subread →
1.6.0+dfsg-1 →
armhf → 2017-11-23 05:53:09
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| subread 1.6.0+dfsg-1 (armhf) Thu, 23 Nov 2017 05:10:01 +0000 |
+==============================================================================+
Package: subread
Version: 1.6.0+dfsg-1
Source Version: 1.6.0+dfsg-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-e0c061ef-3b1f-4ab6-82f7-21f3659e9cf4' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.2 MB]
Fetched 22.6 MB in 24s (905 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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 15.4 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main subread 1.6.0+dfsg-1 (dsc) [2225 B]
Get:2 http://172.17.0.1/private buster-staging/main subread 1.6.0+dfsg-1 (tar) [15.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main subread 1.6.0+dfsg-1 (diff) [7868 B]
Fetched 15.4 MB in 2s (5421 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/subread-XsZU1s/subread-1.6.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/subread-XsZU1s' 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-x4eEqk/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-x4eEqk/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-x4eEqk/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-x4eEqk/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-x4eEqk/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-x4eEqk/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-x4eEqk/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-x4eEqk/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (2887 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 6 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-x4eEqk/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (19.9 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13068 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) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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-x4eEqk/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-x4eEqk/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-x4eEqk/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-x4eEqk/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-x4eEqk/apt_archive ./ Sources [509 B]
Get:5 copy:/<<BUILDDIR>>/resolver-x4eEqk/apt_archive ./ Packages [590 B]
Fetched 2432 B in 0s (2996 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install subread build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bc bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1
libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libmagic-mgc
libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libreadline6 libsigsegv2 libssl1.1 libtimedate-perl
libtool libxml2 m4 man-db mime-support po-debconf python python-minimal
python2.7 python2.7-minimal zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser
libmail-box-perl python-doc python-tk python2.7-doc binfmt-support
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bc bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3 libexpat1
libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libmagic-mgc
libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libreadline6 libsigsegv2 libssl1.1 libtimedate-perl
libtool libxml2 m4 man-db mime-support po-debconf python python-minimal
python2.7 python2.7-minimal sbuild-build-depends-subread-dummy zlib1g-dev
0 upgraded, 44 newly installed, 0 to remove and 6 not upgraded.
Need to get 24.3 MB of archives.
After this operation, 83.6 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-x4eEqk/apt_archive ./ sbuild-build-depends-subread-dummy 0.invalid.0 [876 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-3 [95.9 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.14 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.14-2 [393 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.14-2 [1091 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.14-1 [40.7 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.3-2 [73.6 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libssl1.1 armhf 1.1.0g-2 [1100 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.14-2 [1854 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.14-2 [292 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.14-1 [20.1 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.14-1 [155 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libreadline6 armhf 6.3-9 [122 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf bc armhf 1.06.95-9 [96.3 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [225 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.32-1 [105 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-1 [63.7 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-8 [7411 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-5 [609 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1+nmu1 [74.2 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 15 [16.2 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.1-1 [2653 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.10.5 [978 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.5 [162 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
debconf: delaying package configuration, since apt-utils is not installed
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No schema files found: doing nothing.
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Setting up libcroco3:armhf (0.6.12-1) ...
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Setting up autotools-dev (20161112.1+nmu1) ...
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Setting up help2man (1.47.5) ...
Setting up bsdmainutils (9.0.14) ...
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 (2.7.14-2) ...
Setting up autopoint (0.19.8.1-4) ...
Setting up libreadline6:armhf (6.3-9) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.040-1) ...
Setting up gettext (0.19.8.1-4) ...
Setting up python2.7 (2.7.14-2) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.32-1) ...
Setting up libpython-stdlib:armhf (2.7.14-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15.1-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up bc (1.06.95-9) ...
Setting up python (2.7.14-1) ...
Setting up libtool (2.4.6-2) ...
Setting up po-debconf (1.0.20) ...
Setting up dh-autoreconf (15) ...
Setting up dh-strip-nondeterminism (0.040-1) ...
Setting up debhelper (10.10.5) ...
Setting up sbuild-build-depends-subread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-17) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.29.1-6+rpi1 dpkg-dev_1.19.0.4 g++-7_7.2.0-14 gcc-7_7.2.0-14 libc6-dev_2.24-17 libstdc++-7-dev_7.2.0-14 libstdc++6_7.2.0-14 linux-libc-dev_4.9.51-1+rpi3+b1
Package versions: adduser_3.116 apt_1.6~alpha5 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1+nmu1 base-files_10+rpi1 base-passwd_3.5.44 bash_4.4-5 bc_1.06.95-9 binutils_2.29.1-6+rpi1 binutils-arm-linux-gnueabihf_2.29.1-6+rpi1 binutils-common_2.29.1-6+rpi1 bsdmainutils_9.0.14 bsdutils_1:2.30.2-0.1 build-essential_12.4 bzip2_1.0.6-8.1 coreutils_8.28-1 cpio_2.11+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-14 dash_0.5.8-2.5 debconf_1.5.65 debhelper_10.10.5 debianutils_4.8.3 dh-autoreconf_15 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.2-1+rpi1 dmsetup_2:1.02.145-4 dpkg_1.19.0.4 dpkg-dev_1.19.0.4 e2fslibs_1.43.7-1 e2fsprogs_1.43.7-1 fakeroot_1.22-2 fdisk_2.30.2-0.1 file_1:5.32-1 findutils_4.6.0+git+20170828-2 g++_4:7.2.0-1d1 g++-7_7.2.0-14 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-6-base_6.4.0-10 gcc-7_7.2.0-14 gcc-7-base_7.2.0-14 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.2-1+rpi1 gnupg-l10n_2.2.2-1+rpi1 gnupg-utils_2.2.2-1+rpi1 gpg_2.2.2-1+rpi1 gpg-agent_2.2.2-1+rpi1 gpg-wks-client_2.2.2-1+rpi1 gpg-wks-server_2.2.2-1+rpi1 gpgconf_2.2.2-1+rpi1 gpgsm_2.2.2-1+rpi1 gpgv_2.2.2-1+rpi1 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 help2man_1.47.5 hostname_3.18 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.1-3 libapt-pkg5.0_1.6~alpha5 libarchive-zip-perl_1.59-1 libasan4_7.2.0-14 libassuan0_2.4.3-3 libatomic1_7.2.0-14 libattr1_1:2.4.47-2 libaudit-common_1:2.8.1-2 libaudit1_1:2.8.1-2 libbinutils_2.29.1-6+rpi1 libblkid1_2.30.2-0.1 libbsd0_0.8.6-3 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-17 libc-dev-bin_2.24-17 libc6_2.24-17 libc6-dev_2.24-17 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.1 libcc1-0_7.2.0-14 libcilkrts5_7.2.0-14 libcomerr2_1.43.7-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.0-1 libdebconfclient0_0.232 libdevmapper1.02.1_2:1.02.145-4 libdpkg-perl_1.19.0.4 libdrm-common_2.4.85-1+rpi1 libdrm2_2.4.85-1+rpi1 libexpat1_2.2.3-2 libfakeroot_1.22-2 libfdisk1_2.30.2-0.1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.2.0-14 libgcc1_1:7.2.0-14 libgcrypt20_1.8.1-4 libgdbm3_1.8.3-14 libglib2.0-0_2.54.1-1 libgmp10_2:6.1.2+dfsg-1.1 libgnutls30_3.5.16-1 libgomp1_7.2.0-14 libgpg-error0_1.27-5 libhogweed4_3.3-2 libicu57_57.1-8 libidn11_1.33-2 libidn2-0_2.0.2-5 libip4tc0_1.6.1-2+b1 libisl15_0.18-1 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.2-0.1 libmpc3_1.0.3-2 libmpfr4_3.1.6-1 libncurses5_6.0+20170902-1 libncursesw5_6.0+20170902-1 libnettle6_3.3-2 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-4 libperl5.26_5.26.1-2 libpipeline1_1.5.0-1 libplymouth4_0.9.3-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3 libpython-stdlib_2.7.14-1 libpython2.7-minimal_2.7.14-2 libpython2.7-stdlib_2.7.14-2 libreadline6_6.3-9 libreadline7_7.0-3 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libsmartcols1_2.30.2-0.1 libsqlite3-0_3.21.0-1 libss2_1.43.7-1 libssl1.1_1.1.0g-2 libstdc++-7-dev_7.2.0-14 libstdc++6_7.2.0-14 libsystemd0_235-3 libtasn1-6_4.12-2.1 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170902-1 libtool_2.4.6-2 libubsan0_7.2.0-14 libudev1_235-3 libunistring2_0.9.7-2 libuuid1_2.30.2-0.1 libxml2_2.9.4+dfsg1-5 linux-base_4.5 linux-libc-dev_4.9.51-1+rpi3+b1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mime-support_3.60 mount_2.30.2-0.1 mountall_2.54 multiarch-support_2.24-17 ncurses-base_6.0+20170902-1 ncurses-bin_6.0+20170902-1 passwd_1:4.5-1 patch_2.7.5-1 perl_5.26.1-2 perl-base_5.26.1-2 perl-modules-5.26_5.26.1-2 pinentry-curses_1.0.0-3 plymouth_0.9.3-1 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.14-1 python-minimal_2.7.14-1 python2.7_2.7.14-2 python2.7-minimal_2.7.14-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-subread-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.11 systemd_235-3 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2017c-1 udev_235-3 util-linux_2.30.2-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| 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 Nov 17 16:03:42 2017 UTC
gpgv: using RSA key 1CF792111B5228B0
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./subread_1.6.0+dfsg-1.dsc
dpkg-source: info: extracting subread in /<<BUILDDIR>>/subread-1.6.0+dfsg
dpkg-source: info: unpacking subread_1.6.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking subread_1.6.0+dfsg-1.debian.tar.xz
dpkg-source: info: applying typo.patch
dpkg-source: info: applying fix_ftbfs_kfreebsd.patch
dpkg-source: info: applying arch_specific_flags.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-e0c061ef-3b1f-4ab6-82f7-21f3659e9cf4
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package subread
dpkg-buildpackage: info: source version 1.6.0+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build subread-1.6.0+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --parallel
dh_auto_clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.6.0+dfsg'
cd src; make -f Makefile.Linux clean
make[2]: Entering directory '/<<BUILDDIR>>/subread-1.6.0+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-1.6.0+dfsg/src'
dh_clean
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.6.0+dfsg'
debian/rules build-arch
dh build-arch --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-1.6.0+dfsg'
cd src; make -f Makefile.Linux
make[2]: Entering directory '/<<BUILDDIR>>/subread-1.6.0+dfsg/src'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c
core.c: In function 'print_in_box':
core.c:159:7: warning: variable 'is_R_linebreak' set but not used [-Wunused-but-set-variable]
char is_R_linebreak=0, * content, *out_line_buff;
^~~~~~~~~~~~~~
core.c: In function 'convert_GZ_to_FQ':
core.c:898:19: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
gzFile * rawfp = gzopen(fname, "r");
^~~~~~
core.c:909:25: warning: passing argument 1 of 'gzgets' from incompatible pointer type [-Wincompatible-pointer-types]
char * bufr =gzgets(rawfp, linebuff, 3000);
^~~~~
In file included from subread.h:26:0,
from core.c:43:
/usr/include/zlib.h: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:920:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(rawfp);
^~~~~
In file included from subread.h:26:0,
from core.c:43:
/usr/include/zlib.h: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 'add_head_tail_cut_softclipping':
core.c:1216:24: warning: implicit declaration of function 'get_offset_maximum_chro_pos' [-Wimplicit-function-declaration]
is_start_in_chro = get_offset_maximum_chro_pos(global_context,linear_cursor);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:1215:27: warning: variable 'is_end_in_chro' set but not used [-Wunused-but-set-variable]
int is_start_in_chro, is_end_in_chro;
^~~~~~~~~~~~~~
core.c:1215:9: warning: variable 'is_start_in_chro' set but not used [-Wunused-but-set-variable]
int is_start_in_chro, is_end_in_chro;
^~~~~~~~~~~~~~~~
core.c: In function 'calc_tlen':
core.c:1604:16: 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:2274:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret;
^~~
core.c: In function 'write_realignments_for_fragment':
core.c:2490:21: warning: variable 'raw_r2' set but not used [-Wunused-but-set-variable]
mapping_result_t * raw_r2 = NULL;
^~~~~~
core.c:2487:21: 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:2584:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret;
^~~
core.c: In function 'do_voting':
core.c:3234:9: 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:3144:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret, xk1;
^~~
core.c: In function 'convert_BAM_to_SAM':
core.c:829:28: warning: '%s' directive writing up to 299 bytes into a region of size 200 [-Wformat-overflow=]
sprintf(temp_file_name, "%s.sam", global_context->config.temp_file_prefix);
^~
In file included from /usr/include/stdio.h:938:0,
from core.c:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 304 bytes into a destination of size 200
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:829:28: warning: '%s' directive writing up to 299 bytes into a region of size 200 [-Wformat-overflow=]
sprintf(temp_file_name, "%s.sam", global_context->config.temp_file_prefix);
^~
In file included from /usr/include/stdio.h:938:0,
from core.c:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 304 bytes into a destination of size 200
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:829:28: warning: '%s' directive writing up to 299 bytes into a region of size 200 [-Wformat-overflow=]
sprintf(temp_file_name, "%s.sam", global_context->config.temp_file_prefix);
^~
In file included from /usr/include/stdio.h:938:0,
from core.c:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 5 and 304 bytes into a destination of size 200
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c: In function 'convert_GZ_to_FQ':
core.c:903:28: warning: '%s' directive writing up to 299 bytes into a region of size 200 [-Wformat-overflow=]
sprintf(temp_file_name, "%s-%d.fq", global_context->config.temp_file_prefix, half_n);
^~
In file included from /usr/include/stdio.h:938:0,
from core.c:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 6 and 315 bytes into a destination of size 200
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c: In function 'write_single_fragment':
core.c:2080:71: warning: '%s' directive output may be truncated writing up to 299 bytes into a region of size 94 [-Wformat-truncation=]
snprintf(extra_additional_1+strlen(extra_additional_1),100, "\tRG:Z:%s", global_context->config.read_group_id);
^~
In file included from /usr/include/stdio.h:938:0,
from core.c:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 7 and 306 bytes into a destination of size 100
return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:2081:71: warning: '%s' directive output may be truncated writing up to 299 bytes into a region of size 94 [-Wformat-truncation=]
snprintf(extra_additional_2+strlen(extra_additional_2),100, "\tRG:Z:%s", global_context->config.read_group_id);
^~
In file included from /usr/include/stdio.h:938:0,
from core.c:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 7 and 306 bytes into a destination of size 100
return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c: In function 'write_sam_headers':
core.c:3945:32: warning: '%s' directive output may be truncated writing up to 299 bytes into a region of size 292 [-Wformat-truncation=]
snprintf(obuf,299, "@RG\tID:%s%s",context->config.read_group_id, context->config.read_group_txt);
^~
In file included from /usr/include/stdio.h:938:0,
from core.c:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 8 and 606 bytes into a destination of size 299
return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c: In function 'load_global_context':
core.c:4186:21: warning: '.reads' directive writing 6 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.reads", context->config.index_prefix);
^~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from core.c:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 7 and 306 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:4200:22: warning: '.00.c.tab' directive writing 9 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.00.c.tab", context->config.index_prefix);
^~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from core.c:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 10 and 309 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:4202:22: warning: '.00.b.tab' directive writing 9 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.00.b.tab", context->config.index_prefix);
^~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from core.c:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 10 and 309 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:4213:26: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b');
^~~~
In file included from /usr/include/stdio.h:938:0,
from core.c:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 10 and 318 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c: In function 'read_chunk_circles':
core.c:3663:26: warning: '%02d' directive writing between 2 and 10 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
^~~~
core.c:3663:22: note: directive argument in the range [0, 2147483647]
sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
^~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from core.c:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 12 and 319 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:3680:28: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.%02d.%c.tab", global_context->config.index_prefix, global_context->current_index_block_number, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
^~~~
In file included from /usr/include/stdio.h:938:0,
from core.c:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 10 and 318 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:3684:28: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, global_context->current_index_block_number, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
^~~~
In file included from /usr/include/stdio.h:938:0,
from core.c:26:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 12 and 320 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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:995:12: 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:2046:8: warning: variable 'sp2s' set but not used [-Wunused-but-set-variable]
char sp2s[200];
^~~~
core-junction.c: In function 'final_CIGAR_quality':
core-junction.c:2905:13: warning: variable 'debug_ptr' set but not used [-Wunused-but-set-variable]
char * debug_ptr = read_text;
^~~~~~~~~
core-junction.c:2938:13: warning: variable 'debug_ptr' set but not used [-Wunused-but-set-variable]
char * debug_ptr = read_text + read_cursor;
^~~~~~~~~
core-junction.c: In function 'finalise_explain_CIGAR':
core-junction.c:3294:94: warning: variable 'total_coverage_length' set but not used [-Wunused-but-set-variable]
int final_qual = 0, applied_mismatch = 0, non_clipped_length = 0, total_indel_length = 0, total_coverage_length = 0, final_MATCH = 0, chromosomal_length = 0, full_section_clipped = 0;
^~~~~~~~~~~~~~~~~~~~~
core-junction.c:3272:28: warning: variable 'isCigarOK' set but not used [-Wunused-but-set-variable]
int mismatch_bases = 0, isCigarOK = 0;
^~~~~~~~~
core-junction.c:3110:23: 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:5676:23: warning: variable 'candBrkPlist' set but not used [-Wunused-but-set-variable]
chromosome_event_t * candBrkPlist [_PQR_LIST_SIZE];
^~~~~~~~~~~~
core-junction.c: In function 'write_fusion_final_results':
core-junction.c:4125:38: warning: '.breakpoints.txt' directive output may be truncated writing 16 bytes into a region of size between 1 and 300 [-Wformat-truncation=]
snprintf(fn2, MAX_FILE_NAME_LENGTH, "%s.breakpoints.txt", global_context->config.output_prefix);
^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from core-junction.c:21:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 17 and 316 bytes into a destination of size 300
return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-junction.c: In function 'write_junction_final_results':
core-junction.c:4248:38: warning: '.junction.bed' directive output may be truncated writing 13 bytes into a region of size between 1 and 300 [-Wformat-truncation=]
snprintf(fn2, MAX_FILE_NAME_LENGTH, "%s.junction.bed", global_context->config.output_prefix);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from core-junction.c:21:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 14 and 313 bytes into a destination of size 300
return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c
core-indel.c: In function 'find_new_indels':
core-indel.c:2051:9: warning: variable 'best_j' set but not used [-Wunused-but-set-variable]
int best_j=0, best_score=-99999, is_ambiguous_indel= 0;
^~~~~~
core-indel.c: In function 'print_indel_table':
core-indel.c:2255:24: warning: unused variable 'event_body' [-Wunused-variable]
chromosome_event_t * event_body = indel_context -> event_space_dynamic +xk1;
^~~~~~~~~~
core-indel.c:2269:26: warning: unused variable 'event_body' [-Wunused-variable]
chromosome_event_t * event_body = indel_context -> event_space_dynamic + (env_array[env_i]-1);
^~~~~~~~~~
core-indel.c:2265:17: warning: unused variable 'entry_pos' [-Wunused-variable]
unsigned int entry_pos = cursor->key - NULL;
^~~~~~~~~
core-indel.c: In function 'full_indel_alignment':
core-indel.c:3436:41: warning: variable 'best_right' set but not used [-Wunused-but-set-variable]
int best_edge_score = -1, best_left, best_right;
^~~~~~~~~~
core-indel.c:3436:30: warning: variable 'best_left' set but not used [-Wunused-but-set-variable]
int best_edge_score = -1, best_left, best_right;
^~~~~~~~~
core-indel.c: In function 'find_potential_ultralong_indels':
core-indel.c:3535:24: warning: variable 'best_c2_location' set but not used [-Wunused-but-set-variable]
int best_match = -1, best_c2_location = -1;
^~~~~~~~~~~~~~~~
core-indel.c: In function 'finalise_pileup_file':
core-indel.c:3813:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3814:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_text, sizeof(char), read_len, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3815:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3892:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3893:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_text, sizeof(char), read_len, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3894:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c: In function 'finalise_pileup_file_by_debrujin':
core-indel.c:4256:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:4257:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_text, sizeof(char), read_len, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:4258:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c: In function 'write_indel_final_results':
core-indel.c:2288:38: warning: '.indel' directive output may be truncated writing 6 bytes into a region of size between 1 and 300 [-Wformat-truncation=]
snprintf(fn2, MAX_FILE_NAME_LENGTH, "%s.indel", global_context->config.output_prefix);
^~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from subread.h:25,
from gene-value-index.h:24,
from core-indel.c:29:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 7 and 306 bytes into a destination of size 300
return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c: In function 'write_local_reassembly':
core-indel.c:2498:26: warning: '-' directive writing 1 byte into a region of size between 0 and 299 [-Wformat-overflow=]
sprintf(temp_file_name,"%s@%s-%04u.bin", global_context -> config.temp_file_prefix, chro_name , chro_offset / BASE_BLOCK_LENGTH );
^~~~~~~~~~~~~~~~
core-indel.c:2498:26: note: using the range [0, 4294967295] for directive argument
In file included from /usr/include/stdio.h:938:0,
from subread.h:25,
from gene-value-index.h:24,
from core-indel.c:29:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output 11 or more bytes (assuming 310) into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c: In function 'finalise_long_insertions_by_hashtable':
core-indel.c:4291:20: warning: '.reassembly.fa' directive writing 14 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf(tmp_fname,"%s.reassembly.fa", global_context->config.output_prefix);
^~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from subread.h:25,
from gene-value-index.h:24,
from core-indel.c:29:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 15 and 314 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:4303:27: warning: '-' directive writing 1 byte into a region of size between 0 and 299 [-Wformat-overflow=]
sprintf(temp_file_name,"%s@%s-%04u.bin", global_context -> config.temp_file_prefix, global_context -> chromosome_table.read_names+chro_i*MAX_CHROMOSOME_NAME_LEN , block_no );
^~~~~~~~~~~~~~~~
core-indel.c:4303:27: note: using the range [0, 4294967295] for directive argument
In file included from /usr/include/stdio.h:938:0,
from subread.h:25,
from gene-value-index.h:24,
from core-indel.c:29:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output 11 or more bytes (assuming 310) into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c
sambam-file.c: In function 'PBam_get_next_zchunk':
sambam-file.c:356:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&ID1, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:357:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&ID2, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:358:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&CM, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:359:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&FLG, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:368:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&XLEN,1, 2, bam_fp );
^~~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:376:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SI1, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:377:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SI2, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:383:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&BSIZE_MID, 1,2 , bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:395:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(buffer, 1, CDATA_READING, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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:785:6: warning: variable 'last_end' set but not used [-Wunused-but-set-variable]
int last_end=0, last_offset = 0, cursor = 0;
^~~~~~~~
gene-algorithms.c:784:9: 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:1197:28: 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:1746:6: 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:2387:7: 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-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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'; did you mean 'gzopen64'? [-Wimplicit-function-declaration]
return fopen64(fname, mode);
^~~~~~~
gzopen64
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:2784:11: warning: variable 'ref_name' set but not used [-Wunused-but-set-variable]
char ref_name[MAX_CHROMOSOME_NAME_LEN];
^~~~~~~~
input-files.c: In function 'SAM_pairer_make_dummy':
input-files.c:3439:31: warning: pointer targets in passing argument 1 of 'SAM_pairer_iterate_int_tags' differ in signedness [-Wpointer-sign]
SAM_pairer_iterate_int_tags(bin1+bin1ptr,block1len + 4 - bin1ptr, "NH", &NHtag);
^~~~
input-files.c:3284:5: note: expected 'unsigned char *' but argument is of type 'char *'
int SAM_pairer_iterate_int_tags(unsigned char * bin, int bin_len, char * tag_name, int * saved_value){
^~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:3440:31: warning: pointer targets in passing argument 1 of 'SAM_pairer_iterate_int_tags' differ in signedness [-Wpointer-sign]
SAM_pairer_iterate_int_tags(bin1+bin1ptr,block1len + 4 - bin1ptr, "HI", &HItag);
^~~~
input-files.c:3284:5: note: expected 'unsigned char *' but argument is of type 'char *'
int SAM_pairer_iterate_int_tags(unsigned char * bin, int bin_len, char * tag_name, int * saved_value){
^~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:3408:9: warning: unused variable 'tmptr' [-Wunused-variable]
char * tmptr = NULL;
^~~~~
input-files.c: In function 'fix_write_block':
input-files.c:4464:23: 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:5014:9: warning: variable 'ref_name' set but not used [-Wunused-but-set-variable]
char ref_name[MAX_CHROMOSOME_NAME_LEN];
^~~~~~~~
input-files.c: In function 'SAM_pairer_long_cigar_run':
input-files.c:5259:20: warning: unused variable 'is_longcigar' [-Wunused-variable]
int x1, nch = 0, is_longcigar = 0, binptr = 0;
^~~~~~~~~~~~
input-files.c:5254:7: warning: unused variable 'out_bin_ptr' [-Wunused-variable]
int out_bin_ptr = 0;
^~~~~~~~~~~
input-files.c:5252:7: warning: unused variable 'disk_is_full' [-Wunused-variable]
int disk_is_full = 0;
^~~~~~~~~~~~
input-files.c: In function 'geinput_next_char':
input-files.c:532:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(out_buf, 1999,input->input_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'SAM_pairer_writer_reset':
input-files.c:3558:2: 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:3768:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:3780:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 4, fp);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'SAM_pairer_osr_next_bin':
input-files.c:3789:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:3793:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 4, fp);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:3795:2: 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:4443:4: 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:5473:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:5479:6: 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:5482:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len,2,1,bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:5488:6: 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:5541:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:5547:6: 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:5551:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, 2,1 , bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:5554:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_line_buf, 1, read_len, bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'SAM_pairer_rescure_orphants_max_FP':
input-files.c:4038:22: warning: '-LEVELMERGE.tmp' directive writing 15 bytes into a region of size between 0 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s-LEVELMERGE.tmp", pairer->tmp_file_prefix);
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from input-files.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 16 and 316 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:4046:24: warning: '-TH' directive writing 3 bytes into a region of size between 0 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s-TH%02d-BK%06d.tmp", pairer->tmp_file_prefix, thno, bkno);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:4046:24: note: directive argument in the range [0, 2147483647]
input-files.c:4046:24: note: directive argument in the range [0, 2147483647]
In file included from /usr/include/stdio.h:938:0,
from input-files.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 19 and 331 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'merge_level_fps':
input-files.c:3821:21: warning: '-MERGE-TMP.tmp' directive writing 14 bytes into a region of size between 0 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s-MERGE-TMP.tmp", pairer->tmp_file_prefix);
^~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from input-files.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 15 and 315 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'SAM_pairer_probe_maxfp':
input-files.c:3934:23: warning: '-TH' directive writing 3 bytes into a region of size between 0 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s-TH%02d-BK%06d.tmp", pairer->tmp_file_prefix, thno, bkno);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:3934:23: note: directive argument in the range [0, 2147483647]
input-files.c:3934:23: note: directive argument in the range [0, 2147483647]
In file included from /usr/include/stdio.h:938:0,
from input-files.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 19 and 331 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:3948:22: warning: '-FTEST-' directive writing 7 bytes into a region of size between 0 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s-FTEST-%d.tmp", pairer->tmp_file_prefix, bkno);
^~~~~~~~~~~~~~~~~
input-files.c:3948:22: note: directive argument in the range [0, 5]
In file included from /usr/include/stdio.h:938:0,
from input-files.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 13 and 313 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:3960:23: warning: '-TH' directive writing 3 bytes into a region of size between 0 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s-TH%02d-BK%06d.tmp", pairer->tmp_file_prefix, thno, bkno);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:3960:23: note: directive argument in the range [0, 2147483647]
input-files.c:3960:23: note: directive argument in the range [0, 2147483647]
In file included from /usr/include/stdio.h:938:0,
from input-files.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 19 and 331 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:3988:24: warning: '-TH' directive writing 3 bytes into a region of size between 0 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s-TH%02d-BK%06d.tmp", pairer->tmp_file_prefix, thno, bkno);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:3988:24: note: directive argument in the range [0, 2147483647]
input-files.c:3988:24: note: directive argument in the range [0, 2147483647]
In file included from /usr/include/stdio.h:938:0,
from input-files.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 19 and 331 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:3998:25: warning: '-LEVELMERGE.tmp' directive writing 15 bytes into a region of size between 0 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s-LEVELMERGE.tmp", pairer->tmp_file_prefix);
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from input-files.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 16 and 316 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'SAM_pairer_update_orphant_table':
input-files.c:4180:21: warning: '-TH' directive writing 3 bytes into a region of size between 0 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s-TH%02d-BK%06d.tmp", pairer->tmp_file_prefix, thread_context -> thread_id, thread_context -> orphant_block_no++);
^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from input-files.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 19 and 333 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'SAM_pairer_fix_format':
input-files.c:4546:20: warning: '.fixbam' directive writing 7 bytes into a region of size between 0 and 300 [-Wformat-overflow=]
sprintf(tmpfname, "%s.fixbam", pairer -> tmp_file_prefix);
^~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from input-files.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 8 and 308 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c: In function 'SAM_nosort_run_once':
input-files.c:5002:10: warning: argument 1 value '4294967295' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
char * header_txt = malloc(max(1000000,pairer->BAM_l_text));
^~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/bits/string2.h:319:0,
from /usr/include/string.h:630,
from input-files.c:23:
/usr/include/stdlib.h:427:14: note: in a call to allocation function 'malloc' declared here
extern void *malloc (size_t __size) __THROW __attribute_malloc__ __wur;
^~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c
gene-value-index.c: In function 'is_offset_in_chro':
gene-value-index.c:60:7: warning: unused variable 'padding' [-Wunused-variable]
int padding = offsets -> appendix2 - NULL;
^~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-bigtable.c: In function 'init_bigtable_results':
core-bigtable.c:127:26: warning: '%02d' directive writing 2 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
sprintf(tmpfname, "%s-%02d-align.bin", global_context -> config.temp_file_prefix, 0);
^~~~
In file included from /usr/include/stdio.h:938:0,
from core-bigtable.c:1:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 14 and 313 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-bigtable.c: In function 'finalise_bigtable_results':
core-bigtable.c:317:26: warning: '%02d' directive writing 2 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
sprintf(tmpfname, "%s-%02d-align.bin", global_context -> config.temp_file_prefix, 0);
^~~~
In file included from /usr/include/stdio.h:938:0,
from core-bigtable.c:1:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 14 and 313 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c
echo " " > longread-mapping/make.version
rm -f longread-mapping/*.o
cd longread-mapping && make
make[3]: Entering directory '/<<BUILDDIR>>/subread-1.6.0+dfsg/src/longread-mapping'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.0"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMsorted-hashtable.o LRMsorted-hashtable.c
LRMsorted-hashtable.c: In function 'LRMgehash_load_option':
LRMsorted-hashtable.c:271:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
LRMsorted-hashtable.c:276:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
LRMsorted-hashtable.c:279:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LRMsorted-hashtable.c:283:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(result ,option_length,1,fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LRMsorted-hashtable.c: In function 'LRMgehash_load':
LRMsorted-hashtable.c:310:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
LRMsorted-hashtable.c:323:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
LRMsorted-hashtable.c:326:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LRMsorted-hashtable.c:329:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&(the_table -> index_gap),2,1,fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LRMsorted-hashtable.c:331:5: 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-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.0"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMbase-index.o LRMbase-index.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.0"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMchro-event.o LRMchro-event.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.0"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMhelper.o LRMhelper.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.0"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.0"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMfile-io.o LRMfile-io.c
LRMfile-io.c: In function 'LRMload_offsets':
LRMfile-io.c:423:14: warning: '.reads' directive writing 6 bytes into a region of size between 1 and 500 [-Wformat-overflow=]
sprintf(fn, "%s.reads", context->index_prefix);
^~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from LRMfile-io.c:19:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 7 and 506 bytes into a destination of size 500
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LRMfile-io.c: In function 'LRMsambam_write_header':
LRMfile-io.c:501:102: warning: '%s' directive writing up to 9999 bytes into a region of size 9935 [-Wformat-overflow=]
wrlen = sprintf(header_line, "@PG\tID:subread-long-read-mapping\tPN:subread-long-read-mapping\tCL:%s\n", context -> user_command_line);
^~
In file included from /usr/include/stdio.h:938:0,
from LRMfile-io.c:19:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 67 and 10066 bytes into a destination of size 10000
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.0"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -D SUBREAD_VERSION=\""1.6.0"\" -fmessage-length=0 -ggdb -o sublong longread-mapping.c LRMsorted-hashtable.o LRMbase-index.o LRMchro-event.o LRMhelper.o seek-zlib.o LRMfile-io.o hashtable.o -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
longread-mapping.c: In function 'LRMread_final_result_merge':
longread-mapping.c:1174:68: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=]
LRMprintf("INIT_LOC of SEG %d, CAND %d: strand: %s read_pos: %ld + %d, chro_pos: %s\tV=%d\n",x1,x2,(iteration_context -> segment_best_masks[x1][x2] & LRMIS_NEGATIVE_STRAND)?"NEG":"POS" , iteration_context -> segment_texts[x1] - iteration_context -> read_text, LRMfind_leftS_size(iteration_context -> segment_cigars[x1][x2]) ,ptxt, seg_cand_votes);
~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
%d
longread-mapping.c: In function 'LRMload_index':
longread-mapping.c:383:26: warning: '.00.b.tab' directive writing 9 bytes into a region of size between 1 and 500 [-Wformat-overflow=]
sprintf(indextab_fname, "%s.00.b.tab", context -> index_prefix);
^~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from longread-mapping.c:19:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 10 and 509 bytes into a destination of size 500
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
longread-mapping.c:386:26: warning: '.00.b.array' directive writing 11 bytes into a region of size between 1 and 500 [-Wformat-overflow=]
sprintf(indextab_fname, "%s.00.b.array", context -> index_prefix);
^~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from longread-mapping.c:19:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 12 and 511 bytes into a destination of size 500
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
longread-mapping.c:386:26: warning: '.00.b.array' directive writing 11 bytes into a region of size between 1 and 500 [-Wformat-overflow=]
sprintf(indextab_fname, "%s.00.b.array", context -> index_prefix);
^~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from longread-mapping.c:19:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 12 and 511 bytes into a destination of size 500
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mv sublong ../
make[3]: Leaving directory '/<<BUILDDIR>>/subread-1.6.0+dfsg/src/longread-mapping'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
tx-unique.c: In function 'txunique_parse_options':
tx-unique.c:391:6: warning: unused variable 'sort_needed' [-Wunused-variable]
int sort_needed = 0;
^~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
readSummary.c: In function 'calc_junctions_from_cigar':
readSummary.c:382:15: 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:1873:15: 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:1871:16: 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:1870:16: 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:1868:15: warning: variable 'merged_section_start_positions' set but not used [-Wunused-but-set-variable]
unsigned int merged_section_start_positions[ MAXIMUM_INSERTION_IN_SECTION * 3 ];
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function 'compress_read_detail_BAM':
readSummary.c:2474:8: warning: unused variable 'write_ptr' [-Wunused-variable]
int write_ptr, bin_len = write_end - write_start;
^~~~~~~~~
In file included from readSummary.c:41:0:
readSummary.c: In function 'vote_and_add_count':
readSummary.c:3368:22: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'long int' [-Wformat=]
SUBREADprintf("OVERLAP TO %ld : %u >= %u ; EXON_SPAN=%ld ( %ld ~ %ld)\n", tested_exon_id, tested_exon_overlap_any_read, applied_overlapping_threshold, exon_span, global_context -> exontable_start[tested_exon_id], global_context -> exontable_stop[tested_exon_id]);
^
subread.h:122:44: note: in definition of macro 'SUBREADprintf'
#define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
^~~~~~~~~~~
readSummary.c: In function 'fc_thread_start_threads':
readSummary.c:4009:23: warning: too many arguments for format [-Wformat-extra-args]
sprintf(tmp_fname, "%s.featureCounts%s", global_context -> raw_input_file_name, global_context -> input_file_short_name, global_context -> is_read_details_out == FILE_TYPE_BAM?".bam":(global_context -> is_read_details_out == FILE_TYPE_SAM?".sam":""));
^~~~~~~~~~~~~~~~~~~~
readSummary.c: In function 'readSummary':
readSummary.c:5173:9: warning: variable 'curchr_name' set but not used [-Wunused-but-set-variable]
char * curchr_name, * fasta_contigs_fname;
^~~~~~~~~~~
readSummary.c:5172:15: warning: variable 'curpos' set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^~~~~~
readSummary.c:5172:7: warning: variable 'curchr' set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^~~~~~
readSummary.c: In function 'load_feature_info':
readSummary.c:960:3: 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:1627:3: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(global_context -> read_details_out_FP), 0);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function 'process_pairer_header':
readSummary.c:1690:11: warning: 'id_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(id_end < 1)id_end = rcursor;
^
readSummary.c: In function 'calc_total_frag_len':
readSummary.c:1909:113: 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:1937:113: 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:1969:112: 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:1978:112: warning: array subscript is above array bounds [-Warray-bounds]
CIGAR_intervals_R2[R2_i].insertion_start_pos[ins_dist_i] = CIGAR_intervals_R2[R2_i].insertion_start_pos[insmov_i];
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
readSummary.c: In function 'fc_thread_start_threads':
readSummary.c:4114:23: warning: '/temp-core-' directive writing 11 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf(rand_prefix, "%s/temp-core-%06u-%s.sam", global_context -> temp_file_dir, getpid(), MAC_or_random);
^~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:4114:23: note: using the range [0, 4294967295] for directive argument
In file included from /usr/include/stdio.h:938:0,
from readSummary.c:23:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output 23 or more bytes (assuming 322) into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:4115:55: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
if(global_context -> use_stdin_file) sprintf(new_fn, "<%s", global_context -> input_file_name );
^~~~~
In file included from /usr/include/stdio.h:938:0,
from readSummary.c:23:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 301 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function 'main':
readSummary.c:6159:34: warning: '%g' directive writing between 1 and 13 bytes into a region of size 11 [-Wformat-overflow=]
sprintf(strFeatureFracOverlap, "%g", fracOverlapFeature);
^~
readSummary.c:6159:33: note: assuming directive output of 12 bytes
sprintf(strFeatureFracOverlap, "%g", fracOverlapFeature);
^~~~
In file included from /usr/include/stdio.h:938:0,
from readSummary.c:23:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 14 bytes into a destination of size 11
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
removeDupReads.c: In function 'parse_base_blocks':
removeDupReads.c:88:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_record, sizeof(base_block_temp_read_t), 1, block_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
removeDupReads.c:97:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_record, sizeof(base_block_temp_read_t), 1, block_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
SNPCalling.c: In function 'read_tmp_block':
SNPCalling.c:276:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SNP_rec, sizeof(SNP_rec),1 , tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SNPCalling.c:295:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_rec, sizeof(read_rec), 1, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SNPCalling.c:296:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SNPCalling.c:297:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read, sizeof(char), read_len, tmp_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
index-builder.c: In function 'scan_gene_index':
index-builder.c:474:19: warning: variable 'table_no' set but not used [-Wunused-but-set-variable]
int file_number, table_no, i ,j;
^~~~~~~~
index-builder.c: In function 'main':
index-builder.c:1210:2: warning: ignoring return value of 'mkstemp', declared with attribute warn_unused_result [-Wunused-result]
mkstemp(tmp_fa_file);
^~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
SUBindel.c: In function 'load_global_context_forindel':
SUBindel.c:66:21: warning: '.reads' directive writing 6 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.reads", context->config.index_prefix);
^~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 7 and 306 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c:75:22: warning: '.00.c.tab' directive writing 9 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.00.c.tab", context->config.index_prefix);
^~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 10 and 309 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c:77:22: warning: '.00.b.tab' directive writing 9 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.00.b.tab", context->config.index_prefix);
^~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 10 and 309 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c:87:26: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b');
^~~~
In file included from /usr/include/stdio.h:938:0,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 10 and 318 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBindel.c: In function 'load_indexes_forindel':
SUBindel.c:110:26: warning: '%02d' directive writing between 2 and 10 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
^~~~
SUBindel.c:110:22: note: directive argument in the range [0, 2147483647]
sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
^~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from SUBindel.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 12 and 319 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
qualityScores.c: In function 'finalise_qs_context':
qualityScores.c:82:12: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(qs_context -> gzfq_reader);
^~~~~~~~~~
In file included from qualityScores.c:24:0:
/usr/include/zlib.h: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-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
propmapped.c: In function 'prop_PE':
propmapped.c:369:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len,1,1,fp);
^~~~~~~~~~~~~~~~~~~~~~~
propmapped.c:372:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_name,read_len,1,fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
propmapped.c:376:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&flags,1, sizeof(short), fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
propmapped.c: In function 'get_FP_by_read_name':
propmapped.c:243:22: warning: '%llu' directive writing between 1 and 20 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
sprintf(fname, "%s-%llu.bin", context->temp_file_prefix, hash_key);
^~~~
propmapped.c:243:18: note: directive argument in the range [0, 18446744073709551614]
sprintf(fname, "%s-%llu.bin", context->temp_file_prefix, hash_key);
^~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from propmapped.c:21:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 7 and 325 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
propmapped.c: In function 'prop_PE':
propmapped.c:360:22: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
sprintf(fname, "%s-%d.bin", context->temp_file_prefix, bini);
^~
propmapped.c:360:18: note: directive argument in the range [0, 2147483647]
sprintf(fname, "%s-%d.bin", context->temp_file_prefix, bini);
^~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
from propmapped.c:21:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 7 and 315 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.0+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=\""1.6.0"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o coverageCount coverage_calc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o -Wl,-z,relro -Wl,-z,now -pthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE
mkdir -p ../bin/utilities
mv sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/
mv repair coverageCount propmapped qualityScores removeDup subread-fullscan txUnique ../bin/utilities
###########################################################
# #
# Installation successfully completed. #
# #
# Generated executables were copied to directory ../bin/ #
# #
###########################################################
make[2]: Leaving directory '/<<BUILDDIR>>/subread-1.6.0+dfsg/src'
dh_auto_build -- CC=arm-linux-gnueabihf-gcc
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.6.0+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.6.0+dfsg'
debian/tests/subread-tests /<<BUILDDIR>>/subread-1.6.0+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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.0
//=========================== 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=103.5k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=124.1k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=148.9k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=169.9k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=190.5k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=208.7k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=217.6k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=231.9k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=245.7k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=258.4k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=272.4k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=282.0k bps/s, total=0m ||
|| 52 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=69.7k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=83.6k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=98.3k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=112.9k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=128.7k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=144.4k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=159.6k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=172.6k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=183.9k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=196.9k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=207.6k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=219.2k 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: 0.2 minutes. ||
|| Index ../small1 was successfully built! ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.0
//========================== 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 (23-Nov-2017 05:21:24, pid=30611) =================\\
|| ||
|| 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, 0.2 mins elapsed, rate=3.4k reads per second ||
|| 39% completed, 0.2 mins elapsed, rate=3.4k reads per second ||
|| 46% completed, 0.2 mins elapsed, rate=3.7k reads per second ||
|| 53% completed, 0.3 mins elapsed, rate=3.9k reads per second ||
|| 60% completed, 0.3 mins elapsed, rate=4.0k reads per second ||
|| 74% completed, 0.3 mins elapsed, rate=0.9k reads per second ||
|| 83% completed, 0.3 mins elapsed, rate=1.0k reads per second ||
|| 91% completed, 0.3 mins elapsed, rate=1.1k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 reads ||
|| Mapped : 18758 reads (93.8%), wherein ||
|| Uniquely mapped : 18758 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 1240 ||
|| ||
|| Indels : 5 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 1.6 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.0
//========================== 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 (23-Nov-2017 05:23:04, pid=30621) =================\\
|| ||
|| 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, 0.2 mins elapsed, rate=4.1k reads per second ||
|| 39% completed, 0.2 mins elapsed, rate=4.3k reads per second ||
|| 46% completed, 0.2 mins elapsed, rate=4.4k reads per second ||
|| 53% completed, 0.2 mins elapsed, rate=4.6k reads per second ||
|| 60% completed, 0.2 mins elapsed, rate=4.7k reads per second ||
|| 74% completed, 0.3 mins elapsed, rate=0.9k reads per second ||
|| 83% completed, 0.3 mins elapsed, rate=1.0k reads per second ||
|| 91% completed, 0.3 mins elapsed, rate=1.1k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 reads ||
|| Mapped : 18758 reads (93.8%), wherein ||
|| Uniquely mapped : 18758 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 1240 ||
|| ||
|| Indels : 5 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 1.7 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.0
//========================== 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 (23-Nov-2017 05:24:46, pid=30643) =================\\
|| ||
|| 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=2.3k fragments per second ||
|| 39% completed, 0.3 mins elapsed, rate=2.3k fragments per second ||
|| 46% completed, 0.3 mins elapsed, rate=2.3k fragments per second ||
|| 53% completed, 0.3 mins elapsed, rate=2.4k fragments per second ||
|| 60% completed, 0.3 mins elapsed, rate=2.4k fragments per second ||
|| 74% completed, 0.3 mins elapsed, rate=0.8k fragments per second ||
|| 83% completed, 0.3 mins elapsed, rate=0.8k fragments per second ||
|| 91% completed, 0.3 mins elapsed, rate=0.9k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 fragments ||
|| Mapped : 19216 fragments (96.1%), wherein ||
|| Uniquely mapped : 19216 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 782 ||
|| ||
|| Correctly paired : 18830 fragments ||
|| Not mapped in pairs : 386 fragments, wherein ||
|| Only one end mapped : 1 fragments ||
|| Multi-chromosomes : 0 fragments ||
|| Different strands : 0 fragments ||
|| Not in PE distance : 385 fragments ||
|| Abnormal order : 0 fragments ||
|| ||
|| Indels : 22 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 1.7 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.0
//========================== 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 (23-Nov-2017 05:26:32, pid=30670) =================\\
|| ||
|| 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=2.4k fragments per second ||
|| 39% completed, 0.3 mins elapsed, rate=2.4k fragments per second ||
|| 46% completed, 0.3 mins elapsed, rate=2.5k fragments per second ||
|| 53% completed, 0.3 mins elapsed, rate=2.5k fragments per second ||
|| 60% completed, 0.3 mins elapsed, rate=2.5k fragments per second ||
|| 74% completed, 0.3 mins elapsed, rate=0.8k fragments per second ||
|| 83% completed, 0.3 mins elapsed, rate=0.8k fragments per second ||
|| 91% completed, 0.4 mins elapsed, rate=0.9k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 fragments ||
|| Mapped : 19216 fragments (96.1%), wherein ||
|| Uniquely mapped : 19216 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 782 ||
|| ||
|| Correctly paired : 18830 fragments ||
|| Not mapped in pairs : 386 fragments, wherein ||
|| Only one end mapped : 1 fragments ||
|| Multi-chromosomes : 0 fragments ||
|| Different strands : 0 fragments ||
|| Not in PE distance : 385 fragments ||
|| Abnormal order : 0 fragments ||
|| ||
|| Indels : 22 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 1.7 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.0
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : data/test-error-r1.fq ||
|| Input file 2 : data/test-error-r2.fq ||
|| Output file : result/test-tmp.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================ Running (23-Nov-2017 05:28:22, pid=30697) =================\\
|| ||
|| The input file contains base space reads. ||
|| WARNING - The specified Phred score offset (33) seems incorrect. ||
|| ASCII values of the quality scores of read bases included in ||
|| the first 3000 reads were found to be within the range of ||
|| [50,50]. ||
|| ||
|| Load the 1-th index block... ||
|| 33% completed, 0.3 mins elapsed, rate=2.0k fragments per second ||
|| 39% completed, 0.3 mins elapsed, rate=2.1k fragments per second ||
|| 46% completed, 0.3 mins elapsed, rate=2.2k fragments per second ||
|| 53% completed, 0.3 mins elapsed, rate=2.3k fragments per second ||
|| 60% completed, 0.3 mins elapsed, rate=2.3k fragments per second ||
|| 74% completed, 0.4 mins elapsed, rate=0.7k fragments per second ||
|| 83% completed, 0.4 mins elapsed, rate=0.8k fragments per second ||
|| 91% completed, 0.4 mins elapsed, rate=0.8k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 20000 fragments ||
|| Mapped : 18698 fragments (93.5%), wherein ||
|| Uniquely mapped : 18698 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 1302 ||
|| ||
|| Correctly paired : 13915 fragments ||
|| Not mapped in pairs : 4783 fragments, wherein ||
|| Only one end mapped : 4506 fragments ||
|| Multi-chromosomes : 0 fragments ||
|| Different strands : 0 fragments ||
|| Not in PE distance : 273 fragments ||
|| Abnormal order : 4 fragments ||
|| ||
|| Indels : 53 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 1.7 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.0
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : data/test-err-mut-r1.fq.gz ||
|| Input file 2 : data/test-err-mut-r2.fq.gz ||
|| Output file : result/test-tmp.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| Read group name : MyTestGroup ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================ Running (23-Nov-2017 05:30:10, pid=30727) =================\\
|| ||
|| The input file contains base space reads. ||
|| WARNING - The specified Phred score offset (33) seems incorrect. ||
|| ASCII values of the quality scores of read bases included in ||
|| the first 3000 reads were found to be within the range of ||
|| [50,50]. ||
|| ||
|| Load the 1-th index block... ||
|| 34% completed, 0.3 mins elapsed, rate=2.6k fragments per second ||
|| 40% completed, 0.3 mins elapsed, rate=2.7k fragments per second ||
|| 48% completed, 0.3 mins elapsed, rate=2.8k fragments per second ||
|| 53% completed, 0.3 mins elapsed, rate=2.9k fragments per second ||
|| 59% completed, 0.3 mins elapsed, rate=2.8k fragments per second ||
|| 67% completed, 0.3 mins elapsed, rate=2.9k fragments per second ||
|| 75% completed, 0.3 mins elapsed, rate=0.8k fragments per second ||
|| 83% completed, 0.3 mins elapsed, rate=0.8k fragments per second ||
|| 92% completed, 0.3 mins elapsed, rate=0.9k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 20001 fragments ||
|| Mapped : 18659 fragments (93.3%), wherein ||
|| Uniquely mapped : 18659 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 1342 ||
|| ||
|| Correctly paired : 13557 fragments ||
|| Not mapped in pairs : 5102 fragments, wherein ||
|| Only one end mapped : 4788 fragments ||
|| Multi-chromosomes : 0 fragments ||
|| Different strands : 0 fragments ||
|| Not in PE distance : 309 fragments ||
|| Abnormal order : 5 fragments ||
|| ||
|| Indels : 172 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 1.7 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
492ef95a6caec249c79db5106cdd7788 ../small1.00.b.array
3b39eb4b0aad6902d8a1be198cf2478d ../small1.00.b.tab
*************************************************
*** SINGLE-END READS NO ERROR ******
*************************************************
unmatched= 0 ; matched= 18758 ; unmapped= 1240 ; reads= 19998 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.93799379938
paired_match= 0 ; paired= 0.0
*************************************************
*** SINGLE-END READS NO ERROR NO DUP ******
*************************************************
unmatched= 0 ; matched= 18758 ; unmapped= 1240 ; reads= 19998 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.93799379938
paired_match= 0 ; paired= 0.0
*************************************************
*** READS WITH NO ERROR ******
*************************************************
unmatched= 0 ; matched= 38431 ; unmapped= 1565 ; reads= 39996 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.960871087109
paired_match= 38430 ; paired= 0.99997397934
*************************************************
*** READS NO ERROR, NO DUPLICATED REPORT ******
*************************************************
unmatched= 0 ; matched= 38431 ; unmapped= 1565 ; reads= 39996 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.960871087109
paired_match= 38430 ; paired= 0.99997397934
*************************************************
*** READS WITH ONLY SEQUENCING ERROR ******
*************************************************
unmatched= 10 ; matched= 32880 ; unmapped= 7110 ; reads= 40000 ;NN= 0
accuracy= 0.999695956218 ; sensitivity= 0.82225
paired_match= 28374 ; paired= 0.86295620438
*************************************************
*** READS WITH SEQUENCING ERROR AND MUTATION ***
*** SUBREAD IS RUN WITH LONG INDEL DETECTION ***
*************************************************
unmatched= 13 ; matched= 32515 ; unmapped= 7472 ; reads= 40002 ;NN= 0
accuracy= 0.999600344319 ; sensitivity= 0.813159342033
paired_match= 27730 ; paired= 0.852837152084
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.0
//=========================== 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=244.3k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=279.1k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=309.7k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=334.3k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=358.5k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=379.9k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=397.0k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=415.8k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=432.4k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=447.2k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=463.8k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=474.3k bps/s, total=0m ||
|| 2 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=180.0k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=187.4k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=200.3k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=212.5k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=224.9k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=237.9k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=251.6k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=265.4k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=279.7k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=293.3k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=308.4k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=321.6k bps/s, total=0m ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
|| [ 20.0% finished ] ||
|| [ 30.0% finished ] ||
|| [ 40.0% finished ] ||
|| [ 50.0% finished ] ||
|| [ 60.0% finished ] ||
|| [ 70.0% finished ] ||
|| [ 80.0% finished ] ||
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
|| Total running time: 0.1 minutes. ||
|| Index ../small1 was successfully built! ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.0
//============================= subjunc setting ==============================\\
|| ||
|| Function : Read alignment + Junction detection (RNA-Seq) ||
|| Input file 1 : data/junction-reads-A.fq ||
|| Input file 2 : data/junction-reads-B.fq ||
|| Output file : result/junctions.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 14 ||
|| Min read1 vote : 1 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================ Running (23-Nov-2017 05:32:02, pid=30734) =================\\
|| ||
|| 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, 0.4 mins elapsed, rate=1.5k fragments per second ||
|| 48% completed, 0.4 mins elapsed, rate=1.5k fragments per second ||
|| 54% completed, 0.4 mins elapsed, rate=1.6k fragments per second ||
|| 61% completed, 0.4 mins elapsed, rate=1.6k fragments per second ||
|| 77% completed, 0.5 mins elapsed, rate=0.4k fragments per second ||
|| 87% completed, 0.5 mins elapsed, rate=0.5k fragments per second ||
|| 97% completed, 0.5 mins elapsed, rate=0.5k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 16052 fragments ||
|| Mapped : 15251 fragments (95.0%), wherein ||
|| Uniquely mapped : 15251 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 801 ||
|| ||
|| Correctly paired : 13853 fragments ||
|| Not mapped in pairs : 1398 fragments, wherein ||
|| Only one end mapped : 967 fragments ||
|| Multi-chromosomes : 0 fragments ||
|| Different strands : 37 fragments ||
|| Not in PE distance : 332 fragments ||
|| Abnormal order : 62 fragments ||
|| ||
|| Junctions : 416 ||
|| Indels : 182 ||
|| ||
|| Running time : 2.5 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.0
//============================= subjunc setting ==============================\\
|| ||
|| Function : Read alignment + Junction/Fusion detection (RNA-Seq) ||
|| Input file 1 : data/junction-reads-A.fq ||
|| Input file 2 : data/junction-reads-B.fq ||
|| Output file : result/junctionsNfusions.bam (BAM) ||
|| Index name : ../small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 28 ||
|| Min read1 vote : 1 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================ Running (23-Nov-2017 05:34:31, pid=30759) =================\\
|| ||
|| 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, 0.4 mins elapsed, rate=1.1k fragments per second ||
|| 48% completed, 0.5 mins elapsed, rate=1.1k fragments per second ||
|| 54% completed, 0.5 mins elapsed, rate=1.1k fragments per second ||
|| 61% completed, 0.5 mins elapsed, rate=1.1k fragments per second ||
|| 77% completed, 0.5 mins elapsed, rate=0.4k fragments per second ||
|| 87% completed, 0.6 mins elapsed, rate=0.4k fragments per second ||
|| 97% completed, 0.6 mins elapsed, rate=0.4k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 16052 fragments ||
|| Mapped : 15235 fragments (94.9%), wherein ||
|| Uniquely mapped : 15235 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 817 ||
|| ||
|| Correctly paired : 13761 fragments ||
|| Not mapped in pairs : 1474 fragments, wherein ||
|| Only one end mapped : 1010 fragments ||
|| Multi-chromosomes : 0 fragments ||
|| Different strands : 35 fragments ||
|| Not in PE distance : 366 fragments ||
|| Abnormal order : 63 fragments ||
|| ||
|| Junctions : 434 ||
|| Fusions : 92 ||
|| Indels : 183 ||
|| ||
|| Running time : 2.5 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
================================================================================
FeatureCounts Basic Test
http://subread.sourceforge.net/
================================================================================
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.0
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 SAM file ||
|| P data/test-minimum.sam ||
|| ||
|| Output file : result/test-minimum.FC ||
|| Summary : result/test-minimum.FC.summary ||
|| Annotation : data/test-minimum.GTF (GTF) ||
|| Dir for temp files : result ||
|| ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Strand specific : no ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================================= Running ==================================\\
|| ||
|| Load annotation file data/test-minimum.GTF ... ||
|| Features : 23 ||
|| Meta-features : 7 ||
|| Chromosomes/contigs : 3 ||
|| ||
|| Process SAM file data/test-minimum.sam... ||
|| Paired-end reads are included. ||
|| Assign reads to features... ||
|| Total reads : 998 ||
|| Successfully assigned reads : 389 (39.0%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Read assignment finished. ||
|| ||
|| Summary of counting results can be found in file "result/test-minimum.FC. ||
|| summary" ||
|| ||
\\===================== 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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.0
//============================= 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 (23-Nov-2017 05:37:11) ======================\\
|| ||
|| Split BAM file into result/temp-snps-031573-001F7BB4051E-* ... ||
|| 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-1.6.0+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --parallel
dh_testroot -a -O--parallel
dh_prep -a -O--parallel
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.6.0+dfsg'
find /<<BUILDDIR>>/subread-1.6.0+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \;
mkdir -p /<<BUILDDIR>>/subread-1.6.0+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-1.6.0+dfsg/bin/subread-align | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.0+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-1.6.0+dfsg/bin/subread-buildindex | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.0+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-1.6.0+dfsg/bin/subjunc | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.0+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-1.6.0+dfsg/bin/featureCounts | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.0+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-1.6.0+dfsg/bin/exactSNP | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.0+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-1.6.0+dfsg/bin/subindel | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.0+dfsg/debian/subread/usr/share/man/man1/subindel.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='long-read aligner that is designed based on seed-and-vote' \
/<<BUILDDIR>>/subread-1.6.0+dfsg/bin/sublong| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.0+dfsg/debian/subread/usr/share/man/man1/sublong.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='scans the entire genome and reports all matches of a specified sequence' \
/<<BUILDDIR>>/subread-1.6.0+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.0+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-1.6.0+dfsg/bin/utilities/coverageCount | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.0+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-1.6.0+dfsg/bin/utilities/propmapped | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.0+dfsg/debian/subread/usr/share/man/man1/propmapped.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='retrieve Phred score for read bases' \
/<<BUILDDIR>>/subread-1.6.0+dfsg/bin/utilities/qualityScores| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.0+dfsg/debian/subread/usr/share/man/man1/qualityScores.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='Find reads that are from the same pair in the input and then place them next \
to each other in the output. A dummy read is added for each singleton read that does not have a pair. \
The output file is compatible with featureCounts program' \
/<<BUILDDIR>>/subread-1.6.0+dfsg/bin/utilities/repair| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.0+dfsg/debian/subread/usr/share/man/man1/repair.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='Remove duplicated reads' \
/<<BUILDDIR>>/subread-1.6.0+dfsg/bin/utilities/removeDup| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.0+dfsg/debian/subread/usr/share/man/man1/removeDup.1;
dh_auto_install
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.6.0+dfsg'
dh_install -a -O--parallel
dh_installdocs -a -O--parallel
dh_installchangelogs -a -O--parallel
dh_installman -a -O--parallel
dh_perl -a -O--parallel
dh_link -a -O--parallel
dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
dh_fixperms -a -O--parallel
dh_missing -a -O--parallel
dh_strip -a -O--parallel
dh_makeshlibs -a -O--parallel
dh_shlibdeps -a -O--parallel
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/subread/usr/bin/featureCounts debian/subread/usr/lib/subread/qualityScores debian/subread/usr/bin/subread-align debian/subread/usr/bin/subindel debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/txUnique debian/subread/usr/bin/subjunc debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/sublong debian/subread/usr/bin/exactSNP debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/coverageCount 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
dh_md5sums -a -O--parallel
dh_builddeb -a -O--parallel
dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_1.6.0+dfsg-1_armhf.deb'.
dpkg-deb: building package 'subread' in '../subread_1.6.0+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../subread_1.6.0+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build subread-1.6.0+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-11-23T05:38:34Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
subread_1.6.0+dfsg-1_armhf.changes:
-----------------------------------
Format: 1.8
Date: Fri, 17 Nov 2017 16:43:55 +0100
Source: subread
Binary: subread subread-data
Architecture: armhf
Version: 1.6.0+dfsg-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
Description:
subread - toolkit for processing next-gen sequencing data
subread-data - data files for subread package
Changes:
subread (1.6.0+dfsg-1) unstable; urgency=medium
.
* Update d/watch to version 4
* New upstream version 1.6.0+dfsg
* Update d/subread.install, add sublong and txUnique binaries
* d/rules:
- add man page generation for sublong binary
- use conditional variable assignment operator for DEB_HOST_ARCH
* d/control:
- bump Standards-Version to 4.1.1
- drop autopkgtest testsuite from d/control as we have d/tests/control
* Update arch_specific_flags patch, fix Makefile for sublong
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Checksums-Sha256:
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Files:
1bf8b7e122c54867595c34a7292ce138 5504640 debug optional subread-dbgsym_1.6.0+dfsg-1_armhf.deb
dbef262440aa11ad623359149c4948c4 4890 science optional subread_1.6.0+dfsg-1_armhf.buildinfo
219cc81be3ec61028ba03f10308f41d8 399472 science optional subread_1.6.0+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
subread-dbgsym_1.6.0+dfsg-1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 5504640 bytes: control archive=1188 bytes.
914 bytes, 12 lines control
1484 bytes, 14 lines md5sums
Package: subread-dbgsym
Source: subread
Version: 1.6.0+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6469
Depends: subread (= 1.6.0+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for subread
Build-Ids: 27dd4adf0ce0dba04755ec3055015f47d05c1378 2c0cc748e9d00f62e1a6652c235e8e48ada9e8f3 331101dc14e2a1542ad708d0ede3a60057caf96d 33e9356cc9102236eee2ea54a115bea06ab7e4d5 44e4a0f365b4e8ea6f90e6b2e398031bced9f3da 660428b935444f7e1ca7fe16ff031bccf7768253 a5343035cd4ce91d5471a4716534695aac4f23af b2913ea35f88a67add1cfd98a7b08eb80d4cfbc1 b9f8ab7fd595cc9805892fda4cc76e11c57f93f7 bfcca2cc844d650627ee73c0cf035a456e6d33d2 c3b520a9cdec0bfc1ef6cf48816c87a61ffe39c5 d14017c606aa105d9d3cc7ffa0485def542c11d0 f10d8b2c49c608d1a63320b236fd0b42dea7557b f4060734b3f04b91076d0d33c5ff56a4c6bf6ff9
drwxr-xr-x root/root 0 2017-11-17 15:43 ./
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/debug/.build-id/27/
-rw-r--r-- root/root 486012 2017-11-17 15:43 ./usr/lib/debug/.build-id/27/dd4adf0ce0dba04755ec3055015f47d05c1378.debug
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/debug/.build-id/2c/
-rw-r--r-- root/root 509576 2017-11-17 15:43 ./usr/lib/debug/.build-id/2c/0cc748e9d00f62e1a6652c235e8e48ada9e8f3.debug
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/debug/.build-id/33/
-rw-r--r-- root/root 487904 2017-11-17 15:43 ./usr/lib/debug/.build-id/33/1101dc14e2a1542ad708d0ede3a60057caf96d.debug
-rw-r--r-- root/root 491840 2017-11-17 15:43 ./usr/lib/debug/.build-id/33/e9356cc9102236eee2ea54a115bea06ab7e4d5.debug
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/debug/.build-id/44/
-rw-r--r-- root/root 499852 2017-11-17 15:43 ./usr/lib/debug/.build-id/44/e4a0f365b4e8ea6f90e6b2e398031bced9f3da.debug
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/debug/.build-id/66/
-rw-r--r-- root/root 483096 2017-11-17 15:43 ./usr/lib/debug/.build-id/66/0428b935444f7e1ca7fe16ff031bccf7768253.debug
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/debug/.build-id/a5/
-rw-r--r-- root/root 126284 2017-11-17 15:43 ./usr/lib/debug/.build-id/a5/343035cd4ce91d5471a4716534695aac4f23af.debug
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/debug/.build-id/b2/
-rw-r--r-- root/root 491868 2017-11-17 15:43 ./usr/lib/debug/.build-id/b2/913ea35f88a67add1cfd98a7b08eb80d4cfbc1.debug
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/debug/.build-id/b9/
-rw-r--r-- root/root 583216 2017-11-17 15:43 ./usr/lib/debug/.build-id/b9/f8ab7fd595cc9805892fda4cc76e11c57f93f7.debug
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/debug/.build-id/bf/
-rw-r--r-- root/root 484148 2017-11-17 15:43 ./usr/lib/debug/.build-id/bf/cca2cc844d650627ee73c0cf035a456e6d33d2.debug
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/debug/.build-id/c3/
-rw-r--r-- root/root 488436 2017-11-17 15:43 ./usr/lib/debug/.build-id/c3/b520a9cdec0bfc1ef6cf48816c87a61ffe39c5.debug
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/debug/.build-id/d1/
-rw-r--r-- root/root 488844 2017-11-17 15:43 ./usr/lib/debug/.build-id/d1/4017c606aa105d9d3cc7ffa0485def542c11d0.debug
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/debug/.build-id/f1/
-rw-r--r-- root/root 488912 2017-11-17 15:43 ./usr/lib/debug/.build-id/f1/0d8b2c49c608d1a63320b236fd0b42dea7557b.debug
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/debug/.build-id/f4/
-rw-r--r-- root/root 484756 2017-11-17 15:43 ./usr/lib/debug/.build-id/f4/060734b3f04b91076d0d33c5ff56a4c6bf6ff9.debug
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/share/
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-11-17 15:43 ./usr/share/doc/subread-dbgsym -> subread
subread_1.6.0+dfsg-1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 399472 bytes: control archive=1512 bytes.
622 bytes, 14 lines control
1994 bytes, 31 lines md5sums
Package: subread
Version: 1.6.0+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4625
Depends: libc6 (>= 2.7), zlib1g (>= 1:1.2.3.3)
Section: science
Priority: optional
Homepage: http://sourceforge.net/projects/subread/
Description: toolkit for processing next-gen sequencing data
Subread aligner can be used to align both gDNA-seq and RNA-seq reads.
Subjunc aligner was specified designed for the detection of exon-exon
junction. For the mapping of RNA-seq reads, Subread performs local
alignments and Subjunc performs global alignments.
drwxr-xr-x root/root 0 2017-11-17 15:43 ./
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/bin/
-rwxr-xr-x root/root 366860 2017-11-17 15:43 ./usr/bin/exactSNP
-rwxr-xr-x root/root 432716 2017-11-17 15:43 ./usr/bin/featureCounts
-rwxr-xr-x root/root 342300 2017-11-17 15:43 ./usr/bin/subindel
-rwxr-xr-x root/root 351356 2017-11-17 15:43 ./usr/bin/subjunc
-rwxr-xr-x root/root 83448 2017-11-17 15:43 ./usr/bin/sublong
-rwxr-xr-x root/root 351260 2017-11-17 15:43 ./usr/bin/subread-align
-rwxr-xr-x root/root 354548 2017-11-17 15:43 ./usr/bin/subread-buildindex
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/lib/subread/
-rwxr-xr-x root/root 342300 2017-11-17 15:43 ./usr/lib/subread/coverageCount
-rwxr-xr-x root/root 342300 2017-11-17 15:43 ./usr/lib/subread/propmapped
-rwxr-xr-x root/root 346508 2017-11-17 15:43 ./usr/lib/subread/qualityScores
-rwxr-xr-x root/root 342252 2017-11-17 15:43 ./usr/lib/subread/removeDup
-rwxr-xr-x root/root 342252 2017-11-17 15:43 ./usr/lib/subread/repair
-rwxr-xr-x root/root 342252 2017-11-17 15:43 ./usr/lib/subread/subread-fullscan
-rwxr-xr-x root/root 342252 2017-11-17 15:43 ./usr/lib/subread/txUnique
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/share/
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/share/doc/subread/
-rw-r--r-- root/root 500 2017-11-17 15:43 ./usr/share/doc/subread/README.Debian
-rw-r--r-- root/root 3850 2017-11-14 03:42 ./usr/share/doc/subread/README.txt
-rw-r--r-- root/root 2384 2017-11-17 15:43 ./usr/share/doc/subread/changelog.Debian.gz
-rw-r--r-- root/root 1138 2017-11-17 15:43 ./usr/share/doc/subread/copyright
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/share/man/
drwxr-xr-x root/root 0 2017-11-17 15:43 ./usr/share/man/man1/
-rw-r--r-- root/root 594 2017-11-17 15:43 ./usr/share/man/man1/coverageCount.1.gz
-rw-r--r-- root/root 1166 2017-11-17 15:43 ./usr/share/man/man1/exactSNP.1.gz
-rw-r--r-- root/root 3129 2017-11-17 15:43 ./usr/share/man/man1/featureCounts.1.gz
-rw-r--r-- root/root 475 2017-11-17 15:43 ./usr/share/man/man1/propmapped.1.gz
-rw-r--r-- root/root 577 2017-11-17 15:43 ./usr/share/man/man1/qualityScores.1.gz
-rw-r--r-- root/root 480 2017-11-17 15:43 ./usr/share/man/man1/removeDup.1.gz
-rw-r--r-- root/root 603 2017-11-17 15:43 ./usr/share/man/man1/repair.1.gz
-rw-r--r-- root/root 368 2017-11-17 15:43 ./usr/share/man/man1/subindel.1.gz
-rw-r--r-- root/root 2101 2017-11-17 15:43 ./usr/share/man/man1/subjunc.1.gz
-rw-r--r-- root/root 696 2017-11-17 15:43 ./usr/share/man/man1/sublong.1.gz
-rw-r--r-- root/root 2181 2017-11-17 15:43 ./usr/share/man/man1/subread-align.1.gz
-rw-r--r-- root/root 707 2017-11-17 15:43 ./usr/share/man/man1/subread-buildindex.1.gz
-rw-r--r-- root/root 368 2017-11-17 15:43 ./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: 113228
Build-Time: 1297
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 357
Job: subread_1.6.0+dfsg-1
Machine Architecture: armhf
Package: subread
Package-Time: 1713
Source-Version: 1.6.0+dfsg-1
Space: 113228
Status: successful
Version: 1.6.0+dfsg-1
--------------------------------------------------------------------------------
Finished at 2017-11-23T05:38:34Z
Build needed 00:28:33, 113228k disc space