read_rec), 1, tmp_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SNPCalling.c:296:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_len, sizeof(short), 1, tmp_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SNPCalling.c:297:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(read, sizeof(char), read_len, tmp_fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -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:474:19: warning: variable ‘table_no’ set but not used [-Wunused-but-set-variable] int file_number, table_no, i ,j; ^~~~~~~~ index-builder.c: In function ‘main’: index-builder.c:1210:2: warning: ignoring return value of ‘mkstemp’, declared with attribute warn_unused_result [-Wunused-result] mkstemp(tmp_fa_file); ^~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -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:1630:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’ ZEXTERN int ZEXPORT gzclose OF((gzFile file)); ^~~~~~~ qualityScores.c: In function ‘rewind_qs_file’: qualityScores.c:275:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types] gzclose(qs_context -> gzfq_reader); ^~~~~~~~~~ In file included from qualityScores.c:24:0: /usr/include/zlib.h:1630:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’ ZEXTERN int ZEXPORT gzclose OF((gzFile file)); ^~~~~~~ qualityScores.c:282:29: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb"); ^ qualityScores.c: In function ‘start_qs_context’: qualityScores.c:313:29: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb"); ^ gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE propmapped.c: In function ‘prop_PE’: propmapped.c:368:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&read_len,1,1,fp); ^~~~~~~~~~~~~~~~~~~~~~~ propmapped.c:371:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(read_name,read_len,1,fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ propmapped.c:375:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&flags,1, sizeof(short), fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/<>/subread-1.5.2+dfsg=. -specs=/usr/share/dpkg/pie-compile.specs -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=\""1.5.2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o coverageCount coverage_calc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/pie-link.specs -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-1.5.2+dfsg/src' dh_auto_build -- CC=arm-linux-gnueabihf-gcc make[1]: Leaving directory '/<>/subread-1.5.2+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/subread-1.5.2+dfsg' debian/tests/subread-tests /<>/subread-1.5.2+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 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.2 //=========================== 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=137.9k bps/s, total=0m || || 16%, 0 mins elapsed, rate=175.0k bps/s, total=0m || || 24%, 0 mins elapsed, rate=209.7k bps/s, total=0m || || 33%, 0 mins elapsed, rate=236.4k bps/s, total=0m || || 41%, 0 mins elapsed, rate=261.8k bps/s, total=0m || || 49%, 0 mins elapsed, rate=284.5k bps/s, total=0m || || 58%, 0 mins elapsed, rate=303.1k bps/s, total=0m || || 66%, 0 mins elapsed, rate=324.8k bps/s, total=0m || || 74%, 0 mins elapsed, rate=342.9k bps/s, total=0m || || 83%, 0 mins elapsed, rate=360.1k bps/s, total=0m || || 91%, 0 mins elapsed, rate=379.8k bps/s, total=0m || || 99%, 0 mins elapsed, rate=394.9k bps/s, total=0m || || 52 uninformative subreads were found. || || These subreads were excluded from index building. || || Build the index... || || 8%, 0 mins elapsed, rate=204.2k bps/s, total=0m || || 16%, 0 mins elapsed, rate=242.6k bps/s, total=0m || || 24%, 0 mins elapsed, rate=245.1k bps/s, total=0m || || 33%, 0 mins elapsed, rate=255.4k bps/s, total=0m || || 41%, 0 mins elapsed, rate=272.8k bps/s, total=0m || || 49%, 0 mins elapsed, rate=294.8k bps/s, total=0m || || 58%, 0 mins elapsed, rate=318.5k bps/s, total=0m || || 66%, 0 mins elapsed, rate=342.0k bps/s, total=0m || || 74%, 0 mins elapsed, rate=364.7k bps/s, total=0m || || 83%, 0 mins elapsed, rate=385.4k bps/s, total=0m || || 91%, 0 mins elapsed, rate=405.3k bps/s, total=0m || || 99%, 0 mins elapsed, rate=423.3k 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: 0.1 minutes. || || Index ../small1 was successfully built! || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.2 //========================== 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 (30-Apr-2017 03:49:08, pid=3528) =================\\ || || || 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, 0.1 mins elapsed, rate=15.3k reads per second || || 39% completed, 0.1 mins elapsed, rate=15.3k reads per second || || 46% completed, 0.1 mins elapsed, rate=15.2k reads per second || || 53% completed, 0.1 mins elapsed, rate=15.2k reads per second || || 60% completed, 0.1 mins elapsed, rate=15.2k reads per second || || 74% completed, 0.1 mins elapsed, rate=2.4k reads per second || || 83% completed, 0.1 mins elapsed, rate=2.6k reads per second || || 91% completed, 0.1 mins elapsed, rate=2.8k reads per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 19998 reads || || Mapped : 19997 reads (100.0%) || || Indels : 7 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.2 //========================== 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 (30-Apr-2017 03:49:17, pid=3531) =================\\ || || || 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, 0.1 mins elapsed, rate=15.4k reads per second || || 39% completed, 0.1 mins elapsed, rate=15.3k reads per second || || 46% completed, 0.1 mins elapsed, rate=15.3k reads per second || || 53% completed, 0.1 mins elapsed, rate=15.3k reads per second || || 60% completed, 0.1 mins elapsed, rate=15.3k reads per second || || 74% completed, 0.1 mins elapsed, rate=2.8k reads per second || || 83% completed, 0.1 mins elapsed, rate=3.0k reads per second || || 91% completed, 0.1 mins elapsed, rate=3.2k reads per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 19998 reads || || Mapped : 18758 reads (93.8%) || || Indels : 5 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.2 //========================== 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 (30-Apr-2017 03:49:26, pid=3534) =================\\ || || || 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, 0.1 mins elapsed, rate=7.4k fragments per second || || 39% completed, 0.1 mins elapsed, rate=7.4k fragments per second || || 46% completed, 0.1 mins elapsed, rate=7.4k fragments per second || || 53% completed, 0.1 mins elapsed, rate=7.4k fragments per second || || 60% completed, 0.1 mins elapsed, rate=7.4k fragments per second || || 74% completed, 0.1 mins elapsed, rate=2.3k fragments per second || || 83% completed, 0.1 mins elapsed, rate=2.5k fragments per second || || 91% completed, 0.1 mins elapsed, rate=2.6k 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 : 0.2 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.2 //========================== 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 (30-Apr-2017 03:49:36, pid=3537) =================\\ || || || 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, 0.1 mins elapsed, rate=7.2k fragments per second || || 39% completed, 0.1 mins elapsed, rate=7.2k fragments per second || || 46% completed, 0.1 mins elapsed, rate=7.2k fragments per second || || 53% completed, 0.1 mins elapsed, rate=7.2k fragments per second || || 60% completed, 0.1 mins elapsed, rate=7.1k fragments per second || || 74% completed, 0.1 mins elapsed, rate=2.3k fragments per second || || 83% completed, 0.1 mins elapsed, rate=2.4k fragments per second || || 91% completed, 0.1 mins elapsed, rate=2.6k 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 : 0.2 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.2 //========================== 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 (30-Apr-2017 03:49:47, pid=3540) =================\\ || || || 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, 0.1 mins elapsed, rate=7.5k fragments per second || || 39% completed, 0.1 mins elapsed, rate=7.4k fragments per second || || 46% completed, 0.1 mins elapsed, rate=7.4k fragments per second || || 53% completed, 0.1 mins elapsed, rate=7.4k fragments per second || || 60% completed, 0.1 mins elapsed, rate=7.4k fragments per second || || 74% completed, 0.1 mins elapsed, rate=2.3k fragments per second || || 83% completed, 0.1 mins elapsed, rate=2.4k fragments per second || || 91% completed, 0.1 mins elapsed, rate=2.5k 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 : 0.2 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.2 //========================== 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 (30-Apr-2017 03:49:58, pid=3543) =================\\ || || || 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, 0.1 mins elapsed, rate=10.5k fragments per second || || 40% completed, 0.1 mins elapsed, rate=10.6k fragments per second || || 48% completed, 0.1 mins elapsed, rate=10.7k fragments per second || || 53% completed, 0.1 mins elapsed, rate=10.7k fragments per second || || 59% completed, 0.1 mins elapsed, rate=10.6k fragments per second || || 67% completed, 0.1 mins elapsed, rate=10.6k fragments per second || || 75% completed, 0.1 mins elapsed, rate=2.5k fragments per second || || 83% completed, 0.1 mins elapsed, rate=2.7k fragments per second || || 92% completed, 0.1 mins elapsed, rate=2.9k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 20001 fragments || || Mapped : 19528 fragments (97.6%) || || Correctly paired : 14071 fragments || || Indels : 181 || || || || WARNING : Phred offset (33) incorrect? || || || || Running time : 0.1 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// a8672c5cccb9414ef7c2a3b91319aa48 ../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 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.2 //=========================== indexBuilder setting ===========================\\ || || || Index name : ../small1 || || Index space : base-space || || Memory : 3000 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=778.7k bps/s, total=0m || || 24%, 0 mins elapsed, rate=853.1k bps/s, total=0m || || 33%, 0 mins elapsed, rate=903.2k bps/s, total=0m || || 41%, 0 mins elapsed, rate=964.3k bps/s, total=0m || || 49%, 0 mins elapsed, rate=1018.1k bps/s, total=0m || || 58%, 0 mins elapsed, rate=1056.6k bps/s, total=0m || || 66%, 0 mins elapsed, rate=1101.7k bps/s, total=0m || || 74%, 0 mins elapsed, rate=1139.6k bps/s, total=0m || || 83%, 0 mins elapsed, rate=1175.1k bps/s, total=0m || || 91%, 0 mins elapsed, rate=1213.9k bps/s, total=0m || || 99%, 0 mins elapsed, rate=1237.4k bps/s, total=0m || || 2 uninformative subreads were found. || || These subreads were excluded from index building. || || Build the index... || || 8%, 0 mins elapsed, rate=505.0k bps/s, total=0m || || 16%, 0 mins elapsed, rate=527.3k bps/s, total=0m || || 24%, 0 mins elapsed, rate=559.2k bps/s, total=0m || || 33%, 0 mins elapsed, rate=589.9k bps/s, total=0m || || 41%, 0 mins elapsed, rate=617.2k bps/s, total=0m || || 49%, 0 mins elapsed, rate=647.5k bps/s, total=0m || || 58%, 0 mins elapsed, rate=679.0k bps/s, total=0m || || 66%, 0 mins elapsed, rate=711.4k bps/s, total=0m || || 74%, 0 mins elapsed, rate=743.9k bps/s, total=0m || || 83%, 0 mins elapsed, rate=775.0k bps/s, total=0m || || 91%, 0 mins elapsed, rate=808.9k bps/s, total=0m || || 99%, 0 mins elapsed, rate=838.1k 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/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.2 //============================= 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 (30-Apr-2017 03:50:10, pid=3550) =================\\ || || || 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, 0.1 mins elapsed, rate=4.3k fragments per second || || 48% completed, 0.1 mins elapsed, rate=4.3k fragments per second || || 54% completed, 0.1 mins elapsed, rate=4.3k fragments per second || || 61% completed, 0.1 mins elapsed, rate=4.3k fragments per second || || 77% completed, 0.2 mins elapsed, rate=1.3k fragments per second || || 87% completed, 0.2 mins elapsed, rate=1.4k fragments per second || || 97% completed, 0.2 mins elapsed, rate=1.5k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 16052 fragments || || Mapped : 15914 fragments (99.1%) || || Correctly paired : 14375 fragments || || Junctions : 425 || || Indels : 187 || || || || Running time : 0.2 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.2 //============================= 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 (30-Apr-2017 03:50:25, pid=3551) =================\\ || || || 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, 0.1 mins elapsed, rate=2.8k fragments per second || || 48% completed, 0.1 mins elapsed, rate=2.8k fragments per second || || 54% completed, 0.1 mins elapsed, rate=2.8k fragments per second || || 61% completed, 0.2 mins elapsed, rate=2.8k fragments per second || || 77% completed, 0.2 mins elapsed, rate=1.2k fragments per second || || 87% completed, 0.2 mins elapsed, rate=1.3k fragments per second || || 97% completed, 0.2 mins elapsed, rate=1.4k fragments per second || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed : 16052 fragments || || Mapped : 15906 fragments (99.1%) || || Correctly paired : 14291 fragments || || Junctions : 458 || || Fusions : 103 || || Indels : 188 || || || || Running time : 0.3 minutes || || || \\===================== http://subread.sourceforge.net/ ======================// ================================================================================ FeatureCounts Basic Test http://subread.sourceforge.net/ ================================================================================ ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.2 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || P data/test-minimum.sam || || || || Output file : result/test-minimum.FC || || Summary : result/test-minimum.FC.summary || || Annotation : data/test-minimum.GTF (GTF) || || Dir for temp files : result || || || || Threads : 1 || || Level : meta-feature level || || Paired-end : no || || Strand specific : no || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file data/test-minimum.GTF ... || || Features : 23 || || Meta-features : 7 || || Chromosomes/contigs : 3 || || || || Process SAM file data/test-minimum.sam... || || Paired-end reads are included. || || Assign reads to features... || || Total reads : 998 || || Successfully assigned reads : 389 (39.0%) || || Running time : 0.00 minutes || || || || Read assignment finished. || || || || Summary of counting results can be found in file "result/test-minimum.FC" || || || \\===================== http://subread.sourceforge.net/ ======================// ================================================================================ Basic Test finished. The results are in result/test-minimum.FC ================================================================================ ================================================================================ FeatureCounts Chromosome Name Aliases Tests http://subread.sourceforge.net/ ================================================================================ Testing chromosome aliases ... [PASS] ================================================================================ FeatureCounts Chromosome Name Inference Tests http://subread.sourceforge.net/ ================================================================================ Testing automatic inference of chromosome names ... [PASS] ================================================================================ FeatureCounts Corner Case Tests http://subread.sourceforge.net/ ================================================================================ Testing indel reads ... [PASS] Testing junction reads ... [PASS] Testing paired-end reads (fragment counting) ... [PASS] Testing paired-end reads (fragment counting, both ends mapped) ... [PASS] Testing multi-overlapping reads ... [PASS] Testing feature-level summarization ... [PASS] Testing gene-level summarization ... [PASS] Testing multi-mapping reads ... [PASS] Testing multi-mapping reads (primary only) ... [PASS] Testing both ends mapped ... [PASS] Testing disallowing chimeric fragments ... [PASS] Testing Allowing multi-mapped reads ... [PASS] Testing not sorting input file ... [PASS] Testing minimum overlapping length ... [PASS] Testing minimum overlapping fraction ... [PASS] Testing Largest Overlapping ... [PASS] Testing paired-end distance ... [PASS] Testing Read to position (5' end) ... [PASS] Testing Read to position (3' end) ... [PASS] Testing Read extension to the 3' end ... [PASS] Testing Read extension to the 5' end ... [PASS] Testing Low maxOPs value ... [PASS] Testing minimum mapping quality ... [PASS] Testing Ignoring duplicated reads ... [PASS] Testing Fraction counting ... [PASS] Testing Advanced fractions ... [PASS] Testing Junction counting ... [PASS,PASS] Skipping Junction counting (with genome). Testing GTF format annotations ... [PASS] Testing SAF format annotations ... [PASS] Testing SAM format input ... [PASS] Testing BAM format input ... [PASS] Testing unstranded read summarization ... [PASS] Testing stranded read summarization ... [PASS] Testing reversely stranded read summarization ... [PASS] Testing Ignoring duplicate fragments ... [PASS] Testing Junction reads only ... [PASS] Testing Exonic reads only ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] ../../bin/exactSNP -g ../chr901.fa -o result/test-out.VCF -i data/test-in.BAM -b ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.2 //============================= 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 (30-Apr-2017 03:50:43) ======================\\ || || || Split BAM file into result/temp-snps-004316-FA163E790EDE-* ... || || 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-1.5.2+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --parallel dh_testroot -a -O--parallel dh_prep -a -O--parallel debian/rules override_dh_auto_install make[1]: Entering directory '/<>/subread-1.5.2+dfsg' find /<>/subread-1.5.2+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \; mkdir -p /<>/subread-1.5.2+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-1.5.2+dfsg/bin/subread-align | debian/filter.pl > /<>/subread-1.5.2+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-1.5.2+dfsg/bin/subread-buildindex | debian/filter.pl > /<>/subread-1.5.2+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-1.5.2+dfsg/bin/subjunc | debian/filter.pl > /<>/subread-1.5.2+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-1.5.2+dfsg/bin/featureCounts | debian/filter.pl > /<>/subread-1.5.2+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-1.5.2+dfsg/bin/exactSNP | debian/filter.pl > /<>/subread-1.5.2+dfsg/debian/subread/usr/share/man/man1/exactSNP.1; help2man --no-info --help-option="''" --no-discard-stderr --name='detect short and long indels' \ /<>/subread-1.5.2+dfsg/bin/subindel | debian/filter.pl > /<>/subread-1.5.2+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-1.5.2+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /<>/subread-1.5.2+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-1.5.2+dfsg/bin/utilities/coverageCount | debian/filter.pl > /<>/subread-1.5.2+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-1.5.2+dfsg/bin/utilities/propmapped | debian/filter.pl > /<>/subread-1.5.2+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-1.5.2+dfsg/bin/utilities/$i | debian/filter.pl > /<>/subread-1.5.2+dfsg/debian/subread/usr/share/man/man1/$i.1; \ done dh_auto_install make[1]: Leaving directory '/<>/subread-1.5.2+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_makeshlibs -a -O--parallel dh_shlibdeps -a -O--parallel dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-armhf.so.3) twice in a symfile dh_installdeb -a -O--parallel dh_gencontrol -a -O--parallel dh_md5sums -a -O--parallel dh_builddeb -a -O--parallel INFO: pkgstriptranslations version 131 pkgstriptranslations: processing subread-dbgsym (in debian/.debhelper/subread/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/subread/dbgsym-root/DEBIAN/control, package subread-dbgsym, directory debian/.debhelper/subread/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package subread-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'subread-dbgsym' in 'debian/.debhelper/scratch-space/build-subread/subread-dbgsym_1.5.2+dfsg-1_armhf.deb'. Renaming subread-dbgsym_1.5.2+dfsg-1_armhf.deb to subread-dbgsym_1.5.2+dfsg-1_armhf.ddeb 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_1.5.2+dfsg-1_armhf.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../subread_1.5.2+dfsg-1_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build subread-1.5.2+dfsg dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20170430-0351 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ subread_1.5.2+dfsg-1_armhf.changes: ----------------------------------- Format: 1.8 Date: Tue, 21 Mar 2017 16:18:52 +0100 Source: subread Binary: subread subread-data Architecture: armhf Version: 1.5.2+dfsg-1 Distribution: artful-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Alexandre Mestiashvili Description: subread - toolkit for processing next-gen sequencing data subread-data - data files for subread package Changes: subread (1.5.2+dfsg-1) unstable; urgency=medium . * New upstream version 1.5.2+dfsg * Refresh and update patches * Add d/patches/typo.patch fixing a typo in featureCounts Checksums-Sha1: 0096d8a1996d23839ea7de0f0d390263f29f13be 5351014 subread-dbgsym_1.5.2+dfsg-1_armhf.ddeb 347e4beb3895c111e8c9eb8df0fc4308d02831b4 5350 subread_1.5.2+dfsg-1_armhf.buildinfo a3d8f9e07b50fec177b648e73299730f3bbf610d 377896 subread_1.5.2+dfsg-1_armhf.deb Checksums-Sha256: cba647e8239eee074ce67e176d8c31e47247b2f1b9e7128fa977da8fbd8cd5a7 5351014 subread-dbgsym_1.5.2+dfsg-1_armhf.ddeb 4a682ca771b06bd73b2d779652993a748836479fe18f3dbd1afee28c544798cd 5350 subread_1.5.2+dfsg-1_armhf.buildinfo 7234245a78f72636b3f7428033fc44e24d155b2dded8b06a90200cefb8568c53 377896 subread_1.5.2+dfsg-1_armhf.deb Files: 2c18da886530105cdc3f47b9870707b1 5351014 debug extra subread-dbgsym_1.5.2+dfsg-1_armhf.ddeb e4e0aea10605777c5ecfa1160555f01e 5350 science optional subread_1.5.2+dfsg-1_armhf.buildinfo 333e55765aa302399d3763ce976bc732 377896 science optional subread_1.5.2+dfsg-1_armhf.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ subread_1.5.2+dfsg-1_armhf.deb ------------------------------ new debian package, version 2.0. size 377896 bytes: control archive=1436 bytes. 701 bytes, 15 lines control 1819 bytes, 28 lines md5sums Package: subread Version: 1.5.2+dfsg-1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3142 Depends: libc6 (>= 2.7), zlib1g (>= 1:1.2.3.3) Section: science Priority: optional Homepage: http://sourceforge.net/projects/subread/ Description: toolkit for processing next-gen sequencing data Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments. drwxr-xr-x root/root 0 2017-03-21 15:18 ./ drwxr-xr-x root/root 0 2017-03-21 15:18 ./usr/ drwxr-xr-x root/root 0 2017-03-21 15:18 ./usr/bin/ -rwxr-xr-x root/root 272648 2017-03-21 15:18 ./usr/bin/exactSNP -rwxr-xr-x root/root 313880 2017-03-21 15:18 ./usr/bin/featureCounts -rwxr-xr-x root/root 256280 2017-03-21 15:18 ./usr/bin/subindel -rwxr-xr-x root/root 265320 2017-03-21 15:18 ./usr/bin/subjunc -rwxr-xr-x root/root 265224 2017-03-21 15:18 ./usr/bin/subread-align -rwxr-xr-x root/root 268528 2017-03-21 15:18 ./usr/bin/subread-buildindex drwxr-xr-x root/root 0 2017-03-21 15:18 ./usr/lib/ drwxr-xr-x root/root 0 2017-03-21 15:18 ./usr/lib/subread/ -rwxr-xr-x root/root 256280 2017-03-21 15:18 ./usr/lib/subread/coverageCount -rwxr-xr-x root/root 256280 2017-03-21 15:18 ./usr/lib/subread/propmapped -rwxr-xr-x root/root 256392 2017-03-21 15:18 ./usr/lib/subread/qualityScores -rwxr-xr-x root/root 252136 2017-03-21 15:18 ./usr/lib/subread/removeDup -rwxr-xr-x root/root 252136 2017-03-21 15:18 ./usr/lib/subread/repair -rwxr-xr-x root/root 252136 2017-03-21 15:18 ./usr/lib/subread/subread-fullscan drwxr-xr-x root/root 0 2017-03-21 15:18 ./usr/share/ drwxr-xr-x root/root 0 2017-03-21 15:18 ./usr/share/doc/ drwxr-xr-x root/root 0 2017-03-21 15:18 ./usr/share/doc/subread/ -rw-r--r-- root/root 500 2017-03-21 15:18 ./usr/share/doc/subread/README.Debian -rw-r--r-- root/root 3850 2017-03-16 22:08 ./usr/share/doc/subread/README.txt -rw-r--r-- root/root 947 2017-03-21 15:18 ./usr/share/doc/subread/changelog.Debian.gz -rw-r--r-- root/root 1138 2017-03-21 15:18 ./usr/share/doc/subread/copyright drwxr-xr-x root/root 0 2017-03-21 15:18 ./usr/share/man/ drwxr-xr-x root/root 0 2017-03-21 15:18 ./usr/share/man/man1/ -rw-r--r-- root/root 614 2017-03-21 15:18 ./usr/share/man/man1/coverageCount.1.gz -rw-r--r-- root/root 1170 2017-03-21 15:18 ./usr/share/man/man1/exactSNP.1.gz -rw-r--r-- root/root 2818 2017-03-21 15:18 ./usr/share/man/man1/featureCounts.1.gz -rw-r--r-- root/root 457 2017-03-21 15:18 ./usr/share/man/man1/propmapped.1.gz -rw-r--r-- root/root 563 2017-03-21 15:18 ./usr/share/man/man1/qualityScores.1.gz -rw-r--r-- root/root 493 2017-03-21 15:18 ./usr/share/man/man1/removeDup.1.gz -rw-r--r-- root/root 475 2017-03-21 15:18 ./usr/share/man/man1/repair.1.gz -rw-r--r-- root/root 344 2017-03-21 15:18 ./usr/share/man/man1/subindel.1.gz -rw-r--r-- root/root 2110 2017-03-21 15:18 ./usr/share/man/man1/subjunc.1.gz -rw-r--r-- root/root 2212 2017-03-21 15:18 ./usr/share/man/man1/subread-align.1.gz -rw-r--r-- root/root 761 2017-03-21 15:18 ./usr/share/man/man1/subread-buildindex.1.gz -rw-r--r-- root/root 372 2017-03-21 15:18 ./usr/share/man/man1/subread-fullscan.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 107956 Build-Time: 204 Distribution: artful-proposed Host Architecture: armhf Install-Time: 23 Job: subread_1.5.2+dfsg-1.dsc Machine Architecture: arm64 Package: subread Package-Time: 233 Source-Version: 1.5.2+dfsg-1 Space: 107956 Status: successful Version: 1.5.2+dfsg-1 -------------------------------------------------------------------------------- Finished at 20170430-0351 Build needed 00:03:53, 107956k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-12500012'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-12500012/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-12500012'] Unmounting chroot for build PACKAGEBUILD-12500012... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-12500012'] Removing build PACKAGEBUILD-12500012