subread →
1.5.1+dfsg-4 →
armhf → 2016-12-08 07:17:16
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| subread 1.5.1+dfsg-4 (armhf) Thu, 08 Dec 2016 06:07:36 +0000 |
+==============================================================================+
Package: subread
Version: 1.5.1+dfsg-4
Source Version: 1.5.1+dfsg-4
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/stretch-staging-armhf-sbuild-c0a1c6c9-f80e-497c-bac0-75bfec0a8c26' 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 [9580 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.5 MB]
Fetched 21.1 MB in 23s (896 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
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 15.7 MB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main subread 1.5.1+dfsg-4 (dsc) [2243 B]
Get:2 http://172.17.0.1/private stretch-staging/main subread 1.5.1+dfsg-4 (tar) [15.7 MB]
Get:3 http://172.17.0.1/private stretch-staging/main subread 1.5.1+dfsg-4 (diff) [7108 B]
Fetched 15.7 MB in 1s (9495 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/subread-pmrPak/subread-1.5.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/subread-pmrPak' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-5snn2b/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-5snn2b/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-5snn2b/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-5snn2b/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-5snn2b/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-5snn2b/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-5snn2b/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-5snn2b/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-5snn2b/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (3235 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-5snn2b/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-5snn2b/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n libfuse2 manpages
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 9 not upgraded.
Need to get 776 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-5snn2b/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 776 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12988 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in amd64 arm64 armel armhf i386 kfreebsd-amd64 kfreebsd-i386 ppc64el all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: bc, debhelper (>= 10), help2man, python, zlib1g-dev
Filtered Build-Depends: bc, debhelper (>= 10), help2man, python, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-subread-dummy' in '/<<BUILDDIR>>/resolver-5snn2b/apt_archive/sbuild-build-depends-subread-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-subread-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-5snn2b/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-5snn2b/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-5snn2b/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-5snn2b/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-5snn2b/apt_archive ./ Sources [509 B]
Get:5 copy:/<<BUILDDIR>>/resolver-5snn2b/apt_archive ./ Packages [590 B]
Fetched 2432 B in 0s (3770 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-5snn2b/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-5snn2b/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install subread build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n libfuse2 manpages
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bc bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1
libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libicu57
liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib libreadline6 libsigsegv2
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 libicu57
liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib libreadline6 libsigsegv2
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, 47 newly installed, 0 to remove and 9 not upgraded.
Need to get 23.6 MB/24.6 MB of archives.
After this operation, 85.2 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-5snn2b/apt_archive ./ sbuild-build-depends-subread-dummy 0.invalid.0 [800 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf liblocale-gettext-perl armhf 1.07-3+b1 [18.3 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12 [178 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-2 [971 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.12-7 [389 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.12-7 [1177 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-2 [40.3 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.12-7 [1853 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.12-7 [284 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-2 [19.8 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-2 [153 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf bc armhf 1.06.95-9 [96.3 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-1 [219 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-1 [104 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-1 [63.3 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-5 [7427 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.1 [804 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-5 [733 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.2-2 [2527 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.2 [826 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf help2man armhf 1.47.4 [162 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../29-zlib1g-dev_1%3a1.2.8.dfsg-2+b1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Selecting previously unselected package sbuild-build-depends-subread-dummy.
Preparing to unpack .../30-sbuild-build-depends-subread-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-subread-dummy (0.invalid.0) ...
Setting up libexpat1:armhf (2.2.0-1) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up mime-support (3.60) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up groff-base (1.22.3-8) ...
Setting up gettext-base (0.19.8.1-1) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up m4 (1.4.17-5) ...
Setting up libicu57:armhf (57.1-5) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2.1) ...
Setting up libmagic-mgc (1:5.29-1) ...
Setting up libmagic1:armhf (1:5.29-1) ...
Setting up libssl1.0.2:armhf (1.0.2j-4) ...
Processing triggers for libc-bin (2.24-7+rpi1) ...
Setting up autotools-dev (20161112.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up liblocale-gettext-perl (1.07-3+b1) ...
Setting up libffi6:armhf (3.2.1-6) ...
Setting up bsdmainutils (9.0.12) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libpython2.7-stdlib:armhf (2.7.12-7) ...
Setting up autopoint (0.19.8.1-1) ...
Setting up libreadline6:armhf (6.3-9) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libfile-stripnondeterminism-perl (0.028-1) ...
Setting up libglib2.0-0:armhf (2.50.2-2) ...
No schema files found: doing nothing.
Setting up python2.7 (2.7.12-7) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.29-1) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up libpython-stdlib:armhf (2.7.11-2) ...
Setting up automake (1:1.15-5) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up help2man (1.47.4) ...
Setting up man-db (2.7.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up bc (1.06.95-9) ...
Setting up python (2.7.11-2) ...
Setting up libtool (2.4.6-2) ...
Setting up gettext (0.19.8.1-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.20) ...
Setting up dh-autoreconf (12) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
Setting up debhelper (10.2.2) ...
Setting up sbuild-build-depends-subread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-7+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.6.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27.51.20161127-1 dpkg-dev_1.18.15 g++-6_6.2.1-5+rpi1 gcc-6_6.2.1-5+rpi1 libc6-dev_2.24-7+rpi1 libstdc++-6-dev_6.2.1-5+rpi1 libstdc++6_6.2.1-5+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.4~beta1 autoconf_2.69-10 automake_1:1.15-5 autopoint_0.19.8.1-1 autotools-dev_20161112.1 base-files_9.7+rpi1 base-passwd_3.5.41 bash_4.4-2 bc_1.06.95-9 binutils_2.27.51.20161127-1 bsdmainutils_9.0.12 bsdutils_1:2.29-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-6 cpp_4:6.1.1-1 cpp-6_6.2.1-5+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.2 debianutils_4.8.1 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dmsetup_2:1.02.136-1 dpkg_1.18.15 dpkg-dev_1.18.15 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.29-1 findutils_4.6.0+git+20161106-1 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.2.1-5+rpi1 gcc_4:6.1.1-1 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-6_6.2.1-5+rpi1 gcc-6-base_6.2.1-5+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_2.1.16-2 gnupg-agent_2.1.16-2 gnupg-l10n_2.1.16-2 gpgv_2.1.16-2 grep_2.26-1 groff-base_1.22.3-8 gzip_1.6-5 help2man_1.47.4 hostname_3.18 init_1.46 init-system-helpers_1.46 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_23-1 libacl1_2.2.52-3 libapparmor1_2.10.95-6 libapt-pkg5.0_1.4~beta1 libarchive-zip-perl_1.59-1 libasan3_6.2.1-5+rpi1 libassuan0_2.4.3-2 libatomic1_6.2.1-5+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblkid1_2.29-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-7+rpi1 libc-dev-bin_2.24-7+rpi1 libc6_2.24-7+rpi1 libc6-dev_2.24-7+rpi1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.2.1-5+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.3-2 libdb5.3_5.3.28-12 libdbus-1-3_1.10.14-1 libdebconfclient0_0.218 libdevmapper1.02.1_2:1.02.136-1 libdpkg-perl_1.18.15 libdrm2_2.4.74-1 libexpat1_2.2.0-1 libfakeroot_1.21-2 libfdisk1_2.29-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.1-5+rpi1 libgcc1_1:6.2.1-5+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libglib2.0-0_2.50.2-2 libgmp10_2:6.1.1+dfsg-1 libgomp1_6.2.1-5+rpi1 libgpg-error0_1.25-1 libicu57_57.1-5 libidn11_1.33-1 libip4tc0_1.6.0-4 libisl15_0.17.1-1 libklibc_2.0.4-9+rpi1 libkmod2_23-1 libksba8_1.3.5-2 liblocale-gettext-perl_1.07-3+b1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-1 libmagic1_1:5.29-1 libmount1_2.29-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnpth0_1.3-1 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre3_2:8.39-2 libperl5.24_5.24.1~rc4-1 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-3 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.12-7 libpython2.7-stdlib_2.7.12-7 libreadline6_6.3-9 libreadline7_7.0-1 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-1 libsemanage1_2.6-1 libsepol1_2.6-1 libsigsegv2_2.10-5 libsmartcols1_2.29-1 libsqlite3-0_3.15.2-1 libss2_1.43.3-1 libssl1.0.2_1.0.2j-4 libstdc++-6-dev_6.2.1-5+rpi1 libstdc++6_6.2.1-5+rpi1 libsystemd0_232-6 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.2.1-5+rpi1 libudev1_232-6 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1 libxml2_2.9.4+dfsg1-2.1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.3 lsb-base_9.20161125+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-2 manpages_4.08-1 mawk_1.3.3-17 mime-support_3.60 mount_2.29-1 multiarch-support_2.24-7+rpi1 nano_2.7.1-1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 passwd_1:4.2-3.3 patch_2.7.5-1 perl_5.24.1~rc4-1 perl-base_5.24.1~rc4-1 perl-modules-5.24_5.24.1~rc4-1 pinentry-curses_0.9.7-9 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.11-2 python-minimal_2.7.11-2 python2.7_2.7.12-7 python2.7-minimal_2.7.12-7 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-subread-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_232-6 systemd-sysv_232-6 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1.1 tzdata_2016j-2 udev_232-6 util-linux_2.29-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Dec 2 07:47:25 2016 UTC
gpgv: using RSA key 578A0494D1C646D1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./subread_1.5.1+dfsg-4.dsc
dpkg-source: info: extracting subread in /<<BUILDDIR>>/subread-1.5.1+dfsg
dpkg-source: info: unpacking subread_1.5.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking subread_1.5.1+dfsg-4.debian.tar.xz
dpkg-source: info: applying fix_ftbfs_kfreebsd.patch
dpkg-source: info: applying arch_specific_flags.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
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-c0a1c6c9-f80e-497c-bac0-75bfec0a8c26
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 1.5.1+dfsg-4
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build subread-1.5.1+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --parallel
dh_testdir
dh_auto_clean
dh_autoreconf_clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.5.1+dfsg'
cd src; make -f Makefile.Linux clean
make[2]: Entering directory '/<<BUILDDIR>>/subread-1.5.1+dfsg/src'
rm -f core featureCounts exactSNP removeDup subread-buildindex core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o
make[2]: Leaving directory '/<<BUILDDIR>>/subread-1.5.1+dfsg/src'
dh_clean
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.5.1+dfsg'
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
dh_update_autotools_config -a -O--parallel
dh_autoreconf -a -O--parallel
dh_auto_configure -a -O--parallel
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.5.1+dfsg'
cd src; make -f Makefile.Linux
make[2]: Entering directory '/<<BUILDDIR>>/subread-1.5.1+dfsg/src'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c
core.c: In function 'print_in_box':
core.c:158:7: warning: variable 'is_R_linebreak' set but not used [-Wunused-but-set-variable]
char is_R_linebreak=0, * content, *out_line_buff;
^~~~~~~~~~~~~~
core.c: In function 'convert_GZ_to_FQ':
core.c:853:19: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
gzFile * rawfp = gzopen(fname, "r");
^~~~~~
core.c:864:25: warning: passing argument 1 of 'gzgets' from incompatible pointer type [-Wincompatible-pointer-types]
char * bufr =gzgets(rawfp, linebuff, 3000);
^~~~~
In file included from subread.h:26:0,
from core.c:43:
/usr/include/zlib.h:1372:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^~~~~~
core.c:875:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(rawfp);
^~~~~
In file included from subread.h:26:0,
from core.c:43:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
core.c: In function 'calc_tlen':
core.c:1548:16: warning: variable 'section_start' set but not used [-Wunused-but-set-variable]
unsigned int section_start = smaller_head_pos, section_end = 0;
^~~~~~~~~~~~~
core.c: In function 'do_iteration_one':
core.c:2174:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret;
^~~
core.c: In function 'write_realignments_for_fragment':
core.c:2386:21: warning: variable 'raw_r2' set but not used [-Wunused-but-set-variable]
mapping_result_t * raw_r2 = NULL;
^~~~~~
core.c:2383:21: warning: variable 'raw_r1' set but not used [-Wunused-but-set-variable]
mapping_result_t * raw_r1 = NULL;
^~~~~~
core.c: In function 'do_iteration_two':
core.c:2452:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret;
^~~
core.c: In function 'do_voting':
core.c:3021:9: warning: variable 'allsubreads_for_each_gap' set but not used [-Wunused-but-set-variable]
int allsubreads_for_each_gap [GENE_SLIDING_STEP], noninformative_subreads_for_each_gap[GENE_SLIDING_STEP];
^~~~~~~~~~~~~~~~~~~~~~~~
core.c:2940:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret, xk1;
^~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c
core-junction.c: In function 'copy_vote_to_alignment_res':
core-junction.c:945:12: warning: variable 'current_piece_minor_score' set but not used [-Wunused-but-set-variable]
int i,j, current_piece_minor_score = 0;
^~~~~~~~~~~~~~~~~~~~~~~~~
core-junction.c: In function 'find_donor_receptor':
core-junction.c:1996:8: warning: variable 'sp2s' set but not used [-Wunused-but-set-variable]
char sp2s[200];
^~~~
core-junction.c: In function 'finalise_explain_CIGAR':
core-junction.c:3119:10: warning: variable 'is_front_search' set but not used [-Wunused-but-set-variable]
int is_front_search = 0;
^~~~~~~~~~~~~~~
core-junction.c:3255:94: warning: variable 'total_coverage_length' set but not used [-Wunused-but-set-variable]
int final_qual = 0, applied_mismatch = 0, non_clipped_length = 0, total_indel_length = 0, total_coverage_length = 0, final_MATCH = 0, chromosomal_length = 0;
^~~~~~~~~~~~~~~~~~~~~
core-junction.c:3235:28: warning: variable 'isCigarOK' set but not used [-Wunused-but-set-variable]
int mismatch_bases = 0, isCigarOK = 0;
^~~~~~~~~
core-junction.c:3049:23: warning: variable 'tmp_cigar_exonic' set but not used [-Wunused-but-set-variable]
char tmp_cigar[120], tmp_cigar_exonic[120];
^~~~~~~~~~~~~~~~
core-junction.c: In function 'find_translocation_brk_PQR':
core-junction.c:5635:23: warning: variable 'candBrkPlist' set but not used [-Wunused-but-set-variable]
chromosome_event_t * candBrkPlist [_PQR_LIST_SIZE];
^~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c
core-indel.c: In function 'find_new_indels':
core-indel.c:1589:9: warning: variable 'best_j' set but not used [-Wunused-but-set-variable]
int best_j=0, best_score=-99999, is_ambiguous_indel= 0;
^~~~~~
core-indel.c: In function 'full_indel_alignment':
core-indel.c:2936:41: warning: variable 'best_right' set but not used [-Wunused-but-set-variable]
int best_edge_score = -1, best_left, best_right;
^~~~~~~~~~
core-indel.c:2936:30: warning: variable 'best_left' set but not used [-Wunused-but-set-variable]
int best_edge_score = -1, best_left, best_right;
^~~~~~~~~
core-indel.c: In function 'find_potential_ultralong_indels':
core-indel.c:3035:24: warning: variable 'best_c2_location' set but not used [-Wunused-but-set-variable]
int best_match = -1, best_c2_location = -1;
^~~~~~~~~~~~~~~~
core-indel.c: In function 'finalise_pileup_file':
core-indel.c:3313:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3314:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_text, sizeof(char), read_len, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3315:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3392:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3393:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_text, sizeof(char), read_len, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3394:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c: In function 'finalise_pileup_file_by_debrujin':
core-indel.c:3756:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3757:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_text, sizeof(char), read_len, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3758:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c
sambam-file.c: In function 'PBam_get_next_zchunk':
sambam-file.c:352:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&ID1, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:353:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&ID2, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:354:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&CM, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:355:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&FLG, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:364:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&XLEN,1, 2, bam_fp );
^~~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:372:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SI1, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:373:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SI2, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:374:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SLEN, 1, 2, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:378:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&BSIZE_MID, 1,2 , bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:390:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(buffer, 1, CDATA_READING, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:394:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&real_len, 4, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c
gene-algorithms.c: In function 'show_cigar':
gene-algorithms.c:771:6: warning: variable 'last_end' set but not used [-Wunused-but-set-variable]
int last_end=0, last_offset = 0, cursor = 0;
^~~~~~~~
gene-algorithms.c:770:9: warning: variable 'is_error' set but not used [-Wunused-but-set-variable]
int i, is_error = 0;
^~~~~~~~
gene-algorithms.c: In function 'match_chro_indel':
gene-algorithms.c:1183:28: warning: variable 'last_section_indels' set but not used [-Wunused-but-set-variable]
int last_section_end = 0, last_section_indels=0;
^~~~~~~~~~~~~~~~~~~
gene-algorithms.c: In function 'search_DP_branch':
gene-algorithms.c:1732:6: warning: variable 'table_mask2_j_1' set but not used [-Wunused-but-set-variable]
int table_mask2_j_1 = 0, table_mask2_i_1 = 0;
^~~~~~~~~~~~~~~
gene-algorithms.c: In function 'final_mapping_quality':
gene-algorithms.c:2373:7: warning: variable 'is_match_begin' set but not used [-Wunused-but-set-variable]
int is_match_begin = 0;
^~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c
input-files.c: In function 'f_subr_open':
input-files.c:53:10: warning: implicit declaration of function 'fopen64' [-Wimplicit-function-declaration]
return fopen64(fname, mode);
^~~~~~~
input-files.c:53:10: warning: return makes pointer from integer without a cast [-Wint-conversion]
return fopen64(fname, mode);
^~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'SAM_pairer_get_next_read_BIN':
input-files.c:2754:11: warning: variable 'ref_name' set but not used [-Wunused-but-set-variable]
char ref_name[MAX_CHROMOSOME_NAME_LEN];
^~~~~~~~
input-files.c: In function 'fix_write_block':
input-files.c:4297:23: warning: variable 'retbam' set but not used [-Wunused-but-set-variable]
int x1, bam_len = 0, retbam;
^~~~~~
input-files.c: In function 'SAM_nosort_run_once':
input-files.c:4755:9: warning: variable 'ref_name' set but not used [-Wunused-but-set-variable]
char ref_name[MAX_CHROMOSOME_NAME_LEN];
^~~~~~~~
input-files.c: In function 'geinput_next_char':
input-files.c:523:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(out_buf, 1999,input->input_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'SAM_pairer_writer_reset':
input-files.c:3406:2: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(bam_main -> bam_fp), 0);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'SAM_pairer_osr_next_name':
input-files.c:3613:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:3625:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'SAM_pairer_osr_next_bin':
input-files.c:3635:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:3639:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:3642:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(bin, 1, rlen, fp);
^~~~~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'fix_load_next_block':
input-files.c:4273:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(bam_buf, 1, bsize - xlen - 19, in);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'sort_SAM_finalise':
input-files.c:5067:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:5073:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_name, 1, read_name_len, bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:5076:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len,2,1,bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:5082:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(new_line_mem, 1, read_len, bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:5135:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:5141:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_name_buf, 1, read_name_len, bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:5145:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, 2,1 , bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:5148:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_line_buf, 1, read_len, bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c
sorted-hashtable.c: In function 'gehash_load_option':
sorted-hashtable.c:1264:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1269:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1272:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1276:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(result ,option_length,1,fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c: In function 'gehash_load':
sorted-hashtable.c:1303:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1326:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1329:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1332:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&(the_table -> index_gap),2,1,fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1334:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&(the_table -> padding),2,1,fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c
long-hashtable.c: In function 'lnhash_create':
long-hashtable.c:43:45: warning: large integer implicitly truncated to unsigned type [-Woverflow]
the_table -> key_repeated_numbers = malloc(sizeof(short) * 0x100000000llu);
^~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c
core-bigtable.c: In function 'bigtable_readonly_result':
core-bigtable.c:70:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(write_ptr, loadjunc?sizeof(subjunc_result_t):sizeof(mapping_result_t), 1, global_context -> bigtable_cache_file_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-bigtable.c: In function 'bigtable_retrieve_cache':
core-bigtable.c:227:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread( current_cache -> big_margin_data , sizeof(short) * 3 * global_context -> config.big_margin_record_size , 1, global_context -> bigtable_cache_file_fp );
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-bigtable.c:228:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread( current_cache -> alignment_res , sizeof(mapping_result_t) * global_context -> config.multi_best_reads , 1, global_context -> bigtable_cache_file_fp );
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-bigtable.c:231:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread( current_cache -> subjunc_res , sizeof(subjunc_result_t) * global_context -> config.multi_best_reads , 1, global_context -> bigtable_cache_file_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-bigtable.c:237:5: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(global_context -> bigtable_cache_file_fp), new_file_size);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
readSummary.c: In function 'calc_junctions_from_cigar':
readSummary.c:347:15: warning: variable 'right_boundary' set but not used [-Wunused-but-set-variable]
unsigned int right_boundary = 0;
^~~~~~~~~~~~~~
readSummary.c: In function 'calc_total_frag_len':
readSummary.c:1804:15: warning: variable 'merged_section_indel_positions' set but not used [-Wunused-but-set-variable]
unsigned int merged_section_indel_positions[ MAXIMUM_INSERTION_IN_SECTION * 3 ][ MAXIMUM_INSERTION_IN_SECTION ];
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:1802:16: warning: variable 'merged_section_belong_R2' set but not used [-Wunused-but-set-variable]
unsigned char merged_section_belong_R2[ MAXIMUM_INSERTION_IN_SECTION * 3 ];
^~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:1801:16: warning: variable 'merged_section_belong_R1' set but not used [-Wunused-but-set-variable]
unsigned char merged_section_belong_R1[ MAXIMUM_INSERTION_IN_SECTION * 3 ];
^~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:1799:15: warning: variable 'merged_section_start_positions' set but not used [-Wunused-but-set-variable]
unsigned int merged_section_start_positions[ MAXIMUM_INSERTION_IN_SECTION * 3 ];
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function 'readSummary':
readSummary.c:4442:9: warning: variable 'curchr_name' set but not used [-Wunused-but-set-variable]
char * curchr_name, * fasta_contigs_fname;
^~~~~~~~~~~
readSummary.c:4441:15: warning: variable 'curpos' set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^~~~~~
readSummary.c:4441:7: warning: variable 'curchr' set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^~~~~~
readSummary.c: In function 'load_feature_info':
readSummary.c:927:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(file_line, MAX_LINE_LENGTH, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function 'process_pairer_reset':
readSummary.c:1555:3: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(global_context -> SAM_output_fp), 0);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function 'load_feature_info':
readSummary.c:865:10: warning: 'token_temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
char * token_temp, *chro_name;
^~~~~~~~~~
readSummary.c:929:10: warning: 'token_temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
char * token_temp;
^~~~~~~~~~
readSummary.c: In function 'calc_total_frag_len':
readSummary.c:1840:113: warning: array subscript is above array bounds [-Warray-bounds]
CIGAR_intervals_R2[R2_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R2[R2_i].insertion_start_pos[insmov_i];
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
readSummary.c:1868:113: warning: array subscript is above array bounds [-Warray-bounds]
CIGAR_intervals_R1[R1_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R1[R1_i].insertion_start_pos[insmov_i];
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
readSummary.c:1900:112: warning: array subscript is above array bounds [-Warray-bounds]
CIGAR_intervals_R1[R1_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R1[R1_i].insertion_start_pos[insmov_i];
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
readSummary.c:1909:112: warning: array subscript is above array bounds [-Warray-bounds]
CIGAR_intervals_R2[R2_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R2[R2_i].insertion_start_pos[insmov_i];
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
removeDupReads.c: In function 'parse_base_blocks':
removeDupReads.c:88:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_record, sizeof(base_block_temp_read_t), 1, block_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
removeDupReads.c:97:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_record, sizeof(base_block_temp_read_t), 1, block_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
SNPCalling.c: In function 'read_tmp_block':
SNPCalling.c:275:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SNP_rec, sizeof(SNP_rec),1 , tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SNPCalling.c:294:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_rec, sizeof(read_rec), 1, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SNPCalling.c:295:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SNPCalling.c:296:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read, sizeof(char), read_len, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SNPCalling.c:297:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qual, sizeof(char), read_len, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
index-builder.c: In function 'scan_gene_index':
index-builder.c:458:19: warning: variable 'table_no' set but not used [-Wunused-but-set-variable]
int file_number, table_no, i ,j;
^~~~~~~~
index-builder.c: In function 'main':
index-builder.c:1179:2: warning: ignoring return value of 'mkstemp', declared with attribute warn_unused_result [-Wunused-result]
mkstemp(tmp_fa_file);
^~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
qualityScores.c: In function 'finalise_qs_context':
qualityScores.c:82:12: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(qs_context -> gzfq_reader);
^~~~~~~~~~
In file included from qualityScores.c:24:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
qualityScores.c: In function 'rewind_qs_file':
qualityScores.c:275:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(qs_context -> gzfq_reader);
^~~~~~~~~~
In file included from qualityScores.c:24:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
qualityScores.c:282:29: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb");
^
qualityScores.c: In function 'start_qs_context':
qualityScores.c:313:29: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb");
^
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
propmapped.c: In function 'prop_PE':
propmapped.c:349:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len,1,1,fp);
^~~~~~~~~~~~~~~~~~~~~~~
propmapped.c:352:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_name,read_len,1,fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
propmapped.c:356:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&flags,1, sizeof(short), fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.5.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o coverageCount coverage_calc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
mkdir -p ../bin/utilities
mv subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/
mv repair coverageCount propmapped qualityScores removeDup subread-fullscan ../bin/utilities
###########################################################
# #
# Installation complete. #
# #
# Generated executables were copied to directory ../bin/ #
# #
###########################################################
make[2]: Leaving directory '/<<BUILDDIR>>/subread-1.5.1+dfsg/src'
dh_auto_build -- CC=arm-linux-gnueabihf-gcc
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.5.1+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.5.1+dfsg'
debian/tests/subread-tests /<<BUILDDIR>>/subread-1.5.1+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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.1
//=========================== indexBuilder setting ===========================\\
|| ||
|| Index name : ../small1 ||
|| Index space : base-space ||
|| Memory : 100 Mbytes ||
|| Repeat threshold : 100 repeats ||
|| Distance to next subread : 1 ||
|| ||
|| Input files : 1 file in total ||
|| o ../chr901.fa ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================================= Running ==================================\\
|| ||
|| Check the integrity of provided reference sequences ... ||
|| There were 4 notes for reference sequences. ||
|| The notes can be found in the log file, '../small1.log'. ||
|| Scan uninformative subreads in reference sequences ... ||
|| 8%, 0 mins elapsed, rate=111.7k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=140.4k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=168.5k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=190.1k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=211.4k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=230.4k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=245.6k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=262.8k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=277.7k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=291.1k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=304.6k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=314.4k bps/s, total=0m ||
|| 52 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=75.8k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=91.7k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=109.1k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=126.4k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=143.4k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=160.2k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=176.5k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=191.9k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=206.5k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=220.2k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=233.1k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=245.0k 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: 0.2 minutes. ||
|| Index ../small1 was successfully built! ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file : data/test-noerror-r1.fq ||
|| Output file : result/test-tmp.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| Min votes : 3 / 10 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (08-Dec-2016 06:19:33) ======================\\
|| ||
|| 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=2.2k reads per second ||
|| 39% completed, 0.3 mins elapsed, rate=2.4k reads per second ||
|| 46% completed, 0.3 mins elapsed, rate=2.6k reads per second ||
|| 53% completed, 0.3 mins elapsed, rate=2.7k reads per second ||
|| 60% completed, 0.3 mins elapsed, rate=2.9k reads per second ||
|| 74% completed, 0.3 mins elapsed, rate=0.8k reads per second ||
|| 83% completed, 0.3 mins elapsed, rate=0.8k reads per second ||
|| 91% completed, 0.3 mins elapsed, rate=0.9k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 reads ||
|| Mapped : 19997 reads (100.0%) ||
|| Indels : 7 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 5.8 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file : data/test-noerror-r1.fq ||
|| Output file : result/test-tmp.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| Min votes : 3 / 10 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (08-Dec-2016 06:25:29) ======================\\
|| ||
|| The input file contains base space reads. ||
|| WARNING - The specified Phred score offset (33) seems incorrect. ||
|| ASCII values of the quality scores of read bases included in ||
|| the first 3000 reads were found to be within the range of ||
|| [73,73]. ||
|| ||
|| Load the 1-th index block... ||
|| 33% completed, 0.7 mins elapsed, rate=1.3k reads per second ||
|| 39% completed, 0.8 mins elapsed, rate=1.3k reads per second ||
|| 46% completed, 0.8 mins elapsed, rate=1.3k reads per second ||
|| 53% completed, 0.8 mins elapsed, rate=1.4k reads per second ||
|| 60% completed, 0.8 mins elapsed, rate=1.3k reads per second ||
|| 74% completed, 0.9 mins elapsed, rate=0.3k reads per second ||
|| 83% completed, 0.9 mins elapsed, rate=0.3k reads per second ||
|| 91% completed, 0.9 mins elapsed, rate=0.4k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 reads ||
|| Mapped : 18758 reads (93.8%) ||
|| Indels : 5 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 7.5 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : data/test-noerror-r1.fq ||
|| Input file 2 : data/test-noerror-r2.fq ||
|| Output file : result/test-tmp.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (08-Dec-2016 06:33:08) ======================\\
|| ||
|| 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, 0.6 mins elapsed, rate=0.5k fragments per second ||
|| 39% completed, 0.6 mins elapsed, rate=0.6k fragments per second ||
|| 46% completed, 0.7 mins elapsed, rate=0.6k fragments per second ||
|| 53% completed, 0.7 mins elapsed, rate=0.6k fragments per second ||
|| 60% completed, 0.7 mins elapsed, rate=0.6k fragments per second ||
|| 74% completed, 0.8 mins elapsed, rate=0.3k fragments per second ||
|| 83% completed, 0.8 mins elapsed, rate=0.4k fragments per second ||
|| 91% completed, 0.8 mins elapsed, rate=0.4k 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 : 7.8 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : data/test-noerror-r1.fq ||
|| Input file 2 : data/test-noerror-r2.fq ||
|| Output file : result/test-tmp.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (08-Dec-2016 06:41:04) ======================\\
|| ||
|| 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, 0.7 mins elapsed, rate=0.6k fragments per second ||
|| 39% completed, 0.7 mins elapsed, rate=0.6k fragments per second ||
|| 46% completed, 0.7 mins elapsed, rate=0.6k fragments per second ||
|| 53% completed, 0.8 mins elapsed, rate=0.6k fragments per second ||
|| 60% completed, 0.8 mins elapsed, rate=0.7k fragments per second ||
|| 74% completed, 0.8 mins elapsed, rate=0.3k fragments per second ||
|| 83% completed, 0.9 mins elapsed, rate=0.3k fragments per second ||
|| 91% completed, 0.9 mins elapsed, rate=0.4k 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 : 7.4 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : data/test-error-r1.fq ||
|| Input file 2 : data/test-error-r2.fq ||
|| Output file : result/test-tmp.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (08-Dec-2016 06:48:37) ======================\\
|| ||
|| 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, 0.4 mins elapsed, rate=1.7k fragments per second ||
|| 39% completed, 0.4 mins elapsed, rate=1.7k fragments per second ||
|| 46% completed, 0.4 mins elapsed, rate=1.8k fragments per second ||
|| 53% completed, 0.4 mins elapsed, rate=1.8k fragments per second ||
|| 60% completed, 0.4 mins elapsed, rate=1.9k fragments per second ||
|| 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second ||
|| 83% completed, 0.4 mins elapsed, rate=0.6k fragments per second ||
|| 91% completed, 0.5 mins elapsed, rate=0.7k 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 : 5.6 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : data/test-err-mut-r1.fq.gz ||
|| Input file 2 : data/test-err-mut-r2.fq.gz ||
|| Output file : result/test-tmp.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : no ||
|| Read group name : MyTestGroup ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (08-Dec-2016 06:54:24) ======================\\
|| ||
|| The input file contains base space reads. ||
|| WARNING - The specified Phred score offset (33) seems incorrect. ||
|| ASCII values of the quality scores of read bases included in ||
|| the first 3000 reads were found to be within the range of ||
|| [50,50]. ||
|| ||
|| Load the 1-th index block... ||
|| 34% completed, 0.9 mins elapsed, rate=0.5k fragments per second ||
|| 40% completed, 1.0 mins elapsed, rate=0.5k fragments per second ||
|| 48% completed, 1.0 mins elapsed, rate=0.6k fragments per second ||
|| 53% completed, 1.0 mins elapsed, rate=0.6k fragments per second ||
|| 59% completed, 1.1 mins elapsed, rate=0.5k fragments per second ||
|| 67% completed, 1.2 mins elapsed, rate=0.4k fragments per second ||
|| 75% completed, 1.3 mins elapsed, rate=0.2k fragments per second ||
|| 83% completed, 1.3 mins elapsed, rate=0.2k fragments per second ||
|| 92% completed, 1.3 mins elapsed, rate=0.2k 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 : 6.3 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
307d561834a35eed71872011179c898d ../small1.00.b.array
3b39eb4b0aad6902d8a1be198cf2478d ../small1.00.b.tab
*************************************************
*** SINGLE-END READS NO ERROR ******
*************************************************
unmatched= 532 ; matched= 19465 ; unmapped= 1 ; reads= 19998 ;NN= 0
accuracy= 0.973396009401 ; sensitivity= 0.999949994999
paired_match= 0 ; paired= 0.0
*************************************************
*** SINGLE-END READS NO ERROR NO DUP ******
*************************************************
unmatched= 0 ; matched= 18758 ; unmapped= 1240 ; reads= 19998 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.93799379938
paired_match= 0 ; paired= 0.0
*************************************************
*** READS WITH NO ERROR ******
*************************************************
unmatched= 563 ; matched= 39432 ; unmapped= 1 ; reads= 39996 ;NN= 0
accuracy= 0.985923240405 ; sensitivity= 0.9999749975
paired_match= 39414 ; paired= 0.999543517955
*************************************************
*** READS NO ERROR, NO DUPLICATED REPORT ******
*************************************************
unmatched= 0 ; matched= 38431 ; unmapped= 1565 ; reads= 39996 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.960871087109
paired_match= 38430 ; paired= 0.99997397934
*************************************************
*** READS WITH ONLY SEQUENCING ERROR ******
*************************************************
unmatched= 454 ; matched= 33883 ; unmapped= 5663 ; reads= 40000 ;NN= 0
accuracy= 0.986778111076 ; sensitivity= 0.858425
paired_match= 29154 ; paired= 0.860431484815
*************************************************
*** READS WITH SEQUENCING ERROR AND MUTATION ***
*** SUBREAD IS RUN WITH LONG INDEL DETECTION ***
*************************************************
unmatched= 499 ; matched= 33456 ; unmapped= 6045 ; reads= 40002 ;NN= 0
accuracy= 0.985304078928 ; sensitivity= 0.848832558372
paired_match= 28432 ; paired= 0.849832615973
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.1
//=========================== indexBuilder setting ===========================\\
|| ||
|| Index name : ../small1 ||
|| Index space : base-space ||
|| Memory : 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=262.8k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=300.2k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=337.8k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=363.8k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=390.1k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=411.4k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=428.8k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=448.5k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=465.5k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=481.0k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=498.1k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=509.3k bps/s, total=0m ||
|| 2 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=186.0k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=194.2k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=207.8k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=220.3k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=233.1k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=246.6k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=260.6k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=274.9k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=289.6k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=303.7k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=319.4k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=333.2k bps/s, total=0m ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
|| [ 20.0% finished ] ||
|| [ 30.0% finished ] ||
|| [ 40.0% finished ] ||
|| [ 50.0% finished ] ||
|| [ 60.0% finished ] ||
|| [ 70.0% finished ] ||
|| [ 80.0% finished ] ||
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
|| Total running time: 0.1 minutes. ||
|| Index ../small1 was successfully built! ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.1
//============================= subjunc setting ==============================\\
|| ||
|| Function : Read alignment + Junction detection (RNA-Seq) ||
|| Input file 1 : data/junction-reads-A.fq ||
|| Input file 2 : data/junction-reads-B.fq ||
|| Output file : result/junctions.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 14 ||
|| Min read1 vote : 1 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (08-Dec-2016 07:00:57) ======================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [2,41] ||
|| Load the 1-th index block... ||
|| 41% completed, 0.9 mins elapsed, rate=0.6k fragments per second ||
|| 48% completed, 0.9 mins elapsed, rate=0.6k fragments per second ||
|| 54% completed, 0.9 mins elapsed, rate=0.6k fragments per second ||
|| 61% completed, 1.0 mins elapsed, rate=0.6k fragments per second ||
|| 77% completed, 1.0 mins elapsed, rate=0.2k fragments per second ||
|| 87% completed, 1.0 mins elapsed, rate=0.2k fragments per second ||
|| 97% completed, 1.0 mins elapsed, rate=0.3k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 16052 fragments ||
|| Mapped : 15914 fragments (99.1%) ||
|| Correctly paired : 14370 fragments ||
|| Junctions : 425 ||
|| Indels : 187 ||
|| ||
|| Running time : 8.6 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.1
//============================= subjunc setting ==============================\\
|| ||
|| Function : Read alignment + Junction/Fusion detection (RNA-Seq) ||
|| Input file 1 : data/junction-reads-A.fq ||
|| Input file 2 : data/junction-reads-B.fq ||
|| Output file : result/junctionsNfusions.bam (BAM) ||
|| Index name : ../small1 ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 28 ||
|| Min read1 vote : 1 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : no ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (08-Dec-2016 07:09:35) ======================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [2,41] ||
|| Load the 1-th index block... ||
|| 41% completed, 0.7 mins elapsed, rate=0.4k fragments per second ||
|| 48% completed, 0.7 mins elapsed, rate=0.4k fragments per second ||
|| 54% completed, 0.8 mins elapsed, rate=0.4k fragments per second ||
|| 61% completed, 0.8 mins elapsed, rate=0.4k fragments per second ||
|| 77% completed, 0.8 mins elapsed, rate=0.2k fragments per second ||
|| 87% completed, 0.9 mins elapsed, rate=0.3k fragments per second ||
|| 97% completed, 0.9 mins elapsed, rate=0.3k 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 : 4.3 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
================================================================================
FeatureCounts Basic Test
http://subread.sourceforge.net/
================================================================================
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.1
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 SAM file ||
|| P data/test-minimum.sam ||
|| ||
|| Output file : result/test-minimum.FC ||
|| Summary : result/test-minimum.FC.summary ||
|| Annotation : data/test-minimum.GTF (GTF) ||
|| Dir for temp files : result ||
|| ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Strand specific : no ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| Overlapping bases : 0.0% ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================================= Running ==================================\\
|| ||
|| Load annotation file data/test-minimum.GTF ... ||
|| Features : 23 ||
|| Meta-features : 7 ||
|| Chromosomes/contigs : 3 ||
|| ||
|| Process SAM file data/test-minimum.sam... ||
|| Paired-end reads are included. ||
|| Assign reads to features... ||
|| Total reads : 998 ||
|| Successfully assigned reads : 389 (39.0%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Read assignment finished. ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
================================================================================
Basic Test finished.
The results are in result/test-minimum.FC
================================================================================
================================================================================
FeatureCounts Chromosome Name Aliases Tests
http://subread.sourceforge.net/
================================================================================
Testing chromosome aliases ... [[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 minimum overlapping fraction ... [[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 Advanced fractions ... [[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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.1
//============================= exactSNP setting =============================\\
|| ||
|| Input file : data/test-in.BAM (BAM) ||
|| Output file : result/test-out.VCF ||
|| Reference genome : ../chr901.fa ||
|| ||
|| Threads : 1 ||
|| Min supporting reads : 1 ||
|| Min pct. of supporting reads : 0.0% ||
|| Min base quality score : 13 ||
|| Number of trimmed bases : 3 ||
|| ||
|| Q value cutoff : 10E-12.0 ||
|| P value upper bound : 0.00500 ||
|| Flanking windows size : 5 ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (08-Dec-2016 07:14:03) ======================\\
|| ||
|| Split BAM file into ./temp-snps-019422-001F7BB4051A-* ... ||
|| 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-1.5.1+dfsg'
fakeroot debian/rules binary-arch
dh binary-arch --parallel
dh_testroot -a -O--parallel
dh_prep -a -O--parallel
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.5.1+dfsg'
find /<<BUILDDIR>>/subread-1.5.1+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \;
mkdir -p /<<BUILDDIR>>/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1
help2man --no-info --help-option="''" --no-discard-stderr --name='an accurate and efficient aligner for mapping both genomic \
DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \
/<<BUILDDIR>>/subread-1.5.1+dfsg/bin/subread-align | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/subread-align.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='builds an base-space or color-space index using the reference sequences' \
/<<BUILDDIR>>/subread-1.5.1+dfsg/bin/subread-buildindex | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/subread-buildindex.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='an RNA-seq aligner suitable for all purposes of RNA-seq analyses' \
/<<BUILDDIR>>/subread-1.5.1+dfsg/bin/subjunc | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/subjunc.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='a highly efficient and accurate read summarization program' \
/<<BUILDDIR>>/subread-1.5.1+dfsg/bin/featureCounts | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/featureCounts.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='a SNP caller that discovers SNPs by testing signals against local background noises' \
/<<BUILDDIR>>/subread-1.5.1+dfsg/bin/exactSNP | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/exactSNP.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='detect short and long indels' \
/<<BUILDDIR>>/subread-1.5.1+dfsg/bin/subindel | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/subindel.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='scans the entire genome and reports all matches of a specified sequence' \
/<<BUILDDIR>>/subread-1.5.1+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/subread-fullscan.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='counting the coverage of mapped reads at each location on the entire reference genome' \
/<<BUILDDIR>>/subread-1.5.1+dfsg/bin/utilities/coverageCount | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/coverageCount.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='calculate the proportion of mapped reads/fragments' \
/<<BUILDDIR>>/subread-1.5.1+dfsg/bin/utilities/propmapped | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/propmapped.1;
for i in removeDup repair qualityScores ; do \
help2man --no-info --help-option="''" --no-discard-stderr --name='a component of subread suite' /<<BUILDDIR>>/subread-1.5.1+dfsg/bin/utilities/$i | debian/filter.pl > /<<BUILDDIR>>/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/$i.1; \
done
dh_auto_install
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.5.1+dfsg'
dh_install -a -O--parallel
dh_installdocs -a -O--parallel
dh_installchangelogs -a -O--parallel
dh_installman -a -O--parallel
dh_perl -a -O--parallel
dh_link -a -O--parallel
dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
dh_fixperms -a -O--parallel
dh_strip -a -O--parallel
dh_makeshlibs -a -O--parallel
dh_shlibdeps -a -O--parallel
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/removeDup debian/subread/usr/bin/subread-align debian/subread/usr/bin/subjunc debian/subread/usr/bin/subread-buildindex debian/subread/usr/lib/subread/coverageCount debian/subread/usr/lib/subread/repair debian/subread/usr/bin/exactSNP debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
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_1.5.1+dfsg-4_armhf.deb'.
dpkg-deb: building package 'subread' in '../subread_1.5.1+dfsg-4_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../subread_1.5.1+dfsg-4_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build subread-1.5.1+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2016-12-08T07:15:51Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
subread_1.5.1+dfsg-4_armhf.changes:
-----------------------------------
Format: 1.8
Date: Fri, 02 Dec 2016 08:22:05 +0100
Source: subread
Binary: subread subread-data
Architecture: armhf
Version: 1.5.1+dfsg-4
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
subread - toolkit for processing next-gen sequencing data
subread-data - data files for subread package
Changes:
subread (1.5.1+dfsg-4) unstable; urgency=medium
.
* Fix watch file
* debhelper 10
* remove outdated information from README.source
Checksums-Sha1:
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b6fcd9b41a4e801d65da6fbcca6f08a078669345 424334 subread_1.5.1+dfsg-4_armhf.deb
Checksums-Sha256:
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448be8e777af799ae95e71ca548e2e01152a62593daa55b897265cb530f40e9c 4907 subread_1.5.1+dfsg-4_armhf.buildinfo
786efe161996a1e4f5658358dcaa10aa1f4bd87cdd880d6883e6b2eaac1d0f28 424334 subread_1.5.1+dfsg-4_armhf.deb
Files:
d919857185931b9365d009c61c17a5eb 5543760 debug extra subread-dbgsym_1.5.1+dfsg-4_armhf.deb
fe4c065956c2f102c6f4ba234f698530 4907 science optional subread_1.5.1+dfsg-4_armhf.buildinfo
f5c9737774a72c24a31d0f019f337a24 424334 science optional subread_1.5.1+dfsg-4_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
subread-dbgsym_1.5.1+dfsg-4_armhf.deb
-------------------------------------
new debian package, version 2.0.
size 5543760 bytes: control archive=1088 bytes.
880 bytes, 13 lines control
1272 bytes, 12 lines md5sums
Package: subread-dbgsym
Source: subread
Version: 1.5.1+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6085
Depends: subread (= 1.5.1+dfsg-4)
Section: debug
Priority: extra
Homepage: http://sourceforge.net/projects/subread/
Description: Debug symbols for subread
Auto-Built-Package: debug-symbols
Build-Ids: 0ebbae63734582beaf042bd6cdc269bc4076db55 26ff1dbe8338a4f209e996606a2ddb1fb22855ef 5a9a0123270943025f1ee9318b607bb3b26df5e2 7334acfe14db6f7ce855d126f7d380edc0f0c5c4 8042ac5f1d3226ca9e3e36755055b89e07601267 962b1f7061b84d3df1f8994fc90bc09472d1b6ae 975161a57fe76cba4701f8b4914ea41b3690aef0 e57ba3f8842f6611e8b20ff3f881fd796ec016f6 e7ea9706b0531d3544c743b3a12ff9cc9e0c3c2f ecb8b6f11628b4468068afe0ac96254a433f5434 f7abd73ab8b4cb0b5384c6a377b76a43148d0edd f9bfb8262b816b871494dc85f0145552227f24f8
drwxr-xr-x root/root 0 2016-12-02 07:22 ./
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/debug/.build-id/0e/
-rw-r--r-- root/root 508436 2016-12-02 07:22 ./usr/lib/debug/.build-id/0e/bbae63734582beaf042bd6cdc269bc4076db55.debug
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/debug/.build-id/26/
-rw-r--r-- root/root 508332 2016-12-02 07:22 ./usr/lib/debug/.build-id/26/ff1dbe8338a4f209e996606a2ddb1fb22855ef.debug
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/debug/.build-id/5a/
-rw-r--r-- root/root 502232 2016-12-02 07:22 ./usr/lib/debug/.build-id/5a/9a0123270943025f1ee9318b607bb3b26df5e2.debug
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/debug/.build-id/73/
-rw-r--r-- root/root 504164 2016-12-02 07:22 ./usr/lib/debug/.build-id/73/34acfe14db6f7ce855d126f7d380edc0f0c5c4.debug
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/debug/.build-id/80/
-rw-r--r-- root/root 507044 2016-12-02 07:22 ./usr/lib/debug/.build-id/80/42ac5f1d3226ca9e3e36755055b89e07601267.debug
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/debug/.build-id/96/
-rw-r--r-- root/root 531080 2016-12-02 07:22 ./usr/lib/debug/.build-id/96/2b1f7061b84d3df1f8994fc90bc09472d1b6ae.debug
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/debug/.build-id/97/
-rw-r--r-- root/root 506884 2016-12-02 07:22 ./usr/lib/debug/.build-id/97/5161a57fe76cba4701f8b4914ea41b3690aef0.debug
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/debug/.build-id/e5/
-rw-r--r-- root/root 522296 2016-12-02 07:22 ./usr/lib/debug/.build-id/e5/7ba3f8842f6611e8b20ff3f881fd796ec016f6.debug
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/debug/.build-id/e7/
-rw-r--r-- root/root 506500 2016-12-02 07:22 ./usr/lib/debug/.build-id/e7/ea9706b0531d3544c743b3a12ff9cc9e0c3c2f.debug
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/debug/.build-id/ec/
-rw-r--r-- root/root 597308 2016-12-02 07:22 ./usr/lib/debug/.build-id/ec/b8b6f11628b4468068afe0ac96254a433f5434.debug
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/debug/.build-id/f7/
-rw-r--r-- root/root 504096 2016-12-02 07:22 ./usr/lib/debug/.build-id/f7/abd73ab8b4cb0b5384c6a377b76a43148d0edd.debug
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/debug/.build-id/f9/
-rw-r--r-- root/root 503540 2016-12-02 07:22 ./usr/lib/debug/.build-id/f9/bfb8262b816b871494dc85f0145552227f24f8.debug
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/share/
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-12-02 07:22 ./usr/share/doc/subread-dbgsym -> subread
subread_1.5.1+dfsg-4_armhf.deb
------------------------------
new debian package, version 2.0.
size 424334 bytes: control archive=1389 bytes.
623 bytes, 14 lines control
1819 bytes, 28 lines md5sums
Package: subread
Version: 1.5.1+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5595
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 2016-12-02 07:22 ./
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/bin/
-rwxr-xr-x root/root 489732 2016-12-02 07:22 ./usr/bin/exactSNP
-rwxr-xr-x root/root 563732 2016-12-02 07:22 ./usr/bin/featureCounts
-rwxr-xr-x root/root 461076 2016-12-02 07:22 ./usr/bin/subindel
-rwxr-xr-x root/root 465940 2016-12-02 07:22 ./usr/bin/subjunc
-rwxr-xr-x root/root 465876 2016-12-02 07:22 ./usr/bin/subread-align
-rwxr-xr-x root/root 477420 2016-12-02 07:22 ./usr/bin/subread-buildindex
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/lib/subread/
-rwxr-xr-x root/root 461076 2016-12-02 07:22 ./usr/lib/subread/coverageCount
-rwxr-xr-x root/root 461076 2016-12-02 07:22 ./usr/lib/subread/propmapped
-rwxr-xr-x root/root 461188 2016-12-02 07:22 ./usr/lib/subread/qualityScores
-rwxr-xr-x root/root 456932 2016-12-02 07:22 ./usr/lib/subread/removeDup
-rwxr-xr-x root/root 456932 2016-12-02 07:22 ./usr/lib/subread/repair
-rwxr-xr-x root/root 461028 2016-12-02 07:22 ./usr/lib/subread/subread-fullscan
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/share/
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/share/doc/subread/
-rw-r--r-- root/root 500 2016-12-02 07:22 ./usr/share/doc/subread/README.Debian
-rw-r--r-- root/root 3670 2016-08-25 04:20 ./usr/share/doc/subread/README.txt
-rw-r--r-- root/root 2083 2016-12-02 07:22 ./usr/share/doc/subread/changelog.Debian.gz
-rw-r--r-- root/root 1138 2016-12-02 07:22 ./usr/share/doc/subread/copyright
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/share/man/
drwxr-xr-x root/root 0 2016-12-02 07:22 ./usr/share/man/man1/
-rw-r--r-- root/root 594 2016-12-02 07:22 ./usr/share/man/man1/coverageCount.1.gz
-rw-r--r-- root/root 1173 2016-12-02 07:22 ./usr/share/man/man1/exactSNP.1.gz
-rw-r--r-- root/root 2726 2016-12-02 07:22 ./usr/share/man/man1/featureCounts.1.gz
-rw-r--r-- root/root 461 2016-12-02 07:22 ./usr/share/man/man1/propmapped.1.gz
-rw-r--r-- root/root 565 2016-12-02 07:22 ./usr/share/man/man1/qualityScores.1.gz
-rw-r--r-- root/root 495 2016-12-02 07:22 ./usr/share/man/man1/removeDup.1.gz
-rw-r--r-- root/root 477 2016-12-02 07:22 ./usr/share/man/man1/repair.1.gz
-rw-r--r-- root/root 347 2016-12-02 07:22 ./usr/share/man/man1/subindel.1.gz
-rw-r--r-- root/root 1528 2016-12-02 07:22 ./usr/share/man/man1/subjunc.1.gz
-rw-r--r-- root/root 1617 2016-12-02 07:22 ./usr/share/man/man1/subread-align.1.gz
-rw-r--r-- root/root 764 2016-12-02 07:22 ./usr/share/man/man1/subread-buildindex.1.gz
-rw-r--r-- root/root 377 2016-12-02 07:22 ./usr/share/man/man1/subread-fullscan.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 114024
Build-Time: 3651
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 384
Job: subread_1.5.1+dfsg-4
Machine Architecture: armhf
Package: subread
Package-Time: 4096
Source-Version: 1.5.1+dfsg-4
Space: 114024
Status: successful
Version: 1.5.1+dfsg-4
--------------------------------------------------------------------------------
Finished at 2016-12-08T07:15:52Z
Build needed 01:08:16, 114024k disc space