subread →
1.6.1+dfsg-1 →
armhf → 2018-04-10 06:57:14
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| subread 1.6.1+dfsg-1 (armhf) Tue, 10 Apr 2018 06:25:29 +0000 |
+==============================================================================+
Package: subread
Version: 1.6.1+dfsg-1
Source Version: 1.6.1+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-b3502874-3db8-4414-980f-e604eae5cb76' 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 [10.7 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.4 MB]
Fetched 23.1 MB in 27s (853 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://salsa.debian.org/med-team/subread.git
Please use:
git clone https://salsa.debian.org/med-team/subread.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 15.5 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main subread 1.6.1+dfsg-1 (dsc) [2204 B]
Get:2 http://172.17.0.1/private buster-staging/main subread 1.6.1+dfsg-1 (tar) [15.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main subread 1.6.1+dfsg-1 (diff) [8132 B]
Fetched 15.5 MB in 2s (9300 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/subread-W02Eer/subread-1.6.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/subread-W02Eer' 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-q4IpvW/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-q4IpvW/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-q4IpvW/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-q4IpvW/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-q4IpvW/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-q4IpvW/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-q4IpvW/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-q4IpvW/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2944 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...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session libexpat1 libnss-systemd
libpam-systemd libssl1.1 openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 23 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-q4IpvW/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (21.4 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13929 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-q4IpvW/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-q4IpvW/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-q4IpvW/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-q4IpvW/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-q4IpvW/apt_archive ./ Sources [509 B]
Get:5 copy:/<<BUILDDIR>>/resolver-q4IpvW/apt_archive ./ Packages [588 B]
Fetched 2430 B in 1s (3397 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 packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session libnss-systemd libpam-systemd openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bc bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3
libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libmagic-mgc
libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db
mime-support po-debconf python python-minimal python2.7 python2.7-minimal
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx 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
libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libmagic-mgc
libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db
mime-support po-debconf python python-minimal python2.7 python2.7-minimal
sbuild-build-depends-subread-dummy zlib1g-dev
0 upgraded, 41 newly installed, 0 to remove and 23 not upgraded.
Need to get 14.4 MB/23.2 MB of archives.
After this operation, 80.6 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-q4IpvW/apt_archive ./ sbuild-build-depends-subread-dummy 0.invalid.0 [876 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.2-1 [1145 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.14-8 [393 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.14-8 [1076 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.14-4 [41.0 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.14-8 [1843 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.14-8 [293 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.14-4 [20.4 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.14-4 [155 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf bc armhf 1.07.1-2 [101 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-1 [32.2 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 17 [16.5 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.0-4 [2749 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.1.6 [1009 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.6 [169 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libbsd0:armhf.
(Reading database ... 13929 files and directories currently installed.)
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Unpacking libbsd0:armhf (0.8.7-1) ...
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Preparing to unpack .../02-groff-base_1.22.3-10_armhf.deb ...
Unpacking groff-base (1.22.3-10) ...
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Preparing to unpack .../03-libpipeline1_1.5.0-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.0-1) ...
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Unpacking man-db (2.8.2-1) ...
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Preparing to unpack .../05-libpython2.7-minimal_2.7.14-8_armhf.deb ...
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Preparing to unpack .../06-python2.7-minimal_2.7.14-8_armhf.deb ...
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Preparing to unpack .../07-python-minimal_2.7.14-4_armhf.deb ...
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Unpacking libpython-stdlib:armhf (2.7.14-4) ...
Setting up libpython2.7-minimal:armhf (2.7.14-8) ...
Setting up python2.7-minimal (2.7.14-8) ...
Setting up python-minimal (2.7.14-4) ...
Selecting previously unselected package python.
(Reading database ... 15312 files and directories currently installed.)
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Unpacking python (2.7.14-4) ...
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Setting up libarchive-zip-perl (1.60-1) ...
Setting up mime-support (3.60) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.12-1) ...
Setting up groff-base (1.22.3-10) ...
Setting up libglib2.0-0:armhf (2.56.0-4) ...
No schema files found: removed existing output file.
Setting up gettext-base (0.19.8.1-6) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-9) ...
Setting up libbsd0:armhf (0.8.7-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-6.1) ...
Setting up libmagic-mgc (1:5.32-2) ...
Setting up libmagic1:armhf (1:5.32-2) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Processing triggers for libc-bin (2.27-2+rpi1) ...
Setting up autotools-dev (20180224.1) ...
Setting up help2man (1.47.6) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up bc (1.07.1-2) ...
Setting up libpython2.7-stdlib:armhf (2.7.14-8) ...
Setting up autopoint (0.19.8.1-6) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.040-1) ...
Setting up gettext (0.19.8.1-6) ...
Setting up python2.7 (2.7.14-8) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.32-2) ...
Setting up libpython-stdlib:armhf (2.7.14-4) ...
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 (2.8.2-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up python (2.7.14-4) ...
Setting up libtool (2.4.6-2) ...
Setting up po-debconf (1.0.20) ...
Setting up dh-autoreconf (17) ...
Setting up dh-strip-nondeterminism (0.040-1) ...
Setting up debhelper (11.1.6) ...
Setting up sbuild-build-depends-subread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-2+rpi1) ...
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_2.30-8+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-12 gcc-7_7.3.0-12 libc6-dev_2.27-2+rpi1 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180321-1+rpi1 linux-libc-dev_4.15.11-1+rpi1
Package versions: adduser_3.117 apt_1.6~beta1 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.44 bash_4.4.18-1.1 bc_1.07.1-2 binutils_2.30-8+rpi1 binutils-arm-linux-gnueabihf_2.30-8+rpi1 binutils-common_2.30-8+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.5 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-12 dash_0.5.8-2.10 dbus_1.12.6-2 dbus-user-session_1.12.6-2 debconf_1.5.66 debhelper_11.1.6 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.44.1-1 e2fsprogs_1.44.1-1 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.32-2 findutils_4.6.0+git+20171230-2 g++_4:7.2.0-1d1 g++-7_7.3.0-12 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_4.9.4-2+rpi1 gcc-5-base_5.5.0-8 gcc-6-base_6.4.0-12+rpi1 gcc-7_7.3.0-12 gcc-7-base_7.3.0-12 gcc-8-base_8-20180321-1+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gnupg_2.2.5-1 gnupg-l10n_2.2.5-1 gnupg-utils_2.2.5-1 gpg_2.2.5-1 gpg-agent_2.2.5-1 gpg-wks-client_2.2.5-1 gpg-wks-server_2.2.5-1 gpgconf_2.2.5-1 gpgsm_2.2.5-1 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 help2man_1.47.6 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6~beta1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-1.1 libasan4_7.3.0-12 libassuan0_2.5.1-2 libatomic1_8-20180321-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbinutils_2.30-8+rpi1 libblkid1_2.31.1-0.5 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-2+rpi1 libc-dev-bin_2.27-2+rpi1 libc6_2.27-2+rpi1 libc6-dev_2.27-2+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180321-1+rpi1 libcilkrts5_7.3.0-12 libcom-err2_1.44.1-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.6-2 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.91-2+rpi1 libdrm2_2.4.91-2+rpi1 libexpat1_2.2.5-3 libext2fs2_1.44.1-1 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.3.0-12 libgcc1_1:8-20180321-1+rpi1 libgcrypt20_1.8.1-4 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.56.0-4 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180321-1+rpi1 libgpg-error0_1.28-2 libhogweed4_3.4-1 libicu57_57.1-9 libidn11_1.33-2.1 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl15_0.18-4 libjson-c3_0.12.1-1.3 libklibc_2.0.4-11+rpi1 libkmod2_25-1 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_1:5.32-2 libmagic1_1:5.32-2 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1-1 libncursesw5_6.1-1 libnettle6_3.4-1 libnpth0_1.5-3 libnss-systemd_238-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-3 libpam0g_1.1.8-3.7 libpcre3_2:8.39-9 libperl5.26_5.26.1-5 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-4 libpython-stdlib_2.7.14-4 libpython2.7-minimal_2.7.14-8 libpython2.7-stdlib_2.7.14-8 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_2.12-1 libsmartcols1_2.31.1-0.5 libsqlite3-0_3.22.0-2 libss2_1.44.1-1 libssl1.1_1.1.0h-2 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180321-1+rpi1 libsystemd0_238-3 libtasn1-6_4.13-2 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_6.1-1 libtool_2.4.6-2 libubsan0_7.3.0-12 libudev1_238-3 libunistring2_0.9.8-1 libuuid1_2.31.1-0.5 libxml2_2.9.4+dfsg1-6.1 linux-base_4.5 linux-libc-dev_4.15.11-1+rpi1 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_2.8.2-1 mawk_1.3.3-17 mime-support_3.60 mount_2.31.1-0.5 multiarch-support_2.27-2+rpi1 nano_2.9.4-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 netbase_5.4 openssl_1.1.0h-2 passwd_1:4.5-1 patch_2.7.6-1 perl_5.26.1-5 perl-base_5.26.1-5 perl-modules-5.26_5.26.1-5 pinentry-curses_1.1.0-1 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.12-4 python_2.7.14-4 python-minimal_2.7.14-4 python2.7_2.7.14-8 python2.7-minimal_2.7.14-8 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_4.4-2 sensible-utils_0.0.12 systemd_238-3 systemd-sysv_238-3 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018d-1 udev_238-3 util-linux_2.31.1-0.5 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 Wed Apr 4 17:16:21 2018 UTC
gpgv: using RSA key 1CF792111B5228B0
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./subread_1.6.1+dfsg-1.dsc
dpkg-source: info: extracting subread in /<<BUILDDIR>>/subread-1.6.1+dfsg
dpkg-source: info: unpacking subread_1.6.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking subread_1.6.1+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=buildd
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-b3502874-3db8-4414-980f-e604eae5cb76
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package subread
dpkg-buildpackage: info: source version 1.6.1+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build subread-1.6.1+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --parallel
debian/rules override_dh_clean
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.6.1+dfsg'
cd src; make -f Makefile.Linux clean
make[2]: Entering directory '/<<BUILDDIR>>/subread-1.6.1+dfsg/src'
rm -f core featureCounts exactSNP removeDup subread-buildindex core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o
make[2]: Leaving directory '/<<BUILDDIR>>/subread-1.6.1+dfsg/src'
dh_clean
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.6.1+dfsg'
debian/rules build-arch
dh build-arch --parallel
dh_update_autotools_config -a -O--parallel
dh_autoreconf -a -O--parallel
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.6.1+dfsg'
cd src; make -f Makefile.Linux
make[2]: Entering directory '/<<BUILDDIR>>/subread-1.6.1+dfsg/src'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c
core.c: In function 'print_in_box':
core.c: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 'add_head_tail_cut_softclipping':
core.c:1241:27: 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:1241:9: 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:1630:16: 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:2300:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret;
^~~
core.c: In function 'write_realignments_for_fragment':
core.c:2517:21: warning: variable 'raw_r2' set but not used [-Wunused-but-set-variable]
mapping_result_t * raw_r2 = NULL;
^~~~~~
core.c:2514:21: 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:2611:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret;
^~~
core.c: In function 'do_voting':
core.c:3274:9: 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:3185:6: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret, xk1;
^~~
core.c: In function 'convert_BAM_to_SAM':
core.c:855:28: 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:862:0,
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:855:28: 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:862:0,
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:855:28: 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:862:0,
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:929:28: 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:862:0,
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:2106:71: 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:862:0,
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:2107:71: 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:862:0,
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:3957:32: 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:862:0,
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:4198:24: 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:862:0,
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:4212:25: 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:862:0,
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:4214:25: 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:862:0,
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:4225:26: 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:862:0,
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:3675:26: 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:3675:22: 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:862:0,
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:3692:28: 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:862:0,
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:3696:28: 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:862:0,
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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c
core-junction.c: In function 'is_long_del_high_quality':
core-junction.c:986:6: warning: unused variable 'total_gap' [-Wunused-variable]
int total_gap = mid_gap + min( p1_start, p2_start ) + ( read_len - max(p1_end, p2_end) );
^~~~~~~~~
core-junction.c: In function 'copy_vote_to_alignment_res':
core-junction.c:1009:12: 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:2065:8: 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:2924:13: warning: variable 'debug_ptr' set but not used [-Wunused-but-set-variable]
char * debug_ptr = read_text;
^~~~~~~~~
core-junction.c:2957:13: 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:3313:94: 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:3291:28: warning: variable 'isCigarOK' set but not used [-Wunused-but-set-variable]
int mismatch_bases = 0, isCigarOK = 0;
^~~~~~~~~
core-junction.c:3129:23: 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_new_junctions':
core-junction.c:4034:95: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
int new_event_type = ((global_context -> config.entry_program_name == CORE_PROGRAM_SUBJUNC && global_context -> config.do_fusion_detection || global_context -> config.entry_program_name == CORE_PROGRAM_SUBJUNC && global_context -> config.do_long_del_detection) && !global_context -> config.prefer_donor_receptor_junctions)?CHRO_EVENT_TYPE_FUSION:CHRO_EVENT_TYPE_JUNCTION;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-junction.c: In function 'find_translocation_brk_PQR':
core-junction.c:5727:23: 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:4151:41: warning: '.breakpoints.vcf' 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.vcf", global_context->config.output_prefix);
^~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
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:4298:41: 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:862:0,
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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c
core-indel.c: In function 'remove_neighbour':
core-indel.c:567:11: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
if((1 && global_context-> config.do_fusion_detection || 1 && global_context-> config.do_long_del_detection) && event_body -> event_type == CHRO_EVENT_TYPE_FUSION)
~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c: In function 'find_new_indels':
core-indel.c:2040:9: 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:2244:24: warning: unused variable 'event_body' [-Wunused-variable]
chromosome_event_t * event_body = indel_context -> event_space_dynamic +xk1;
^~~~~~~~~~
core-indel.c:2258:26: 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:2254:17: 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:3425:41: warning: variable 'best_right' set but not used [-Wunused-but-set-variable]
int best_edge_score = -1, best_left, best_right;
^~~~~~~~~~
core-indel.c:3425:30: 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:3524:24: 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:3802:3: 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:3803:3: 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:3804:3: 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:3881:3: 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:3882:3: 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:3883:3: 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:4245:3: 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:4246:3: 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:4247:3: 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:2277:41: warning: '.indel.vcf' directive output may be truncated writing 10 bytes into a region of size between 1 and 300 [-Wformat-truncation=]
snprintf(fn2, MAX_FILE_NAME_LENGTH, "%s.indel.vcf", global_context->config.output_prefix);
^~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
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 11 and 310 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:2487:32: 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:2487:26: note: using the range [0, 4294967295] for directive argument
sprintf(temp_file_name,"%s@%s-%04u.bin", global_context -> config.temp_file_prefix, chro_name , chro_offset / BASE_BLOCK_LENGTH );
^~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
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:4280:23: 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:862:0,
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:4292:33: 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:4292:27: note: using the range [0, 4294967295] for directive argument
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 );
^~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c
sambam-file.c: In function 'is_paired_end_BAM':
sambam-file.c:88:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(h2, 1,2,fp);
^~~~~~~~~~~~~~~~~
sambam-file.c: In function 'PBam_get_next_zchunk':
sambam-file.c:378:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&ID1, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:379:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&ID2, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:380:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&CM, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:381:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&FLG, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:390:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&XLEN,1, 2, bam_fp );
^~~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:398:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SI1, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:399:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SI2, 1, 1, bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:405:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&BSIZE_MID, 1,2 , bam_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:417:3: 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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c
gene-algorithms.c: In function 'show_cigar':
gene-algorithms.c: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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c
input-files.c: In function 'f_subr_open':
input-files.c:53:10: warning: implicit declaration of function 'fopen64'; 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:2796:11: 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:3456:31: 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:3301:5: 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:3457:31: 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:3301:5: 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:3425:9: warning: unused variable 'tmptr' [-Wunused-variable]
char * tmptr = NULL;
^~~~~
input-files.c: In function 'fix_write_block':
input-files.c:4480:23: 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:5030:9: 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:5275:20: warning: unused variable 'is_longcigar' [-Wunused-variable]
int x1, nch = 0, is_longcigar = 0, binptr = 0;
^~~~~~~~~~~~
input-files.c:5270:7: warning: unused variable 'out_bin_ptr' [-Wunused-variable]
int out_bin_ptr = 0;
^~~~~~~~~~~
input-files.c:5268:7: 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:3571:2: 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:3781:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:3793:3: 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:3802:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:3806:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 4, fp);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:3808:2: 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:4459:4: 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:5501:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:5507:6: 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:5510:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len,2,1,bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:5516:6: 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:5569:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:5575:6: 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:5579:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, 2,1 , bbfp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:5582:6: 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:4053:25: 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:862:0,
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:4061:27: 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:4061:24: note: directive argument in the range [0, 2147483647]
sprintf(tmp_fname, "%s-TH%02d-BK%06d.tmp", pairer->tmp_file_prefix, thno, bkno);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:4061:24: note: directive argument in the range [0, 2147483647]
In file included from /usr/include/stdio.h:862:0,
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:3834:24: 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:862:0,
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:3949:26: 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:3949:23: note: directive argument in the range [0, 2147483647]
sprintf(tmp_fname, "%s-TH%02d-BK%06d.tmp", pairer->tmp_file_prefix, thno, bkno);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:3949:23: note: directive argument in the range [0, 2147483647]
In file included from /usr/include/stdio.h:862:0,
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:3963:25: 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:3963:22: note: directive argument in the range [0, 5]
sprintf(tmp_fname, "%s-FTEST-%d.tmp", pairer->tmp_file_prefix, bkno);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
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:3975:26: 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:3975:23: note: directive argument in the range [0, 2147483647]
sprintf(tmp_fname, "%s-TH%02d-BK%06d.tmp", pairer->tmp_file_prefix, thno, bkno);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:3975:23: note: directive argument in the range [0, 2147483647]
In file included from /usr/include/stdio.h:862:0,
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:4003:27: 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:4003:24: note: directive argument in the range [0, 2147483647]
sprintf(tmp_fname, "%s-TH%02d-BK%06d.tmp", pairer->tmp_file_prefix, thno, bkno);
^~~~~~~~~~~~~~~~~~~~~~
input-files.c:4003:24: note: directive argument in the range [0, 2147483647]
In file included from /usr/include/stdio.h:862:0,
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:4013:28: 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:862:0,
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:4196:24: 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, thread_context -> thread_id, thread_context -> orphant_block_no++);
^~~
In file included from /usr/include/stdio.h:862:0,
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:4562:23: 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:862:0,
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:5018:10: 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 input-files.c:24:0:
/usr/include/stdlib.h:539:14: 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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c
sorted-hashtable.c: In function 'gehash_load_option':
sorted-hashtable.c:1292:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1297:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1300:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1304:6: 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:1331:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1354:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1357:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1360:6: 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:1362:6: 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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c
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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c
long-hashtable.c: In function 'lnhash_create':
long-hashtable.c:43:45: warning: large integer implicitly truncated to unsigned type [-Woverflow]
the_table -> key_repeated_numbers = malloc(sizeof(short) * 0x100000000llu);
^~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c
core-bigtable.c: In function 'bigtable_readonly_result':
core-bigtable.c:70:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(write_ptr, loadjunc?sizeof(subjunc_result_t):sizeof(mapping_result_t), 1, global_context -> bigtable_cache_file_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-bigtable.c: In function 'bigtable_retrieve_cache':
core-bigtable.c:227:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread( current_cache -> big_margin_data , sizeof(short) * 3 * global_context -> config.big_margin_record_size , 1, global_context -> bigtable_cache_file_fp );
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-bigtable.c:228:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread( current_cache -> alignment_res , sizeof(mapping_result_t) * global_context -> config.multi_best_reads , 1, global_context -> bigtable_cache_file_fp );
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-bigtable.c:231:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread( current_cache -> subjunc_res , sizeof(subjunc_result_t) * global_context -> config.multi_best_reads , 1, global_context -> bigtable_cache_file_fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-bigtable.c:237:5: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(global_context -> bigtable_cache_file_fp), new_file_size);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:862:0,
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:862:0,
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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -D_FILE_OFFSET_BITS=64 -ggdb -fmessage-length=0 -o detectionCall detection-calls.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
In file included from detection-calls.c:8:0:
detection-calls.c: In function 'DTCprint_lentab_items':
detection-calls.c:160:16: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'void *' [-Wformat=]
SUBREADprintf("%s => %ld\n", key, hashed_obj - NULL);
^
subread.h:122:44: note: in definition of macro 'SUBREADprintf'
#define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
^~~~~~~~~~~
detection-calls.c:160:16: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=]
SUBREADprintf("%s => %ld\n", key, hashed_obj - NULL);
^
subread.h:122:44: note: in definition of macro 'SUBREADprintf'
#define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
^~~~~~~~~~~
detection-calls.c: In function 'DTCparse_GTF_and_Genome':
detection-calls.c:324:19: warning: unused variable 'tmp_gene_info' [-Wunused-variable]
unsigned int * tmp_gene_info = HashTableGet(genename_to_3int_table , tmpexon -> gene_name);
^~~~~~~~~~~~~
In file included from detection-calls.c:8:0:
detection-calls.c:396:18: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
SUBREADprintf("%s has %d merged genes from %ld item hashtable\n", current_chro, merged_gene_list -> numOfElements, genename_to_3int_table -> numOfElements);
^ ~~~~~~~~~~~~~~~~~~~~~
subread.h:122:44: note: in definition of macro 'SUBREADprintf'
#define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
^~~~~~~~~~~
detection-calls.c: In function 'DTCinit_context':
detection-calls.c:497:19: warning: '-bins' directive writing 5 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
sprintf(binfn,"%s-bins", ret -> out_file_name);
^~~~~
In file included from /usr/include/stdio.h:862:0,
from detection-calls.c:1:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 6 and 305 bytes into a destination of size 300
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
echo " " > longread-one/make.version
rm -f longread-one/*.o
cd longread-one && make
make[3]: Entering directory '/<<BUILDDIR>>/subread-1.6.1+dfsg/src/longread-one'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+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=\""1.6.1"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+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:269:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
LRMsorted-hashtable.c:274:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
LRMsorted-hashtable.c:277:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LRMsorted-hashtable.c:281:6: 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:308:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^~~~~~~~~~~~~~~~~~~~~~~~~
LRMsorted-hashtable.c:321:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
LRMsorted-hashtable.c:324:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
LRMsorted-hashtable.c:327:5: 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:329:5: 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-1.6.1+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=\""1.6.1"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+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-1.6.1+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=\""1.6.1"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+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-1.6.1+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=\""1.6.1"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+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-1.6.1+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=\""1.6.1"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMseek-zlib.o LRMseek-zlib.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+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=\""1.6.1"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+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:399:17: 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:862:0,
from LRMfile-io.c:1:
/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:478:102: 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:862:0,
from LRMfile-io.c:1:
/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-1.6.1+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=\""1.6.1"\" -fmessage-length=0 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o LRMhashtable.o LRMhashtable.c
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+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=\""1.6.1"\" -fmessage-length=0 -ggdb -o LRM longread-mapping.c LRMsorted-hashtable.o LRMbase-index.o LRMchro-event.o LRMhelper.o LRMseek-zlib.o LRMfile-io.o LRMhashtable.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 'LRMload_index':
longread-mapping.c:319:29: 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:862:0,
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:322:29: 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:862:0,
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:322:29: 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:862:0,
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 ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/subread-1.6.1+dfsg/src/longread-one'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -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:384:15: 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:1905:15: 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:1903:16: 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:1902:16: 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:1900:15: 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:2506:8: 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:3594:89: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=]
if(0 && FIXLENstrcmp("V0112_0155:7:1102:12486:34235", read_name)==0) SUBREADprintf("Scoring Overlap %s = %d >=%d, score=%d, exonid=%ld ; TOTAL_FRAG_LEN=%d\n", read_name, scoring_overlappings[score_x1], applied_fragment_minimum_overlapping, scoring_numbers[score_x1], scoring_exon_ids[score_x1], total_frag_len);
^
subread.h:122:44: note: in definition of macro 'SUBREADprintf'
#define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__)
^~~~~~~~~~~
readSummary.c: In function 'readSummary':
readSummary.c:5326:9: warning: variable 'curchr_name' set but not used [-Wunused-but-set-variable]
char * curchr_name, * fasta_contigs_fname;
^~~~~~~~~~~
readSummary.c:5325:15: warning: variable 'curpos' set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^~~~~~
readSummary.c:5325:7: warning: variable 'curchr' set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^~~~~~
readSummary.c: In function 'process_pairer_reset':
readSummary.c:1659:3: 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:1722:11: 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:1941:113: 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:1969:113: 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:2001:112: 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:2010:112: 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:4231:26: 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:4231:23: note: using the range [0, 4294967295] for directive argument
sprintf(rand_prefix, "%s/temp-core-%06u-%s.sam", global_context -> temp_file_dir, getpid(), MAC_or_random);
^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862:0,
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:4232:59: 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:862:0,
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:6354:34: warning: '%g' directive writing between 1 and 13 bytes into a region of size 11 [-Wformat-overflow=]
sprintf(strFeatureFracOverlap, "%g", fracOverlapFeature);
^~
readSummary.c:6354:33: note: assuming directive output of 12 bytes
sprintf(strFeatureFracOverlap, "%g", fracOverlapFeature);
^~~~
In file included from /usr/include/stdio.h:862:0,
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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -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:1209:2: 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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -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:66:24: 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:862:0,
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:75:25: 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:862:0,
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:77:25: 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:862:0,
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:862:0,
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:862:0,
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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -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
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/subread-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -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:372:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len,1,1,fp);
^~~~~~~~~~~~~~~~~~~~~~~
propmapped.c:375:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_name,read_len,1,fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
propmapped.c:379:6: 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:862:0,
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:363:22: 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:363:18: 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:862:0,
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-1.6.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.6.1"\" -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 longread-one/LRM longread-one/sublong
mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/
mv detectionCall 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-1.6.1+dfsg/src'
dh_auto_build -- CC=arm-linux-gnueabihf-gcc
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.6.1+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/subread-1.6.1+dfsg'
debian/tests/subread-tests /<<BUILDDIR>>/subread-1.6.1+dfsg
[2J[0;0H[30;47m
**************************************************
**************************************************
*** ***
*** This script will test the major functions ***
*** in our package, including the index build- ***
*** er, subread-align, subjunc, featureCounts ***
*** and exactSNP. ***
*** ***
*** Test will start in seconds. ***
*** ***
**************************************************
**************************************************
[13;26H[33;44m9[13;26H8[13;26H7[13;26H6[13;26H5[13;26H4[13;26H3[13;26H2[13;26H1[13;26H0[0m[2J[0,0H
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.1
//=========================== indexBuilder setting ===========================\\
|| ||
|| Index name : ../small1 ||
|| Index space : base-space ||
|| One block index : yes ||
|| 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=109.5k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=138.3k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=165.7k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=186.4k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=207.4k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=225.8k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=240.6k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=257.5k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=272.0k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=284.8k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=300.2k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=309.9k bps/s, total=0m ||
|| 52 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=69.4k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=86.7k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=103.5k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=120.5k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=137.3k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=154.0k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=170.3k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=185.9k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=201.0k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=215.2k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=228.8k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=241.3k bps/s, total=0m ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
|| [ 20.0% finished ] ||
|| [ 30.0% finished ] ||
|| [ 40.0% finished ] ||
|| [ 50.0% finished ] ||
|| [ 60.0% finished ] ||
|| [ 70.0% finished ] ||
|| [ 80.0% finished ] ||
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
|| Total running time: 0.2 minutes. ||
|| Index ../small1 was successfully built! ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file : data/test-noerror-r1.fq ||
|| Output file : result/test-tmp.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| Min votes : 3 / 10 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================ Running (10-Apr-2018 06:37:24, pid=31785) =================\\
|| ||
|| 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=4.6k reads per second ||
|| 39% completed, 0.3 mins elapsed, rate=4.9k reads per second ||
|| 46% completed, 0.3 mins elapsed, rate=5.2k reads per second ||
|| 53% completed, 0.3 mins elapsed, rate=5.4k reads per second ||
|| 60% completed, 0.3 mins elapsed, rate=5.6k 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=1.0k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 reads ||
|| Mapped : 18784 reads (93.9%), wherein ||
|| Uniquely mapped : 18784 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 1214 ||
|| ||
|| Indels : 0 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 1.9 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file : data/test-noerror-r1.fq ||
|| Output file : result/test-tmp.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| Min votes : 3 / 10 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================ Running (10-Apr-2018 06:39:20, pid=32220) =================\\
|| ||
|| 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=2.1k reads per second ||
|| 39% completed, 0.3 mins elapsed, rate=2.3k reads per second ||
|| 46% completed, 0.3 mins elapsed, rate=2.5k reads per second ||
|| 53% completed, 0.3 mins elapsed, rate=2.8k reads per second ||
|| 60% completed, 0.3 mins elapsed, rate=3.0k reads per second ||
|| 74% completed, 0.4 mins elapsed, rate=0.7k reads per second ||
|| 83% completed, 0.4 mins elapsed, rate=0.8k reads per second ||
|| 91% completed, 0.4 mins elapsed, rate=0.8k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 reads ||
|| Mapped : 18784 reads (93.9%), wherein ||
|| Uniquely mapped : 18784 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 1214 ||
|| ||
|| Indels : 0 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 2.0 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : data/test-noerror-r1.fq ||
|| Input file 2 : data/test-noerror-r2.fq ||
|| Output file : result/test-tmp.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================= Running (10-Apr-2018 06:41:23, pid=874) ==================\\
|| ||
|| 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=2.7k fragments per second ||
|| 39% completed, 0.3 mins elapsed, rate=2.8k fragments per second ||
|| 46% completed, 0.3 mins elapsed, rate=2.9k fragments per second ||
|| 53% completed, 0.3 mins elapsed, rate=3.0k fragments per second ||
|| 60% completed, 0.3 mins elapsed, rate=3.1k 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 : 19238 fragments (96.2%), wherein ||
|| Uniquely mapped : 19238 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 760 ||
|| ||
|| Correctly paired : 18852 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 : 0 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 1.7 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : data/test-noerror-r1.fq ||
|| Input file 2 : data/test-noerror-r2.fq ||
|| Output file : result/test-tmp.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================= Running (10-Apr-2018 06:43:13, pid=1105) =================\\
|| ||
|| The input file contains base space reads. ||
|| WARNING - The specified Phred score offset (33) seems incorrect. ||
|| ASCII values of the quality scores of read bases included in ||
|| the first 3000 reads were found to be within the range of ||
|| [73,73]. ||
|| ||
|| Load the 1-th index block... ||
|| 33% completed, 0.3 mins elapsed, rate=1.7k fragments per second ||
|| 39% completed, 0.4 mins elapsed, rate=1.9k fragments per second ||
|| 46% completed, 0.4 mins elapsed, rate=2.0k fragments per second ||
|| 53% completed, 0.4 mins elapsed, rate=2.1k fragments per second ||
|| 60% completed, 0.4 mins elapsed, rate=2.0k fragments per second ||
|| 74% completed, 0.4 mins elapsed, rate=0.6k fragments per second ||
|| 83% completed, 0.4 mins elapsed, rate=0.7k fragments per second ||
|| 91% completed, 0.4 mins elapsed, rate=0.7k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 19998 fragments ||
|| Mapped : 19238 fragments (96.2%), wherein ||
|| Uniquely mapped : 19238 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 760 ||
|| ||
|| Correctly paired : 18852 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 : 0 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 1.9 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : data/test-error-r1.fq ||
|| Input file 2 : data/test-error-r2.fq ||
|| Output file : result/test-tmp.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================= Running (10-Apr-2018 06:45:13, pid=2444) =================\\
|| ||
|| 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=2.2k fragments per second ||
|| 39% completed, 0.3 mins elapsed, rate=2.3k 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=2.6k 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 : 20000 fragments ||
|| Mapped : 18719 fragments (93.6%), wherein ||
|| Uniquely mapped : 18719 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 1281 ||
|| ||
|| Correctly paired : 13931 fragments ||
|| Not mapped in pairs : 4788 fragments, wherein ||
|| Only one end mapped : 4513 fragments ||
|| Multi-chromosomes : 0 fragments ||
|| Different strands : 0 fragments ||
|| Not in PE distance : 274 fragments ||
|| Abnormal order : 1 fragments ||
|| ||
|| Indels : 0 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 1.7 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.1
//========================== subread-align setting ===========================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : data/test-err-mut-r1.fq.gz ||
|| Input file 2 : data/test-err-mut-r2.fq.gz ||
|| Output file : result/test-tmp.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| Read group name : MyTestGroup ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================= Running (10-Apr-2018 06:47:00, pid=2448) =================\\
|| ||
|| 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=2.9k fragments per second ||
|| 67% completed, 0.3 mins elapsed, rate=3.0k fragments per second ||
|| 75% completed, 0.3 mins elapsed, rate=0.7k 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 : 18637 fragments (93.2%), wherein ||
|| Uniquely mapped : 18637 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 1364 ||
|| ||
|| Correctly paired : 13405 fragments ||
|| Not mapped in pairs : 5232 fragments, wherein ||
|| Only one end mapped : 4923 fragments ||
|| Multi-chromosomes : 0 fragments ||
|| Different strands : 0 fragments ||
|| Not in PE distance : 307 fragments ||
|| Abnormal order : 2 fragments ||
|| ||
|| Indels : 33 ||
|| ||
|| WARNING : Phred offset (33) incorrect? ||
|| ||
|| Running time : 1.9 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
142c7df9c22ca343bc66ba2be6e35eb6 ../small1.00.b.array
3b39eb4b0aad6902d8a1be198cf2478d ../small1.00.b.tab
*************************************************
*** SINGLE-END READS NO ERROR ******
*************************************************
unmatched= 0 ; matched= 18784 ; unmapped= 1214 ; reads= 19998 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.939293929393
paired_match= 0 ; paired= 0.0
*************************************************
*** SINGLE-END READS NO ERROR NO DUP ******
*************************************************
unmatched= 0 ; matched= 18784 ; unmapped= 1214 ; reads= 19998 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.939293929393
paired_match= 0 ; paired= 0.0
*************************************************
*** READS WITH NO ERROR ******
*************************************************
unmatched= 0 ; matched= 38475 ; unmapped= 1521 ; reads= 39996 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.96197119712
paired_match= 38474 ; paired= 0.999974009097
*************************************************
*** READS NO ERROR, NO DUPLICATED REPORT ******
*************************************************
unmatched= 0 ; matched= 38475 ; unmapped= 1521 ; reads= 39996 ;NN= 0
accuracy= 1.0 ; sensitivity= 0.96197119712
paired_match= 38474 ; paired= 0.999974009097
*************************************************
*** READS WITH ONLY SEQUENCING ERROR ******
*************************************************
unmatched= 2 ; matched= 32923 ; unmapped= 7075 ; reads= 40000 ;NN= 0
accuracy= 0.999939255885 ; sensitivity= 0.823125
paired_match= 28410 ; paired= 0.862922576922
*************************************************
*** READS WITH SEQUENCING ERROR AND MUTATION ***
*** SUBREAD IS RUN WITH LONG INDEL DETECTION ***
*************************************************
unmatched= 5 ; matched= 32344 ; unmapped= 7651 ; reads= 40002 ;NN= 0
accuracy= 0.999845435717 ; sensitivity= 0.808684565772
paired_match= 27422 ; paired= 0.847823398466
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.1
//=========================== indexBuilder setting ===========================\\
|| ||
|| Index name : ../small1 ||
|| Index space : base-space ||
|| Memory : 3000 Mbytes ||
|| Repeat threshold : 100 repeats ||
|| Distance to next subread : 3 ||
|| ||
|| Input files : 1 file in total ||
|| o ../chr901.fa ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================================= Running ==================================\\
|| ||
|| Check the integrity of provided reference sequences ... ||
|| There were 4 notes for reference sequences. ||
|| The notes can be found in the log file, '../small1.log'. ||
|| Scan uninformative subreads in reference sequences ... ||
|| 8%, 0 mins elapsed, rate=204.7k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=240.1k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=270.8k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=293.1k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=315.4k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=338.0k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=359.1k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=372.6k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=382.6k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=393.2k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=408.6k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=419.7k bps/s, total=0m ||
|| 2 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=126.0k bps/s, total=0m ||
|| 16%, 0 mins elapsed, rate=146.0k bps/s, total=0m ||
|| 24%, 0 mins elapsed, rate=162.6k bps/s, total=0m ||
|| 33%, 0 mins elapsed, rate=170.1k bps/s, total=0m ||
|| 41%, 0 mins elapsed, rate=182.0k bps/s, total=0m ||
|| 49%, 0 mins elapsed, rate=195.7k bps/s, total=0m ||
|| 58%, 0 mins elapsed, rate=209.3k bps/s, total=0m ||
|| 66%, 0 mins elapsed, rate=223.1k bps/s, total=0m ||
|| 74%, 0 mins elapsed, rate=234.3k bps/s, total=0m ||
|| 83%, 0 mins elapsed, rate=243.3k bps/s, total=0m ||
|| 91%, 0 mins elapsed, rate=257.7k bps/s, total=0m ||
|| 99%, 0 mins elapsed, rate=270.7k 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/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.1
//============================= subjunc setting ==============================\\
|| ||
|| Function : Read alignment + Junction detection (RNA-Seq) ||
|| Input file 1 : data/junction-reads-A.fq ||
|| Input file 2 : data/junction-reads-B.fq ||
|| Output file : result/junctions.sam (SAM) ||
|| Index name : ../small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 14 ||
|| Min read1 vote : 1 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================= Running (10-Apr-2018 06:49:05, pid=3528) =================\\
|| ||
|| 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=1.7k fragments per second ||
|| 48% completed, 0.4 mins elapsed, rate=1.7k fragments per second ||
|| 54% completed, 0.4 mins elapsed, rate=1.8k fragments per second ||
|| 61% completed, 0.5 mins elapsed, rate=1.8k 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 : 15213 fragments (94.8%), wherein ||
|| Uniquely mapped : 15213 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 839 ||
|| ||
|| Correctly paired : 13327 fragments ||
|| Not mapped in pairs : 1886 fragments, wherein ||
|| Only one end mapped : 1125 fragments ||
|| Multi-chromosomes : 0 fragments ||
|| Different strands : 36 fragments ||
|| Not in PE distance : 664 fragments ||
|| Abnormal order : 61 fragments ||
|| ||
|| Junctions : 384 ||
|| Indels : 31 ||
|| ||
|| Running time : 2.5 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.1
//============================= subjunc setting ==============================\\
|| ||
|| Function : Read alignment + Junction/Fusion detection (RNA-Seq) ||
|| Input file 1 : data/junction-reads-A.fq ||
|| Input file 2 : data/junction-reads-B.fq ||
|| Output file : result/junctionsNfusions.bam (BAM) ||
|| Index name : ../small1 ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 28 ||
|| Min read1 vote : 1 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Maximum allowed mismatches : 3 ||
|| Maximum allowed indel bases : 5 ||
|| # of best alignments reported : 1 ||
|| Unique mapping : yes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================= Running (10-Apr-2018 06:51:40, pid=4028) =================\\
|| ||
|| 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=1.2k fragments per second ||
|| 77% completed, 0.5 mins elapsed, rate=0.4k fragments per second ||
|| 87% completed, 0.5 mins elapsed, rate=0.4k fragments per second ||
|| 97% completed, 0.6 mins elapsed, rate=0.5k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed : 16052 fragments ||
|| Mapped : 15159 fragments (94.4%), wherein ||
|| Uniquely mapped : 15159 ||
|| Multi-mapping : 0 ||
|| ||
|| Not mapped : 893 ||
|| ||
|| Correctly paired : 13159 fragments ||
|| Not mapped in pairs : 2000 fragments, wherein ||
|| Only one end mapped : 1175 fragments ||
|| Multi-chromosomes : 0 fragments ||
|| Different strands : 36 fragments ||
|| Not in PE distance : 731 fragments ||
|| Abnormal order : 58 fragments ||
|| ||
|| Junctions : 392 ||
|| Fusions : 47 ||
|| Indels : 30 ||
|| ||
|| Running time : 2.9 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
================================================================================
FeatureCounts Basic Test
http://subread.sourceforge.net/
================================================================================
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.1
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 SAM file ||
|| P data/test-minimum.sam ||
|| ||
|| Output file : result/test-minimum.FC ||
|| Summary : result/test-minimum.FC.summary ||
|| Annotation : data/test-minimum.GTF (GTF) ||
|| Dir for temp files : result ||
|| ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Strand specific : no ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| 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
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.6.1
//============================= exactSNP setting =============================\\
|| ||
|| Input file : data/test-in.BAM (BAM) ||
|| Output file : result/test-out.VCF ||
|| Reference genome : ../chr901.fa ||
|| ||
|| Threads : 1 ||
|| Min supporting reads : 1 ||
|| Min pct. of supporting reads : 0.0% ||
|| Min base quality score : 13 ||
|| Number of trimmed bases : 3 ||
|| ||
|| Q value cutoff : 10E-12.0 ||
|| P value upper bound : 0.00500 ||
|| Flanking windows size : 5 ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (10-Apr-2018 06:54:40) ======================\\
|| ||
|| Split BAM file into result/temp-snps-006308-001F7BB4051E-* ... ||
|| 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-1.6.1+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-1.6.1+dfsg'
find /<<BUILDDIR>>/subread-1.6.1+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \;
mkdir -p /<<BUILDDIR>>/subread-1.6.1+dfsg/debian/subread/usr/share/man/man1
help2man --no-info --help-option="''" --no-discard-stderr --name='an accurate and efficient aligner for mapping both genomic \
DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \
/<<BUILDDIR>>/subread-1.6.1+dfsg/bin/subread-align | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.1+dfsg/debian/subread/usr/share/man/man1/subread-align.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='builds an base-space or color-space index using the reference sequences' \
/<<BUILDDIR>>/subread-1.6.1+dfsg/bin/subread-buildindex | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.1+dfsg/debian/subread/usr/share/man/man1/subread-buildindex.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='an RNA-seq aligner suitable for all purposes of RNA-seq analyses' \
/<<BUILDDIR>>/subread-1.6.1+dfsg/bin/subjunc | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.1+dfsg/debian/subread/usr/share/man/man1/subjunc.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='a highly efficient and accurate read summarization program' \
/<<BUILDDIR>>/subread-1.6.1+dfsg/bin/featureCounts | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.1+dfsg/debian/subread/usr/share/man/man1/featureCounts.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='a SNP caller that discovers SNPs by testing signals against local background noises' \
/<<BUILDDIR>>/subread-1.6.1+dfsg/bin/exactSNP | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.1+dfsg/debian/subread/usr/share/man/man1/exactSNP.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='detect short and long indels' \
/<<BUILDDIR>>/subread-1.6.1+dfsg/bin/subindel | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.1+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-1.6.1+dfsg/bin/sublong| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.1+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-1.6.1+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.1+dfsg/debian/subread/usr/share/man/man1/subread-fullscan.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='counting the coverage of mapped reads at each location on the entire reference genome' \
/<<BUILDDIR>>/subread-1.6.1+dfsg/bin/utilities/coverageCount | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.1+dfsg/debian/subread/usr/share/man/man1/coverageCount.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='calculate the proportion of mapped reads/fragments' \
/<<BUILDDIR>>/subread-1.6.1+dfsg/bin/utilities/propmapped | debian/filter.pl > /<<BUILDDIR>>/subread-1.6.1+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-1.6.1+dfsg/bin/utilities/qualityScores| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.1+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-1.6.1+dfsg/bin/utilities/repair| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.1+dfsg/debian/subread/usr/share/man/man1/repair.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='Remove duplicated reads' \
/<<BUILDDIR>>/subread-1.6.1+dfsg/bin/utilities/removeDup| debian/filter.pl > /<<BUILDDIR>>/subread-1.6.1+dfsg/debian/subread/usr/share/man/man1/removeDup.1;
dh_auto_install
make[1]: Leaving directory '/<<BUILDDIR>>/subread-1.6.1+dfsg'
dh_install -a -O--parallel
dh_installdocs -a -O--parallel
dh_installchangelogs -a -O--parallel
dh_installman -a -O--parallel
dh_perl -a -O--parallel
dh_link -a -O--parallel
dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
dh_fixperms -a -O--parallel
dh_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/lib/subread/removeDup debian/subread/usr/bin/subjunc debian/subread/usr/bin/subindel debian/subread/usr/lib/subread/repair debian/subread/usr/bin/featureCounts debian/subread/usr/lib/subread/txUnique debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/sublong debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/qualityScores debian/subread/usr/bin/exactSNP debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/coverageCount debian/subread/usr/bin/subread-align 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' in '../subread_1.6.1+dfsg-1_armhf.deb'.
dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_1.6.1+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../subread_1.6.1+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-1.6.1+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-04-10T06:56:05Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
subread_1.6.1+dfsg-1_armhf.changes:
-----------------------------------
Format: 1.8
Date: Wed, 04 Apr 2018 17:04:57 +0000
Source: subread
Binary: subread subread-data
Architecture: armhf
Version: 1.6.1+dfsg-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Alexandre Mestiashvili <mestia@debian.org>
Description:
subread - toolkit for processing next-gen sequencing data
subread-data - data files for subread package
Changes:
subread (1.6.1+dfsg-1) unstable; urgency=medium
.
[ Steffen Möller ]
* Added new d/u/metadata file
.
[ Alexandre Mestiashvili ]
* New upstream version 1.6.1+dfsg
* Update d/control, bump Policy to 4.1.3, fix Vcs-* fields to point to salsa
* Refresh patches
* Update copyright years
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Files:
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
subread-dbgsym_1.6.1+dfsg-1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 5452516 bytes: control archive=1200 bytes.
914 bytes, 12 lines control
1484 bytes, 14 lines md5sums
Package: subread-dbgsym
Source: subread
Version: 1.6.1+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6449
Depends: subread (= 1.6.1+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for subread
Build-Ids: 0cbd385c8428cb6ea58a7b6bc2536abf7e572998 1d4bc985516f1383f58bd00e77998b11cecd2b81 20eca14142a887cbca223104a321ba162b3b394f 28234100d372a51724534b8477d90c7c3ed7c7b3 2aac0c1fc2a6bd78d896d122838557a9c62d3653 3df92e247b5a790f920a227aa841ad484f773e6a 85cc14a6410e1e969b3ee58ac0b48868f987be03 a258f014da6d65ff6dc1aad1c8fa6fbb6298b5a3 ab2b1220d3b560a0ff3713d8c9e2b823dc6c5dfb b43a3398112aa6e5923151a22b5e69613a4685e6 d13a15d7735cbdc34283bff54add0693383debdb ea0f93970d1c925737b53ce853cdd2e23c6c441c eb0e9484464a1455cf20a4a645020f784c9c7bba f39a2907236f49e93390dc42f25b9aad20e3131a
drwxr-xr-x root/root 0 2018-04-04 17:04 ./
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/debug/.build-id/0c/
-rw-r--r-- root/root 510668 2018-04-04 17:04 ./usr/lib/debug/.build-id/0c/bd385c8428cb6ea58a7b6bc2536abf7e572998.debug
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/debug/.build-id/1d/
-rw-r--r-- root/root 491360 2018-04-04 17:04 ./usr/lib/debug/.build-id/1d/4bc985516f1383f58bd00e77998b11cecd2b81.debug
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/debug/.build-id/20/
-rw-r--r-- root/root 489624 2018-04-04 17:04 ./usr/lib/debug/.build-id/20/eca14142a887cbca223104a321ba162b3b394f.debug
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/debug/.build-id/28/
-rw-r--r-- root/root 484892 2018-04-04 17:04 ./usr/lib/debug/.build-id/28/234100d372a51724534b8477d90c7c3ed7c7b3.debug
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/debug/.build-id/2a/
-rw-r--r-- root/root 491316 2018-04-04 17:04 ./usr/lib/debug/.build-id/2a/ac0c1fc2a6bd78d896d122838557a9c62d3653.debug
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/debug/.build-id/3d/
-rw-r--r-- root/root 488480 2018-04-04 17:04 ./usr/lib/debug/.build-id/3d/f92e247b5a790f920a227aa841ad484f773e6a.debug
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/debug/.build-id/85/
-rw-r--r-- root/root 98852 2018-04-04 17:04 ./usr/lib/debug/.build-id/85/cc14a6410e1e969b3ee58ac0b48868f987be03.debug
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/debug/.build-id/a2/
-rw-r--r-- root/root 487588 2018-04-04 17:04 ./usr/lib/debug/.build-id/a2/58f014da6d65ff6dc1aad1c8fa6fbb6298b5a3.debug
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/debug/.build-id/ab/
-rw-r--r-- root/root 483856 2018-04-04 17:04 ./usr/lib/debug/.build-id/ab/2b1220d3b560a0ff3713d8c9e2b823dc6c5dfb.debug
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/debug/.build-id/b4/
-rw-r--r-- root/root 500556 2018-04-04 17:04 ./usr/lib/debug/.build-id/b4/3a3398112aa6e5923151a22b5e69613a4685e6.debug
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/debug/.build-id/d1/
-rw-r--r-- root/root 584400 2018-04-04 17:04 ./usr/lib/debug/.build-id/d1/3a15d7735cbdc34283bff54add0693383debdb.debug
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/debug/.build-id/ea/
-rw-r--r-- root/root 489188 2018-04-04 17:04 ./usr/lib/debug/.build-id/ea/0f93970d1c925737b53ce853cdd2e23c6c441c.debug
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/debug/.build-id/eb/
-rw-r--r-- root/root 487136 2018-04-04 17:04 ./usr/lib/debug/.build-id/eb/0e9484464a1455cf20a4a645020f784c9c7bba.debug
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/debug/.build-id/f3/
-rw-r--r-- root/root 485508 2018-04-04 17:04 ./usr/lib/debug/.build-id/f3/9a2907236f49e93390dc42f25b9aad20e3131a.debug
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/share/
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-04-04 17:04 ./usr/share/doc/subread-dbgsym -> subread
subread_1.6.1+dfsg-1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 397580 bytes: control archive=1512 bytes.
622 bytes, 14 lines control
1994 bytes, 31 lines md5sums
Package: subread
Version: 1.6.1+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4633
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 2018-04-04 17:04 ./
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/bin/
-rwxr-xr-x root/root 366860 2018-04-04 17:04 ./usr/bin/exactSNP
-rwxr-xr-x root/root 436860 2018-04-04 17:04 ./usr/bin/featureCounts
-rwxr-xr-x root/root 342300 2018-04-04 17:04 ./usr/bin/subindel
-rwxr-xr-x root/root 355452 2018-04-04 17:04 ./usr/bin/subjunc
-rwxr-xr-x root/root 62968 2018-04-04 17:04 ./usr/bin/sublong
-rwxr-xr-x root/root 355372 2018-04-04 17:04 ./usr/bin/subread-align
-rwxr-xr-x root/root 358644 2018-04-04 17:04 ./usr/bin/subread-buildindex
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/lib/subread/
-rwxr-xr-x root/root 346396 2018-04-04 17:04 ./usr/lib/subread/coverageCount
-rwxr-xr-x root/root 346396 2018-04-04 17:04 ./usr/lib/subread/propmapped
-rwxr-xr-x root/root 346508 2018-04-04 17:04 ./usr/lib/subread/qualityScores
-rwxr-xr-x root/root 342252 2018-04-04 17:04 ./usr/lib/subread/removeDup
-rwxr-xr-x root/root 342252 2018-04-04 17:04 ./usr/lib/subread/repair
-rwxr-xr-x root/root 342252 2018-04-04 17:04 ./usr/lib/subread/subread-fullscan
-rwxr-xr-x root/root 346348 2018-04-04 17:04 ./usr/lib/subread/txUnique
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/share/
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/share/doc/subread/
-rw-r--r-- root/root 500 2018-04-04 17:04 ./usr/share/doc/subread/README.Debian
-rw-r--r-- root/root 3850 2018-04-04 16:50 ./usr/share/doc/subread/README.txt
-rw-r--r-- root/root 2508 2018-04-04 17:04 ./usr/share/doc/subread/changelog.Debian.gz
-rw-r--r-- root/root 1138 2018-04-04 17:04 ./usr/share/doc/subread/copyright
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/share/man/
drwxr-xr-x root/root 0 2018-04-04 17:04 ./usr/share/man/man1/
-rw-r--r-- root/root 594 2018-04-04 17:04 ./usr/share/man/man1/coverageCount.1.gz
-rw-r--r-- root/root 1161 2018-04-04 17:04 ./usr/share/man/man1/exactSNP.1.gz
-rw-r--r-- root/root 3196 2018-04-04 17:04 ./usr/share/man/man1/featureCounts.1.gz
-rw-r--r-- root/root 471 2018-04-04 17:04 ./usr/share/man/man1/propmapped.1.gz
-rw-r--r-- root/root 577 2018-04-04 17:04 ./usr/share/man/man1/qualityScores.1.gz
-rw-r--r-- root/root 480 2018-04-04 17:04 ./usr/share/man/man1/removeDup.1.gz
-rw-r--r-- root/root 601 2018-04-04 17:04 ./usr/share/man/man1/repair.1.gz
-rw-r--r-- root/root 368 2018-04-04 17:04 ./usr/share/man/man1/subindel.1.gz
-rw-r--r-- root/root 2116 2018-04-04 17:04 ./usr/share/man/man1/subjunc.1.gz
-rw-r--r-- root/root 556 2018-04-04 17:04 ./usr/share/man/man1/sublong.1.gz
-rw-r--r-- root/root 2196 2018-04-04 17:04 ./usr/share/man/man1/subread-align.1.gz
-rw-r--r-- root/root 704 2018-04-04 17:04 ./usr/share/man/man1/subread-buildindex.1.gz
-rw-r--r-- root/root 369 2018-04-04 17:04 ./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: 114484
Build-Time: 1382
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 393
Job: subread_1.6.1+dfsg-1
Machine Architecture: armhf
Package: subread
Package-Time: 1836
Source-Version: 1.6.1+dfsg-1
Space: 114484
Status: successful
Version: 1.6.1+dfsg-1
--------------------------------------------------------------------------------
Finished at 2018-04-10T06:56:05Z
Build needed 00:30:36, 114484k disc space