subread →
1.5.0-p3+dfsg-1 →
armhf → 2016-06-10 14:00:29
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on bm-wb-03
+==============================================================================+
| subread 1.5.0-p3+dfsg-1 (armhf) 10 Jun 2016 13:29 |
+==============================================================================+
Package: subread
Version: 1.5.0-p3+dfsg-1
Source Version: 1.5.0-p3+dfsg-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/subread-LmT_V6/subread-1.5.0-p3+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/subread-LmT_V6' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-13d18e5c-76aa-4624-8acb-08468323df3b' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9051 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.0 MB]
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+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
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Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'subread' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/subread.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/subread.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 14.4 MB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main subread 1.5.0-p3+dfsg-1 (dsc) [2263 B]
Get:2 http://172.17.0.1/private stretch-staging/main subread 1.5.0-p3+dfsg-1 (tar) [14.4 MB]
Get:3 http://172.17.0.1/private stretch-staging/main subread 1.5.0-p3+dfsg-1 (diff) [6968 B]
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Download complete and in download only mode
Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-oLmdjv/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-oLmdjv/apt_archive ./ InRelease
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Get:3 file:/<<BUILDDIR>>/resolver-oLmdjv/apt_archive ./ Release.gpg [299 B]
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W: file:///<<BUILDDIR>>/resolver-oLmdjv/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
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Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 48 not upgraded.
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Merged Build-Depends: bc, debhelper (>= 9), help2man, python, zlib1g-dev
Filtered Build-Depends: bc, debhelper (>= 9), help2man, python, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-subread-dummy' in '/<<BUILDDIR>>/resolver-OAZZgl/apt_archive/sbuild-build-depends-subread-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-OAZZgl/apt_archive ./ InRelease
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Get:3 file:/<<BUILDDIR>>/resolver-OAZZgl/apt_archive ./ Release.gpg [299 B]
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Get:4 file:/<<BUILDDIR>>/resolver-OAZZgl/apt_archive ./ Sources [232 B]
Get:5 file:/<<BUILDDIR>>/resolver-OAZZgl/apt_archive ./ Packages [551 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-OAZZgl/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
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
libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libicu55 libmagic1
libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib
libsigsegv2 libsqlite3-0 libssl1.0.2 libtimedate-perl libtool libunistring0
libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7
python2.7-minimal zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser
libmail-box-perl python-doc python-tk python2.7-doc binfmt-support
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bc bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1
libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libicu55 libmagic1
libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib
libsigsegv2 libsqlite3-0 libssl1.0.2 libtimedate-perl libtool libunistring0
libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7
python2.7-minimal sbuild-build-depends-subread-dummy zlib1g-dev
0 upgraded, 45 newly installed, 0 to remove and 48 not upgraded.
Need to get 16.2 MB/24.4 MB of archives.
After this operation, 84.2 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-OAZZgl/apt_archive ./ sbuild-build-depends-subread-dummy 0.invalid.0 [790 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.11-11 [384 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.11-11 [1163 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-2 [40.3 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.1.1-3 [60.3 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-0 armhf 3.13.0-1 [479 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libssl1.0.2 armhf 1.0.2h-1 [889 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.11-11 [1821 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.11-11 [272 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-2 [19.8 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-2 [153 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf bc armhf 1.06.95-9 [96.3 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.7-2 [424 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.1-1 [2548 kB]
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Get:30 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.57-1 [95.1 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.018-1 [12.1 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.018-1 [7196 B]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160403 [800 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf help2man armhf 1.47.4 [162 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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Setting up libffi6:armhf (3.2.1-4) ...
Setting up libsqlite3-0:armhf (3.13.0-1) ...
Setting up libssl1.0.2:armhf (1.0.2h-1) ...
Setting up libpython2.7-stdlib:armhf (2.7.11-11) ...
Setting up python2.7 (2.7.11-11) ...
Setting up libpython-stdlib:armhf (2.7.11-2) ...
Setting up python (2.7.11-2) ...
Setting up bc (1.06.95-9) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up m4 (1.4.17-5) ...
Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20160430.1) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up autopoint (0.19.7-2) ...
Setting up libglib2.0-0:armhf (2.48.1-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.19) ...
Setting up libarchive-zip-perl (1.57-1) ...
Setting up libfile-stripnondeterminism-perl (0.018-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libtool (2.4.6-0.1) ...
Setting up help2man (1.47.4) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up dh-autoreconf (12) ...
Setting up debhelper (9.20160403) ...
Setting up sbuild-build-depends-subread-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.018-1) ...
Processing triggers for libc-bin (2.22-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.7 g++-5_5.3.1-19 gcc-5_5.3.1-19 libc6-dev_2.22-7 libstdc++-5-dev_5.3.1-19 libstdc++6_6.1.1-1+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.114 apt_1.2.12 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-14 bc_1.06.95-9 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.28-5 build-essential_11.7 bzip2_1.0.6-8 console-setup_1.142 console-setup-linux_1.142 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-19 dash_0.5.8-2.2 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160403 debianutils_4.7 dh-autoreconf_12 dh-strip-nondeterminism_0.018-1 diffutils_1:3.3-3 dmsetup_2:1.02.124-1 dpkg_1.18.7 dpkg-dev_1.18.7 e2fslibs_1.43-2 e2fsprogs_1.43-2 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-19 gcc_4:5.3.1-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5_5.3.1-19 gcc-5-base_5.3.1-19 gcc-6-base_6.1.1-1+rpi1 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-6 gpgv_1.4.20-6 grep_2.25-1 groff-base_1.22.3-7 gzip_1.6-5 help2man_1.47.4 hostname_3.17 ifupdown_0.8.11 init_1.33 init-system-helpers_1.33 initscripts_2.88dsf-59.4 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 iproute2_4.3.0-1 kbd_2.0.3-2 keyboard-configuration_1.142 klibc-utils_2.0.4-8+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10-4 libapt-pkg5.0_1.2.12 libarchive-zip-perl_1.57-1 libasan2_5.3.1-19 libatm1_1:2.5.1-1.5 libatomic1_6.1.1-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.5.2-1+rpi1 libaudit1_1:2.5.2-1+rpi1 libblkid1_2.28-5 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.22-7 libc-dev-bin_2.22-7 libc6_2.22-7 libc6-dev_2.22-7 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_6.1.1-1+rpi1 libcomerr2_1.43~WIP.2016.03.15-2 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.210 libdevmapper1.02.1_2:1.02.124-1 libdpkg-perl_1.18.7 libdrm2_2.4.68-1 libexpat1_2.1.1-3 libfakeroot_1.20.2-1 libfdisk1_2.28-5 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.018-1 libfuse2_2.9.6-1 libgc1c2_1:7.4.2-7.4 libgcc-5-dev_5.3.1-19 libgcc1_1:6.1.1-1+rpi1 libgcrypt20_1.7.0-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.48.1-1 libgmp10_2:6.1.0+dfsg-2 libgomp1_6.1.1-1+rpi1 libgpg-error0_1.22-2 libicu55_55.1-7 libisl15_0.16.1-1 libklibc_2.0.4-8+rpi1 libkmod2_22-1.1 liblocale-gettext-perl_1.07-1+b1 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.28-5 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160319-1 libncursesw5_6.0+20160319-1 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpcre3_2:8.38-3.1 libperl5.22_5.22.2-1 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libprocps5_2:3.3.11-3 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.11-11 libpython2.7-stdlib_2.7.11-11 libreadline6_6.3-8+b3 libseccomp2_2.3.0-1 libselinux1_2.5-2 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28-5 libsqlite3-0_3.13.0-1 libss2_1.43~WIP.2016.03.15-2 libssl1.0.2_1.0.2h-1 libstdc++-5-dev_5.3.1-19 libstdc++6_6.1.1-1+rpi1 libsystemd0_229-5 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160319-1 libtool_2.4.6-0.1 libubsan0_6.1.1-1+rpi1 libudev1_229-5 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28-5 libxml2_2.9.3+dfsg1-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.06-1 mawk_1.3.3-17 mime-support_3.60 mount_2.28-5 multiarch-support_2.22-7 ncurses-base_6.0+20160319-1 ncurses-bin_6.0+20160319-1 netbase_5.3 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-1 perl-base_5.22.2-1 perl-modules-5.22_5.22.2-1 po-debconf_1.0.19 procps_2:3.3.11-3 psmisc_22.21-2.1 python_2.7.11-2 python-minimal_2.7.11-2 python2.7_2.7.11-11 python2.7-minimal_2.7.11-11 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-subread-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_229-5 systemd-sysv_229-5 sysv-rc_2.88dsf-59.4 sysvinit-utils_2.88dsf-59.4 tar_1.28-2.2+rpi1 tzdata_2016d-2 udev_229-5 util-linux_2.28-5 xkb-data_2.17-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sat Jun 4 07:24:52 2016 UTC using RSA key ID 1B5228B0
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./subread_1.5.0-p3+dfsg-1.dsc
dpkg-source: info: extracting subread in subread-1.5.0-p3+dfsg
dpkg-source: info: unpacking subread_1.5.0-p3+dfsg.orig.tar.xz
dpkg-source: info: unpacking subread_1.5.0-p3+dfsg-1.debian.tar.xz
dpkg-source: info: applying fix_ftbfs_kfreebsd.patch
dpkg-source: info: applying arch_specific_flags.patch
dpkg-source: info: applying syntax_err.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-13d18e5c-76aa-4624-8acb-08468323df3b
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package subread
dpkg-buildpackage: info: source version 1.5.0-p3+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build subread-1.5.0-p3+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
dh_auto_clean -O--parallel
debian/rules override_dh_clean
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.5.0-p3+dfsg'
cd src; make -f Makefile.Linux clean
make[2]: Entering directory '/<<BUILDDIR>>/subread-1.5.0-p3+dfsg/src'
rm -f core featureCounts exactSNP removeDup subread-buildindex core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o
make[2]: Leaving directory '/<<BUILDDIR>>/subread-1.5.0-p3+dfsg/src'
dh_clean
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.5.0-p3+dfsg'
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
dh_update_autotools_config -a -O--parallel
dh_auto_configure -a -O--parallel
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.5.0-p3+dfsg'
cd src; make -f Makefile.Linux
make[2]: Entering directory '/<<BUILDDIR>>/subread-1.5.0-p3+dfsg/src'
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c
core.c: In function 'print_in_box':
core.c:139:7: warning: variable 'is_R_linebreak' set but not used [-Wunused-but-set-variable]
char is_R_linebreak=0, * content, *out_line_buff;
^
core.c: In function 'convert_GZ_to_FQ':
core.c:834:19: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
gzFile * rawfp = gzopen(fname, "r");
^
core.c:845:25: warning: passing argument 1 of 'gzgets' from incompatible pointer type [-Wincompatible-pointer-types]
char * bufr =gzgets(rawfp, linebuff, 3000);
^
In file included from subread.h:26:0,
from core.c:43:
/usr/include/zlib.h:1372:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
core.c:856:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(rawfp);
^
In file included from subread.h:26:0,
from core.c:43:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
core.c: In function 'calc_tlen':
core.c:1529:16: 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:2155:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret;
^
core.c: In function 'write_realignments_for_fragment':
core.c:2367:21: warning: variable 'raw_r2' set but not used [-Wunused-but-set-variable]
mapping_result_t * raw_r2 = NULL;
^
core.c:2364:21: 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:2433:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret;
^
core.c: In function 'do_voting':
core.c:2977:9: 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:2896:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret, xk1;
^
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c
core-junction.c: In function 'copy_vote_to_alignment_res':
core-junction.c:945:12: warning: variable 'current_piece_minor_score' set but not used [-Wunused-but-set-variable]
int i,j, current_piece_minor_score = 0;
^
core-junction.c: In function 'find_donor_receptor':
core-junction.c:1996:8: warning: variable 'sp2s' set but not used [-Wunused-but-set-variable]
char sp2s[200];
^
core-junction.c: In function 'finalise_explain_CIGAR':
core-junction.c:3119:10: warning: variable 'is_front_search' set but not used [-Wunused-but-set-variable]
int is_front_search = 0;
^
core-junction.c:3255:94: warning: variable 'total_coverage_length' set but not used [-Wunused-but-set-variable]
int final_qual = 0, applied_mismatch = 0, non_clipped_length = 0, total_indel_length = 0, total_coverage_length = 0, final_MATCH = 0, chromosomal_length = 0;
^
core-junction.c:3235:28: warning: variable 'isCigarOK' set but not used [-Wunused-but-set-variable]
int mismatch_bases = 0, isCigarOK = 0;
^
core-junction.c:3049:23: warning: variable 'tmp_cigar_exonic' set but not used [-Wunused-but-set-variable]
char tmp_cigar[120], tmp_cigar_exonic[120];
^
core-junction.c: In function 'find_translocation_brk_PQR':
core-junction.c:5635:23: warning: variable 'candBrkPlist' set but not used [-Wunused-but-set-variable]
chromosome_event_t * candBrkPlist [_PQR_LIST_SIZE];
^
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c
core-indel.c: In function 'find_new_indels':
core-indel.c:1581:9: 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:2928:41: warning: variable 'best_right' set but not used [-Wunused-but-set-variable]
int best_edge_score = -1, best_left, best_right;
^
core-indel.c:2928:30: 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:3027:24: 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:3305:3: 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:3306:3: 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:3307:3: 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:3384:3: 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:3385:3: 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:3386:3: 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:3748:3: 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:3749:3: 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:3750:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c
sambam-file.c: In function 'PBam_get_next_zchunk':
sambam-file.c:352:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&ID1, 1, 1, bam_fp);
^
sambam-file.c:353:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&ID2, 1, 1, bam_fp);
^
sambam-file.c:354:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&CM, 1, 1, bam_fp);
^
sambam-file.c:355:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&FLG, 1, 1, bam_fp);
^
sambam-file.c:364:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&XLEN,1, 2, bam_fp );
^
sambam-file.c:372:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SI1, 1, 1, bam_fp);
^
sambam-file.c:373:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SI2, 1, 1, bam_fp);
^
sambam-file.c:374:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SLEN, 1, 2, bam_fp);
^
sambam-file.c:378:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&BSIZE_MID, 1,2 , bam_fp);
^
sambam-file.c:390:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(buffer, 1, CDATA_READING, bam_fp);
^
sambam-file.c:394:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&real_len, 4, 1, bam_fp);
^
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c
gene-algorithms.c: In function 'show_cigar':
gene-algorithms.c:771:6: warning: variable 'last_end' set but not used [-Wunused-but-set-variable]
int last_end=0, last_offset = 0, cursor = 0;
^
gene-algorithms.c:770:9: warning: variable 'is_error' set but not used [-Wunused-but-set-variable]
int i, is_error = 0;
^
gene-algorithms.c: In function 'match_chro_indel':
gene-algorithms.c:1183:28: warning: variable 'last_section_indels' set but not used [-Wunused-but-set-variable]
int last_section_end = 0, last_section_indels=0;
^
gene-algorithms.c: In function 'search_DP_branch':
gene-algorithms.c:1732:6: warning: variable 'table_mask2_j_1' set but not used [-Wunused-but-set-variable]
int table_mask2_j_1 = 0, table_mask2_i_1 = 0;
^
gene-algorithms.c: In function 'final_mapping_quality':
gene-algorithms.c:2373:7: warning: variable 'is_match_begin' set but not used [-Wunused-but-set-variable]
int is_match_begin = 0;
^
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c
input-files.c: In function '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]
input-files.c: In function 'SAM_pairer_get_next_read_BIN':
input-files.c:2729:11: 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:4271:23: 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:4729:9: 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:509:5: 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:3380:2: 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:3587:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^
input-files.c:3599:3: 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:3609:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^
input-files.c:3613:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^
input-files.c:3616:2: 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:4247:4: 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:5041:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^
input-files.c:5047:6: 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:5050:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len,2,1,bbfp);
^
input-files.c:5056:6: 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:5109:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^
input-files.c:5115:6: 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:5119:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, 2,1 , bbfp);
^
input-files.c:5122:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_line_buf, 1, read_len, bbfp);
^
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c
sorted-hashtable.c: In function 'gehash_load_option':
sorted-hashtable.c:1264:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^
sorted-hashtable.c:1269:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^
sorted-hashtable.c:1272:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^
sorted-hashtable.c:1276:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(result ,option_length,1,fp);
^
sorted-hashtable.c: In function 'gehash_load':
sorted-hashtable.c:1303:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^
sorted-hashtable.c:1326:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^
sorted-hashtable.c:1329:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^
sorted-hashtable.c:1332:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&(the_table -> index_gap),2,1,fp);
^
sorted-hashtable.c:1334:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&(the_table -> padding),2,1,fp);
^
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -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 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c
core-bigtable.c: In function 'bigtable_readonly_result':
core-bigtable.c:70:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(write_ptr, loadjunc?sizeof(subjunc_result_t):sizeof(mapping_result_t), 1, global_context -> bigtable_cache_file_fp);
^
core-bigtable.c: In function 'bigtable_retrieve_cache':
core-bigtable.c:227:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread( current_cache -> big_margin_data , sizeof(short) * 3 * global_context -> config.big_margin_record_size , 1, global_context -> bigtable_cache_file_fp );
^
core-bigtable.c:228:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread( current_cache -> alignment_res , sizeof(mapping_result_t) * global_context -> config.multi_best_reads , 1, global_context -> bigtable_cache_file_fp );
^
core-bigtable.c:231:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread( current_cache -> subjunc_res , sizeof(subjunc_result_t) * global_context -> config.multi_best_reads , 1, global_context -> bigtable_cache_file_fp);
^
core-bigtable.c:237:5: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(global_context -> bigtable_cache_file_fp), new_file_size);
^
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
readSummary.c: In function 'calc_junctions_from_cigar':
readSummary.c:338:15: warning: variable 'right_boundary' set but not used [-Wunused-but-set-variable]
unsigned int right_boundary = 0;
^
readSummary.c: In function 'readSummary':
readSummary.c:3993:9: warning: variable 'curchr_name' set but not used [-Wunused-but-set-variable]
char * curchr_name, * fasta_contigs_fname;
^
readSummary.c:3992:15: warning: variable 'curpos' set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^
readSummary.c:3992:7: warning: variable 'curchr' set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^
readSummary.c: In function 'load_feature_info':
readSummary.c:837:10: warning: 'token_temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
char * token_temp, *chro_name;
^
readSummary.c:901:10: warning: 'token_temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
char * token_temp;
^
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
index-builder.c: In function 'scan_gene_index':
index-builder.c:458:19: warning: variable 'table_no' set but not used [-Wunused-but-set-variable]
int file_number, table_no, i ,j;
^
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
qualityScores.c: In function 'finalise_qs_context':
qualityScores.c:82:12: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(qs_context -> gzfq_reader);
^
In file included from qualityScores.c:24:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
qualityScores.c: In function 'rewind_qs_file':
qualityScores.c:275:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(qs_context -> gzfq_reader);
^
In file included from qualityScores.c:24:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
qualityScores.c:282:29: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb");
^
qualityScores.c: In function 'start_qs_context':
qualityScores.c:313:29: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb");
^
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.0-p3"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o coverageCount coverage_calc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
mkdir -p ../bin/utilities
mv subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/
mv repair coverageCount propmapped qualityScores removeDup subread-fullscan ../bin/utilities
###########################################################
# #
# Installation finished. #
# #
# Generated executables were copied to directory ../bin/ #
# #
###########################################################
make[2]: Leaving directory '/<<BUILDDIR>>/subread-1.5.0-p3+dfsg/src'
dh_auto_build
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.5.0-p3+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.5.0-p3+dfsg'
debian/tests/subread-tests /<<BUILDDIR>>/subread-1.5.0-p3+dfsg
[2J[0;0H[30;47m
**************************************************
**************************************************
*** ***
*** 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. ***
*** ***
**************************************************
**************************************************
[13;26H[33;44m9[13;26H8[13;26H7[13;26H6[13;26H5[13;26H4[13;26H3[13;26H2[13;26H1[13;26H0[0m[2J[0,0H
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p3
//=========================== 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=148.0k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=185.1k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=220.6k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=246.7k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=272.8k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=296.0k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=314.1k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=334.6k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=351.9k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=367.5k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=385.1k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=396.7k bps/s, total=0m ||
|| 52 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=90.1k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=107.8k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=126.5k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=145.5k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=163.7k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=181.4k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=197.9k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=213.8k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=228.9k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=242.8k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=255.6k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=267.3k 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/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p3
//========================== 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 (10-Jun-2016 13:39:27) ======================\\
|| ||
|| 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, 0.3 mins elapsed, rate=3.4k reads per second ||
|| 39% completed, 0.3 mins elapsed, rate=3.5k reads per second ||
|| 46% completed, 0.3 mins elapsed, rate=3.8k reads per second ||
|| 53% completed, 0.3 mins elapsed, rate=3.9k reads per second ||
|| 60% completed, 0.3 mins elapsed, rate=4.0k reads per second ||
|| 74% completed, 0.3 mins elapsed, rate=0.8k reads per second ||
|| 83% completed, 0.3 mins elapsed, rate=0.9k reads per second ||
|| 91% completed, 0.3 mins elapsed, rate=1.0k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 reads ||
|| Mapped : 19997 reads (100.0%) ||
|| Indels : 7 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 0.8 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p3
//========================== 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 (10-Jun-2016 13:40:18) ======================\\
|| ||
|| 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, 0.5 mins elapsed, rate=1.3k reads per second ||
|| 39% completed, 0.6 mins elapsed, rate=0.8k reads per second ||
|| 46% completed, 0.6 mins elapsed, rate=0.9k reads per second ||
|| 53% completed, 0.6 mins elapsed, rate=0.9k reads per second ||
|| 60% completed, 0.6 mins elapsed, rate=0.9k reads per second ||
|| 74% completed, 0.7 mins elapsed, rate=0.4k reads per second ||
|| 83% completed, 0.7 mins elapsed, rate=0.4k reads per second ||
|| 91% completed, 0.7 mins elapsed, rate=0.5k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 reads ||
|| Mapped : 18758 reads (93.8%) ||
|| Indels : 5 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 2.8 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p3
//========================== 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 (10-Jun-2016 13:43:07) ======================\\
|| ||
|| 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, 0.3 mins elapsed, rate=2.0k fragments per second ||
|| 39% completed, 0.3 mins elapsed, rate=2.1k fragments per second ||
|| 46% completed, 0.3 mins elapsed, rate=2.1k fragments per second ||
|| 53% completed, 0.3 mins elapsed, rate=2.1k fragments per second ||
|| 60% completed, 0.3 mins elapsed, rate=2.2k fragments per second ||
|| 74% completed, 0.3 mins elapsed, rate=0.8k fragments per second ||
|| 83% completed, 0.3 mins elapsed, rate=0.8k fragments per second ||
|| 91% completed, 0.4 mins elapsed, rate=0.8k 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 : 1.3 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p3
//========================== 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 (10-Jun-2016 13:44:32) ======================\\
|| ||
|| The input file contains base space reads. ||
|| WARNING - The specified Phred score offset (33) seems incorrect. ||
|| ASCII values of the quality scores of read bases included in ||
|| the first 3000 reads were found to be within the range of ||
|| [73,73]. ||
|| ||
|| Load the 1-th index block... ||
|| 33% completed, 0.3 mins elapsed, rate=1.8k fragments per second ||
|| 39% completed, 0.3 mins elapsed, rate=1.8k fragments per second ||
|| 46% completed, 0.3 mins elapsed, rate=1.9k fragments per second ||
|| 53% completed, 0.3 mins elapsed, rate=2.0k fragments per second ||
|| 60% completed, 0.3 mins elapsed, rate=2.0k fragments per second ||
|| 74% completed, 0.3 mins elapsed, rate=0.7k fragments per second ||
|| 83% completed, 0.4 mins elapsed, rate=0.8k fragments per second ||
|| 91% completed, 0.4 mins elapsed, rate=0.8k 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 : 2.4 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p3
//========================== 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 (10-Jun-2016 13:47:02) ======================\\
|| ||
|| 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, 0.3 mins elapsed, rate=2.0k fragments per second ||
|| 39% completed, 0.3 mins elapsed, rate=2.0k fragments per second ||
|| 46% completed, 0.3 mins elapsed, rate=2.0k fragments per second ||
|| 53% completed, 0.3 mins elapsed, rate=2.1k fragments per second ||
|| 60% completed, 0.3 mins elapsed, rate=2.2k fragments per second ||
|| 74% completed, 0.3 mins elapsed, rate=0.7k fragments per second ||
|| 83% completed, 0.4 mins elapsed, rate=0.8k fragments per second ||
|| 91% completed, 0.4 mins elapsed, rate=0.8k 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 : 1.3 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p3
//========================== 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 (10-Jun-2016 13:48:28) ======================\\
|| ||
|| 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, 0.3 mins elapsed, rate=2.6k fragments per second ||
|| 40% completed, 0.3 mins elapsed, rate=2.7k fragments per second ||
|| 48% completed, 0.3 mins elapsed, rate=2.8k fragments per second ||
|| 53% completed, 0.3 mins elapsed, rate=2.8k fragments per second ||
|| 59% completed, 0.3 mins elapsed, rate=2.8k fragments per second ||
|| 67% completed, 0.3 mins elapsed, rate=2.8k fragments per second ||
|| 75% completed, 0.3 mins elapsed, rate=0.8k fragments per second ||
|| 83% completed, 0.3 mins elapsed, rate=0.9k fragments per second ||
|| 92% completed, 0.3 mins elapsed, rate=0.9k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 20001 fragments ||
|| Mapped : 19528 fragments (97.6%) ||
|| Correctly paired : 14071 fragments ||
|| Indels : 179 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 1.5 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
6a8ad9a8de00d896ebfec11602a02726 ../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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p3
//=========================== 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=227.6k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=294.9k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=345.7k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=381.3k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=413.7k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=442.4k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=465.1k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=489.0k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=509.8k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=528.0k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=547.8k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=561.4k bps/s, total=0m ||
|| 2 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=219.3k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=228.6k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=243.6k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=257.5k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=271.9k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=286.8k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=302.0k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=317.4k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=333.6k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=348.6k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=365.3k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=379.9k 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/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p3
//============================= 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 (10-Jun-2016 13:50:10) ======================\\
|| ||
|| 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, 1.7 mins elapsed, rate=0.4k fragments per second ||
|| 48% completed, 1.7 mins elapsed, rate=0.4k fragments per second ||
|| 54% completed, 1.7 mins elapsed, rate=0.4k fragments per second ||
|| 61% completed, 1.8 mins elapsed, rate=0.4k fragments per second ||
|| 77% completed, 1.8 mins elapsed, rate=0.1k fragments per second ||
|| 87% completed, 1.8 mins elapsed, rate=0.1k fragments per second ||
|| 97% completed, 1.9 mins elapsed, rate=0.1k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 16052 fragments ||
|| Mapped : 15914 fragments (99.1%) ||
|| Correctly paired : 14370 fragments ||
|| Junctions : 425 ||
|| Indels : 187 ||
|| ||
|| Running time : 4.8 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p3
//============================= 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 (10-Jun-2016 13:55:01) ======================\\
|| ||
|| 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, 1.2 mins elapsed, rate=0.6k fragments per second ||
|| 48% completed, 1.2 mins elapsed, rate=0.6k fragments per second ||
|| 54% completed, 1.3 mins elapsed, rate=0.6k fragments per second ||
|| 61% completed, 1.3 mins elapsed, rate=0.7k fragments per second ||
|| 77% completed, 1.3 mins elapsed, rate=0.2k fragments per second ||
|| 87% completed, 1.4 mins elapsed, rate=0.2k fragments per second ||
|| 97% completed, 1.4 mins elapsed, rate=0.2k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 16052 fragments ||
|| Mapped : 15907 fragments (99.1%) ||
|| Correctly paired : 14274 fragments ||
|| Junctions : 455 ||
|| Fusions : 99 ||
|| Indels : 188 ||
|| ||
|| Running time : 3.5 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
================================================================================
FeatureCounts Basic Test
http://subread.sourceforge.net/
================================================================================
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p3
//========================== 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) ||
|| ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Strand specific : no ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================================= Running ==================================\\
|| ||
|| Load annotation file data/test-minimum.GTF ... ||
|| Features : 23 ||
|| Meta-features : 7 ||
|| Chromosomes/contigs : 3 ||
|| ||
|| Process SAM file data/test-minimum.sam... ||
|| Paired-end reads are included. ||
|| Assign reads to features... ||
|| Total reads : 998 ||
|| Successfully assigned reads : 389 (39.0%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Read assignment finished. ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
================================================================================
Basic Test finished.
The results are in result/test-minimum.FC
================================================================================
================================================================================
FeatureCounts Chromosome Name Aliases Tests
http://subread.sourceforge.net/
================================================================================
Testing chromosome aliases ... [[32mPASS[0m]
================================================================================
FeatureCounts Chromosome Name Inference Tests
http://subread.sourceforge.net/
================================================================================
Testing automatic inference of chromosome names ... [[32mPASS[0m]
================================================================================
FeatureCounts Corner Case Tests
http://subread.sourceforge.net/
================================================================================
Testing indel reads ... [[32mPASS[0m]
Testing junction reads ... [[32mPASS[0m]
Testing paired-end reads (fragment counting) ... [[32mPASS[0m]
Testing paired-end reads (fragment counting, both ends mapped) ... [[32mPASS[0m]
Testing multi-overlapping reads ... [[32mPASS[0m]
Testing feature-level summarization ... [[32mPASS[0m]
Testing gene-level summarization ... [[32mPASS[0m]
Testing multi-mapping reads ... [[32mPASS[0m]
Testing multi-mapping reads (primary only) ... [[32mPASS[0m]
Testing both ends mapped ... [[32mPASS[0m]
Testing disallowing chimeric fragments ... [[32mPASS[0m]
Testing Allowing multi-mapped reads ... [[32mPASS[0m]
Testing not sorting input file ... [[32mPASS[0m]
Testing minimum overlapping length ... [[32mPASS[0m]
Testing Largest Overlapping ... [[32mPASS[0m]
Testing paired-end distance ... [[32mPASS[0m]
Testing Read to position (5' end) ... [[32mPASS[0m]
Testing Read to position (3' end) ... [[32mPASS[0m]
Testing Read extension to the 3' end ... [[32mPASS[0m]
Testing Read extension to the 5' end ... [[32mPASS[0m]
Testing Low maxOPs value ... [[32mPASS[0m]
Testing minimum mapping quality ... [[32mPASS[0m]
Testing Ignoring duplicated reads ... [[32mPASS[0m]
Testing Fraction counting ... [[32mPASS[0m]
Testing Junction counting ... [[32mPASS[0m,[32mPASS[0m]
Skipping Junction counting (with genome).
Testing GTF format annotations ... [[32mPASS[0m]
Testing SAF format annotations ... [[32mPASS[0m]
Testing SAM format input ... [[32mPASS[0m]
Testing BAM format input ... [[32mPASS[0m]
Testing unstranded read summarization ... [[32mPASS[0m]
Testing stranded read summarization ... [[32mPASS[0m]
Testing reversely stranded read summarization ... [[32mPASS[0m]
Testing Ignoring duplicate fragments ... [[32mPASS[0m]
Testing Junction reads only ... [[32mPASS[0m]
Testing Exonic reads only ... [[32mPASS[0m]
Testing intron_between ... [[32mPASS[0m]
Testing intron_between ... [[32mPASS[0m]
Testing intron_between ... [[32mPASS[0m]
Testing intron_between ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
../../bin/exactSNP -g ../chr901.fa -o result/test-out.VCF -i data/test-in.BAM -b
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.0-p3
//============================= 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 (10-Jun-2016 13:58:38) ======================\\
|| ||
|| Split BAM file into ./temp-snps-022055-001F7BB4051B-* ... ||
|| 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 : 0.1 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
[30;47m
**************************************************
**************************************************
*** ***
*** Test finished. ***
*** ***
*** Should there be any error, please visit ***
*** [34mhttp://subread.sourceforge.net/[0;30;47m for more ***
*** information. ***
*** ***
**************************************************
**************************************************
[0m
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.5.0-p3+dfsg'
fakeroot debian/rules binary-arch
dh binary-arch --parallel
dh_testroot -a -O--parallel
dh_prep -a -O--parallel
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.5.0-p3+dfsg'
find /<<BUILDDIR>>/subread-1.5.0-p3+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \;
mkdir -p /<<BUILDDIR>>/subread-1.5.0-p3+dfsg/debian/subread/usr/share/man/man1
help2man --no-info --help-option="''" --no-discard-stderr --name='an accurate and efficient aligner for mapping both genomic \
DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \
/<<BUILDDIR>>/subread-1.5.0-p3+dfsg/bin/subread-align | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.0-p3+dfsg/debian/subread/usr/share/man/man1/subread-align.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='builds an base-space or color-space index using the reference sequences' \
/<<BUILDDIR>>/subread-1.5.0-p3+dfsg/bin/subread-buildindex | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.0-p3+dfsg/debian/subread/usr/share/man/man1/subread-buildindex.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='an RNA-seq aligner suitable for all purposes of RNA-seq analyses' \
/<<BUILDDIR>>/subread-1.5.0-p3+dfsg/bin/subjunc | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.0-p3+dfsg/debian/subread/usr/share/man/man1/subjunc.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='a highly efficient and accurate read summarization program' \
/<<BUILDDIR>>/subread-1.5.0-p3+dfsg/bin/featureCounts | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.0-p3+dfsg/debian/subread/usr/share/man/man1/featureCounts.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='a SNP caller that discovers SNPs by testing signals against local background noises' \
/<<BUILDDIR>>/subread-1.5.0-p3+dfsg/bin/exactSNP | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.0-p3+dfsg/debian/subread/usr/share/man/man1/exactSNP.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='detect short and long indels' \
/<<BUILDDIR>>/subread-1.5.0-p3+dfsg/bin/subindel | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.0-p3+dfsg/debian/subread/usr/share/man/man1/subindel.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='scans the entire genome and reports all matches of a specified sequence' \
/<<BUILDDIR>>/subread-1.5.0-p3+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.0-p3+dfsg/debian/subread/usr/share/man/man1/subread-fullscan.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='counting the coverage of mapped reads at each location on the entire reference genome' \
/<<BUILDDIR>>/subread-1.5.0-p3+dfsg/bin/utilities/coverageCount | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.0-p3+dfsg/debian/subread/usr/share/man/man1/coverageCount.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='calculate the proportion of mapped reads/fragments' \
/<<BUILDDIR>>/subread-1.5.0-p3+dfsg/bin/utilities/propmapped | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.0-p3+dfsg/debian/subread/usr/share/man/man1/propmapped.1;
for i in removeDup repair qualityScores ; do \
help2man --no-info --help-option="''" --no-discard-stderr --name='a component of subread suite' /<<BUILDDIR>>/subread-1.5.0-p3+dfsg/bin/utilities/$i | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.0-p3+dfsg/debian/subread/usr/share/man/man1/$i.1; \
done
dh_auto_install
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.5.0-p3+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
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a -O--parallel
dh_builddeb -a -O--parallel
dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_1.5.0-p3+dfsg-1_armhf.deb'.
dpkg-deb: building package 'subread' in '../subread_1.5.0-p3+dfsg-1_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../subread_1.5.0-p3+dfsg-1_armhf.changes
dpkg-genchanges: warning: package subread-dbgsym listed in files list but not in control info
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build subread-1.5.0-p3+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160610-1400
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
subread_1.5.0-p3+dfsg-1_armhf.changes:
--------------------------------------
Format: 1.8
Date: Sat, 04 Jun 2016 09:16:27 +0200
Source: subread
Binary: subread subread-data
Architecture: armhf
Version: 1.5.0-p3+dfsg-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
Description:
subread - toolkit for processing next-gen sequencing data
subread-data - data files for subread package
Changes:
subread (1.5.0-p3+dfsg-1) unstable; urgency=medium
.
* Drop get-orig-source target, update d/watch to repack and use compression xz
* Imported Upstream version 1.5.0-p3+dfsg
Checksums-Sha1:
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fbfaf2ae0b252336c4014908a354f5c7c6521a9a 435178 subread_1.5.0-p3+dfsg-1_armhf.deb
Checksums-Sha256:
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Files:
d0a3892ae037466b016b7c16cb820ac0 5388308 debug extra subread-dbgsym_1.5.0-p3+dfsg-1_armhf.deb
d6d054dcef5a2e3d5d186a8e35d47d6a 435178 science optional subread_1.5.0-p3+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
subread-dbgsym_1.5.0-p3+dfsg-1_armhf.deb
----------------------------------------
new debian package, version 2.0.
size 5388308 bytes: control archive=1100 bytes.
886 bytes, 13 lines control
1272 bytes, 12 lines md5sums
Package: subread-dbgsym
Source: subread
Version: 1.5.0-p3+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5948
Depends: subread (= 1.5.0-p3+dfsg-1)
Section: debug
Priority: extra
Homepage: http://sourceforge.net/projects/subread/
Description: Debug symbols for subread
Auto-Built-Package: debug-symbols
Build-Ids: 110c1c754a5e6ab8c37a5a052aa3064420a32825 26ba1b6edca8a0a06223de9782fdec21dfed1a37 36950090143807f4f9b320936efede5bc6820bbd 5f4aa02d0eeb10e11d23a55576342d23f5492023 78e87f5e6f3a302b7dd4b8f071b3e67c3257e9e1 90510f687928e75a436aaca01e4c5c7fac9e5398 b312be6d8abd5b7740d2188caf61735f70f00fae b64236558a0cbc805084aec2bd745bf8c7c30ebf d5455073c0575c8bf45a636f95a27ed946bc1472 f123e11019bc2a5f2f0aa550197e925216ef5da5 fe9f2cb53b7b01fd7d7d0c08999f16db67368407 fee4bf95f07aabe1843f594fa4ec589d533a3bd2
drwxr-xr-x root/root 0 2016-06-10 13:59 ./
drwxr-xr-x root/root 0 2016-06-10 13:59 ./usr/
drwxr-xr-x root/root 0 2016-06-10 13:59 ./usr/lib/
drwxr-xr-x root/root 0 2016-06-10 13:59 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-06-10 13:59 ./usr/lib/debug/.build-id/
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drwxr-xr-x root/root 0 2016-06-10 13:59 ./usr/lib/debug/.build-id/90/
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subread_1.5.0-p3+dfsg-1_armhf.deb
---------------------------------
new debian package, version 2.0.
size 435178 bytes: control archive=1394 bytes.
626 bytes, 14 lines control
1819 bytes, 28 lines md5sums
Package: subread
Version: 1.5.0-p3+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5770
Depends: libc6 (>= 2.15), zlib1g (>= 1:1.2.3.3)
Section: science
Priority: optional
Homepage: http://sourceforge.net/projects/subread/
Description: toolkit for processing next-gen sequencing data
Subread aligner can be used to align both gDNA-seq and RNA-seq reads.
Subjunc aligner was specified designed for the detection of exon-exon
junction. For the mapping of RNA-seq reads, Subread performs local
alignments and Subjunc performs global alignments.
drwxr-xr-x root/root 0 2016-06-10 13:59 ./
drwxr-xr-x root/root 0 2016-06-10 13:59 ./usr/
drwxr-xr-x root/root 0 2016-06-10 13:59 ./usr/bin/
-rwxr-xr-x root/root 506116 2016-06-10 13:59 ./usr/bin/exactSNP
-rwxr-xr-x root/root 563700 2016-06-10 13:59 ./usr/bin/featureCounts
-rwxr-xr-x root/root 477460 2016-06-10 13:59 ./usr/bin/subindel
-rwxr-xr-x root/root 482324 2016-06-10 13:59 ./usr/bin/subjunc
-rwxr-xr-x root/root 482260 2016-06-10 13:59 ./usr/bin/subread-align
-rwxr-xr-x root/root 497900 2016-06-10 13:59 ./usr/bin/subread-buildindex
drwxr-xr-x root/root 0 2016-06-10 13:59 ./usr/lib/
drwxr-xr-x root/root 0 2016-06-10 13:59 ./usr/lib/subread/
-rwxr-xr-x root/root 477460 2016-06-10 13:59 ./usr/lib/subread/coverageCount
-rwxr-xr-x root/root 477460 2016-06-10 13:59 ./usr/lib/subread/propmapped
-rwxr-xr-x root/root 477572 2016-06-10 13:59 ./usr/lib/subread/qualityScores
-rwxr-xr-x root/root 473316 2016-06-10 13:59 ./usr/lib/subread/removeDup
-rwxr-xr-x root/root 473316 2016-06-10 13:59 ./usr/lib/subread/repair
-rwxr-xr-x root/root 473316 2016-06-10 13:59 ./usr/lib/subread/subread-fullscan
drwxr-xr-x root/root 0 2016-06-10 13:59 ./usr/share/
drwxr-xr-x root/root 0 2016-06-10 13:59 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-06-10 13:59 ./usr/share/doc/subread/
-rw-r--r-- root/root 500 2016-06-04 07:17 ./usr/share/doc/subread/README.Debian
-rw-r--r-- root/root 3670 2016-05-27 04:32 ./usr/share/doc/subread/README.txt
-rw-r--r-- root/root 1711 2016-06-04 07:17 ./usr/share/doc/subread/changelog.Debian.gz
-rw-r--r-- root/root 1137 2016-06-04 07:17 ./usr/share/doc/subread/copyright
drwxr-xr-x root/root 0 2016-06-10 13:59 ./usr/share/man/
drwxr-xr-x root/root 0 2016-06-10 13:59 ./usr/share/man/man1/
-rw-r--r-- root/root 595 2016-06-10 13:59 ./usr/share/man/man1/coverageCount.1.gz
-rw-r--r-- root/root 1172 2016-06-10 13:59 ./usr/share/man/man1/exactSNP.1.gz
-rw-r--r-- root/root 2182 2016-06-10 13:59 ./usr/share/man/man1/featureCounts.1.gz
-rw-r--r-- root/root 459 2016-06-10 13:59 ./usr/share/man/man1/propmapped.1.gz
-rw-r--r-- root/root 564 2016-06-10 13:59 ./usr/share/man/man1/qualityScores.1.gz
-rw-r--r-- root/root 496 2016-06-10 13:59 ./usr/share/man/man1/removeDup.1.gz
-rw-r--r-- root/root 478 2016-06-10 13:59 ./usr/share/man/man1/repair.1.gz
-rw-r--r-- root/root 346 2016-06-10 13:59 ./usr/share/man/man1/subindel.1.gz
-rw-r--r-- root/root 1526 2016-06-10 13:59 ./usr/share/man/man1/subjunc.1.gz
-rw-r--r-- root/root 1617 2016-06-10 13:59 ./usr/share/man/man1/subread-align.1.gz
-rw-r--r-- root/root 763 2016-06-10 13:59 ./usr/share/man/man1/subread-buildindex.1.gz
-rw-r--r-- root/root 376 2016-06-10 13:59 ./usr/share/man/man1/subread-fullscan.1.gz
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 105828
Build-Time: 1510
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 284
Job: subread_1.5.0-p3+dfsg-1
Machine Architecture: armhf
Package: subread
Package-Time: 1847
Source-Version: 1.5.0-p3+dfsg-1
Space: 105828
Status: successful
Version: 1.5.0-p3+dfsg-1
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Finished at 20160610-1400
Build needed 00:30:47, 105828k disc space