subread →
1.4.6-p2+dfsg-2 →
armhf → 2015-05-25 15:28:44
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-01
╔══════════════════════════════════════════════════════════════════════════════╗
║ subread 1.4.6-p2+dfsg-2 (armhf) 25 May 2015 15:17 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: subread
Version: 1.4.6-p2+dfsg-2
Source Version: 1.4.6-p2+dfsg-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/subread-BKLzQz/subread-1.4.6-p2+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/subread-BKLzQz' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-03a4f848-916f-40e4-9292-22b14d790501' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [7902 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [9679 kB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
Fetched 17.6 MB in 33s (525 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
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Checking available source versions...
Download source files with APT
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Reading package lists...
Building dependency tree...
NOTICE: 'subread' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/subread.git
Need to get 13.9 MB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main subread 1.4.6-p2+dfsg-2 (dsc) [2121 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main subread 1.4.6-p2+dfsg-2 (tar) [13.9 MB]
Get:3 http://172.17.0.1/private/ stretch-staging/main subread 1.4.6-p2+dfsg-2 (diff) [6080 B]
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Download complete and in download only mode
Check arch
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-7II0a3/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 51 not upgraded.
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After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
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(Reading database ... 11998 files and directories currently installed.)
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Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), zlib1g-dev, help2man
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), zlib1g-dev, help2man
dpkg-deb: building package `sbuild-build-depends-subread-dummy' in `/«BUILDDIR»/resolver-8cLOFM/apt_archive/sbuild-build-depends-subread-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install subread build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils debhelper file gettext gettext-base groff-base help2man
intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info xdg-user-dirs xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils debhelper file gettext gettext-base groff-base help2man
intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1
libpipeline1 libunistring0 libxml2 man-db po-debconf
sbuild-build-depends-subread-dummy zlib1g-dev
0 upgraded, 20 newly installed, 0 to remove and 51 not upgraded.
Need to get 8724 kB/8725 kB of archives.
After this operation, 24.7 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.0-1 [24.0 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-1 [1085 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.0.2-5 [972 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libasprintf0c2 armhf 0.19.3-2 [31.1 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.22+15-2 [244 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.1+dfsg1-5 [703 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.1-2 [18.1 kB]
Get:9 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.44.1-1 [2314 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:11 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.22+15-2 [59.9 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.3-2 [116 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.3-2 [1167 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.2 [25.9 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150507 [824 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main help2man armhf 1.46.6 [142 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-2 [199 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 8724 kB in 2s (4133 kB/s)
Selecting previously unselected package libpipeline1:armhf.
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Preparing to unpack .../libpipeline1_1.4.0-1_armhf.deb ...
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Unpacking libglib2.0-0:armhf (2.44.1-1) ...
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Setting up libpipeline1:armhf (1.4.0-1) ...
Setting up groff-base (1.22.3-1) ...
Setting up bsdmainutils (9.0.6) ...
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 man-db (2.7.0.2-5) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.19.3-2) ...
Setting up libmagic1:armhf (1:5.22+15-2) ...
Setting up libxml2:armhf (2.9.1+dfsg1-5) ...
Setting up libffi6:armhf (3.1-2) ...
Setting up libglib2.0-0:armhf (2.44.1-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-3) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up file (1:5.22+15-2) ...
Setting up gettext-base (0.19.3-2) ...
Setting up gettext (0.19.3-2) ...
Setting up intltool-debian (0.35.0+20060710.2) ...
Setting up po-debconf (1.0.18) ...
Setting up debhelper (9.20150507) ...
Setting up help2man (1.46.6) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2) ...
Setting up sbuild-build-depends-subread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-18) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.25 g++-4.9_4.9.2-10 gcc-4.9_4.9.2-10 libc6-dev_2.19-18 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 linux-libc-dev_3.16.7-ckt4-1+rpi1
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.8 base-files_8+rpi1 base-passwd_3.5.37 bash_4.3-11 binutils_2.25-5 bsdmainutils_9.0.6 bsdutils_1:2.25.2-6 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:4.9.2-2 cpp-4.9_4.9.2-10 dash_0.5.7-4 debconf_1.5.56 debconf-i18n_1.5.56 debfoster_2.7-2 debhelper_9.20150507 debianutils_4.4 diffutils_1:3.3-1 dmsetup_2:1.02.90-2.2 dpkg_1.17.25 dpkg-dev_1.17.25 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9 g++_4:4.9.2-2 g++-4.9_4.9.2-10 gcc_4:4.9.2-2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-1 gcc-4.9_4.9.2-10 gcc-4.9-base_4.9.2-10 gettext_0.19.3-2 gettext-base_0.19.3-2 gnupg_1.4.18-7 gpgv_1.4.18-7 grep_2.20-4.1 groff-base_1.22.3-1 gzip_1.6-4 help2man_1.46.6 hostname_3.15 init_1.22 init-system-helpers_1.22 initramfs-tools_0.120 initscripts_2.88dsf-59 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.2 klibc-utils_2.0.4-2+rpi1 kmod_18-3 libacl1_2.2.52-2 libapt-pkg4.12_1.0.9.8 libasan1_4.9.2-10 libasprintf0c2_0.19.3-2 libatomic1_4.9.2-10 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1 libblkid1_2.25.2-6 libbz2-1.0_1.0.6-7 libc-bin_2.19-18 libc-dev-bin_2.19-18 libc6_2.19-18 libc6-dev_2.19-18 libcap2_1:2.24-8 libcap2-bin_1:2.24-8 libcloog-isl4_0.18.2-1 libcomerr2_1.42.12-1.1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-9 libdbus-1-3_1.8.16-1 libdebconfclient0_0.192 libdevmapper1.02.1_2:1.02.90-2.2 libdpkg-perl_1.17.25 libdrm2_2.4.58-2 libfakeroot_1.20.2-1 libffi6_3.1-2 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.2-10 libgcc1_1:4.9.2-10 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.44.1-1 libgmp10_2:6.0.0+dfsg-6+rpi1 libgomp1_4.9.2-10 libgpg-error0_1.17-3 libisl10_0.12.2-2 libklibc_2.0.4-2+rpi1 libkmod2_18-3 liblocale-gettext-perl_1.05-8+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.22+15-2 libmount1_2.25.2-6 libmpc3_1.0.2-1 libmpfr4_3.1.2-2 libncurses5_5.9+20140913-1 libncursesw5_5.9+20140913-1 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-3.3 libpipeline1_1.4.0-1 libpng12-0_1.2.50-2 libprocps3_2:3.3.9-9 libreadline6_6.3-8 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2 libsmartcols1_2.25.2-6 libss2_1.42.12-1.1 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 libsystemd0_215-17 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1 libubsan0_4.9.2-10 libudev1_215-17 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3 libuuid1_2.25.2-6 libxml2_2.9.1+dfsg1-5 linux-libc-dev_3.16.7-ckt4-1+rpi1 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.1 makedev_2.3.1-93 man-db_2.7.0.2-5 mawk_1.3.3-17 mount_2.25.2-6 mountall_2.54 multiarch-support_2.19-18 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-3 perl-base_5.20.2-3 perl-modules_5.20.2-3 plymouth_0.9.0-9 po-debconf_1.0.18 procps_2:3.3.9-9 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-subread-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 systemd_215-17 systemd-sysv_215-17 sysv-rc_2.88dsf-59 sysvinit-utils_2.88dsf-59 tar_1.27.1-2 tzdata_2015c-1 udev_215-17 util-linux_2.25.2-6 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-2 zlib1g-dev_1:1.2.8.dfsg-2
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sun May 10 09:04:08 2015 UTC using RSA key ID 1B5228B0
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./subread_1.4.6-p2+dfsg-2.dsc
dpkg-source: info: extracting subread in subread-1.4.6-p2+dfsg
dpkg-source: info: unpacking subread_1.4.6-p2+dfsg.orig.tar.xz
dpkg-source: info: unpacking subread_1.4.6-p2+dfsg-2.debian.tar.xz
dpkg-source: info: applying gcc_flags_cleanup.patch
dpkg-source: info: applying fix_syntax.patch
dpkg-source: info: applying inject_hardening_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
LANG=en_GB.UTF-8
LC_ALL=POSIX
LOGNAME=root
MAIL=/var/mail/root
OLDPWD=/usr/share/debootstrap/scripts
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/root
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-03a4f848-916f-40e4-9292-22b14d790501
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
SHLVL=1
SSH_CLIENT=172.17.0.6 44468 22
SSH_CONNECTION=172.17.0.6 44468 172.17.2.1 22
SSH_TTY=/dev/pts/0
TERM=xterm
USER=buildd
_=/etc/init.d/buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package subread
dpkg-buildpackage: source version 1.4.6-p2+dfsg-2
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build subread-1.4.6-p2+dfsg
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
debian/rules override_dh_clean
make[1]: Entering directory '/«BUILDDIR»/subread-1.4.6-p2+dfsg'
cd src; make -f Makefile.Linux clean
make[2]: Entering directory '/«BUILDDIR»/subread-1.4.6-p2+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
make[2]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p2+dfsg/src'
dh_clean
make[1]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p2+dfsg'
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/«BUILDDIR»/subread-1.4.6-p2+dfsg'
cd src; make -f Makefile.Linux
make[2]: Entering directory '/«BUILDDIR»/subread-1.4.6-p2+dfsg/src'
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o core.o core.c
core.c: In function 'print_in_box':
core.c:89:7: warning: variable 'is_R_linebreak' set but not used [-Wunused-but-set-variable]
char is_R_linebreak=0, * content, *out_line_buff;
^
core.c: In function 'convert_GZ_to_FQ':
core.c:770:25: warning: passing argument 1 of 'gzgets' from incompatible pointer type
char * bufr =gzgets(rawfp, linebuff, 3000);
^
In file included from sambam-file.h:23:0,
from core.h:47,
from core.c:42:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
core.c:781:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(rawfp);
^
In file included from sambam-file.h:23:0,
from core.h:47,
from core.c:42:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
core.c: In function 'convert_read_to_tmp':
core.c:1089:7: warning: variable 'current_repeated_times' set but not used [-Wunused-but-set-variable]
int current_repeated_times;
^
core.c: In function 'do_voting':
core.c:2980:9: 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: In function 'split_read_files':
core.c:3309:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(read_line_buf, 3000, global_context->input_reads.first_read_file.input_fp);
^
core.c:3311:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(read_line_buf2, 3000, global_context->input_reads.second_read_file.input_fp);
^
core.c:3340:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(read_line_buf, 3000, global_context->input_reads.first_read_file.input_fp);
^
core.c:3341:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
fgets(read_line_buf2, 3000, global_context->input_reads.second_read_file.input_fp);
^
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c
core-junction.c: In function 'search_events_to_back':
core-junction.c:388:6: warning: variable 'move_start' set but not used [-Wunused-but-set-variable]
int move_start = read_tail_pos - global_context -> config.realignment_minimum_variant_distance;
^
core-junction.c: In function 'finalise_explain_CIGAR':
core-junction.c:1769:23: warning: variable 'tmp_cigar_exonic' set but not used [-Wunused-but-set-variable]
char tmp_cigar[120], tmp_cigar_exonic[120];
^
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c
core-indel.c: In function 'find_new_indels':
core-indel.c:1486:9: warning: variable 'best_j' set but not used [-Wunused-but-set-variable]
int best_j=0, best_score=-99999, is_ambiguous_indel= 0;
^
core-indel.c: In function 'full_indel_alignment':
core-indel.c:2828:41: warning: variable 'best_right' set but not used [-Wunused-but-set-variable]
int best_edge_score = -1, best_left, best_right;
^
core-indel.c:2828:30: 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:2933:24: 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:3211:3: 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:3212:3: 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:3213:3: 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:3290:3: 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:3291:3: 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:3292:3: 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:3647:3: 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:3648:3: 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:3649:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c
sambam-file.c: In function 'PBam_get_next_zchunk':
sambam-file.c:324:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&ID1, 1, 1, bam_fp);
^
sambam-file.c:325:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&ID2, 1, 1, bam_fp);
^
sambam-file.c:326:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&CM, 1, 1, bam_fp);
^
sambam-file.c:327:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&FLG, 1, 1, bam_fp);
^
sambam-file.c:336:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&XLEN,1, 2, bam_fp );
^
sambam-file.c:344:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SI1, 1, 1, bam_fp);
^
sambam-file.c:345:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SI2, 1, 1, bam_fp);
^
sambam-file.c:346:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&SLEN, 1, 2, bam_fp);
^
sambam-file.c:350:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&BSIZE_MID, 1,2 , bam_fp);
^
sambam-file.c:362:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(buffer, 1, CDATA_READING, bam_fp);
^
sambam-file.c:366:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&real_len, 4, 1, bam_fp);
^
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c
gene-algorithms.c: In function 'show_cigar':
gene-algorithms.c:747:6: warning: variable 'last_end' set but not used [-Wunused-but-set-variable]
int last_end=0, last_offset = 0, cursor = 0;
^
gene-algorithms.c:746:9: 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:1159:28: 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:1703:6: 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:2344:7: warning: variable 'is_match_begin' set but not used [-Wunused-but-set-variable]
int is_match_begin = 0;
^
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c
input-files.c: In function 'f_subr_open':
input-files.c:46:3: warning: implicit declaration of function 'fopen64' [-Wimplicit-function-declaration]
return fopen64(fname, mode);
^
input-files.c:46:3: warning: return makes pointer from integer without a cast
input-files.c: In function 'geinput_next_char':
input-files.c:442:5: 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 'sort_SAM_finalise':
input-files.c:2188:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^
input-files.c:2194:6: 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:2197:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len,2,1,bbfp);
^
input-files.c:2203:6: 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:2256:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^
input-files.c:2262:6: 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:2266:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, 2,1 , bbfp);
^
input-files.c:2269:6: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(read_line_buf, 1, read_len, bbfp);
^
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c
sorted-hashtable.c: In function 'gehash_load':
sorted-hashtable.c:1249:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^
sorted-hashtable.c:1272:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^
sorted-hashtable.c:1275:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^
sorted-hashtable.c:1278:6: 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: In function 'gehash_go_q_tolerable':
sorted-hashtable.c:510:22: warning: array subscript is above array bounds [-Warray-bounds]
mutation_stack[j] = 0;
^
sorted-hashtable.c: In function 'gehash_go_q_CtoT':
sorted-hashtable.c:591:22: warning: array subscript is above array bounds [-Warray-bounds]
mutation_stack[j] = 0;
^
sorted-hashtable.c:609:22: warning: array subscript is above array bounds [-Warray-bounds]
error_pos_stack[j] = error_pos_stack[i] + (j-i);
^
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -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 -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE
readSummary.c: In function 'readSummary':
readSummary.c:2708:9: warning: variable 'curchr_name' set but not used [-Wunused-but-set-variable]
char * curchr_name;
^
readSummary.c:2707:15: warning: variable 'curpos' set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^
readSummary.c:2707:7: warning: variable 'curchr' set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^
readSummary.c: In function 'load_feature_info':
readSummary.c:528:84: warning: 'token_temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(chro_name_len > CHROMOSOME_NAME_LENGTH) seq_name[CHROMOSOME_NAME_LENGTH -1 ] = 0;
^
readSummary.c:485:40: warning: 'token_temp' may be used uninitialized in this function [-Wmaybe-uninitialized]
chro_name[CHROMOSOME_NAME_LENGTH-1]=0;
^
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE
index-builder.c: In function 'scan_gene_index':
index-builder.c:449:19: warning: variable 'table_no' set but not used [-Wunused-but-set-variable]
int file_number, table_no, i ,j;
^
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subtools subtools.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 -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE
qualityScores.c: In function 'finalise_qs_context':
qualityScores.c:82:12: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(qs_context -> gzfq_reader);
^
In file included from qualityScores.c:24:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
qualityScores.c: In function 'rewind_qs_file':
qualityScores.c:275:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(qs_context -> gzfq_reader);
^
In file included from qualityScores.c:24:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
qualityScores.c:282:29: warning: assignment from incompatible pointer type
qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb");
^
qualityScores.c: In function 'start_qs_context':
qualityScores.c:313:29: warning: assignment from incompatible pointer type
qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb");
^
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o coverageCount coverage_calc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE
gcc -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0 -o globalReassembly global-reassembly.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 -fPIE -pie -Wl,-z,relro -Wl,-z,now -lpthread -lz -lm -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE
global-reassembly.c: In function 'GRA_trim_reads':
global-reassembly.c:415:7: warning: variable 'in_flags_1' set but not used [-Wunused-but-set-variable]
int in_flags_1= -1, is_second_read = 0;
^
global-reassembly.c: In function 'GRA_reassemble_reads_LR':
global-reassembly.c:1435:14: warning: variable 'target_votes' set but not used [-Wunused-but-set-variable]
int mm=0, target_votes=0, new_bases_len;
^
mkdir -p ../bin/utilities
mv subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/
mv globalReassembly coverageCount propmapped qualityScores removeDup subread-fullscan subtools ../bin/utilities
make[2]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p2+dfsg/src'
dh_auto_build
make[1]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p2+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/«BUILDDIR»/subread-1.4.6-p2+dfsg'
debian/tests/subread-tests /«BUILDDIR»/subread-1.4.6-p2+dfsg
Version 1.4.6-p2
Usage:
./exactSNP [options] -i input -g reference_genome -o output
Required arguments:
-i <file> Specify name of an input file including read mapping results. The
[-b if BAM] format of input file can be SAM or BAM (-b needs to be specified
if a BAM file is provided).
-g <file> Specify name of the file including all reference sequences. Only
one single FASTA format file should be provided.
-o <file> Specify name of the output file. This program outputs a VCF format
file that includes discovered SNPs.
Optional arguments:
-a <file> Provide a set of annotated SNPs (e.g. SNPs included in the dbSNP
database). The supplied file should be in VCF format. Providing
known SNPs to the program should improve its SNP calling
performance. Note that the provided SNPs may or may not be called.
-b Indicate the input file provided via -i is in BAM format.
-Q <int> Specify the q-value cutoff for SNP calling at sequencing depth of
50X. 12 by default. The corresponding p-value cutoff is 10^(-1*Q).
Note that this program automatically adjusts the q-value cutoff
according to the sequencing depth at each chromosomal location.
-f <float> Specify the minimum fraction of mis-matched bases a SNP-containing
location must have. Its value must between 0 and 1. 0 by default.
-n <int> Specify the minimum number of mis-matched bases a SNP-containing
location must have. 1 by default.
-r <int> Specify the minimum number of mapped reads a SNP-containing
location must have (ie. the minimum coverage). 1 by default.
-x <int> Specify the maximum number of mapped reads a SNP-containing
location have have. 3000 by default. Any location having more than
the threshold number of reads will not be considered for SNP
calling. This option is useful for removing PCR artefacts.
-s <int> Specify the minimum base quality scores (Phred scores) read bases
must satisfy to be used for SNP calling. 13 by default. Read bases
with quality scores less than 13 will be excluded from the
analysis.
-t <int> Specify the number of bases trimmed off from each end of the read.
3 by default.
-T <int> Specify the number of threads. 1 by default.
-v output version of the program.
Example:
./exactSNP -i my-alignment.sam -g mm10.fa -o my-SNPs.txt
make[1]: *** [override_dh_auto_test] Error 255
debian/rules:25: recipe for target 'override_dh_auto_test' failed
make[1]: Leaving directory '/«BUILDDIR»/subread-1.4.6-p2+dfsg'
make: *** [build-arch] Error 2
debian/rules:14: recipe for target 'build-arch' failed
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150525-1526
Finished
────────
E: Build failure (dpkg-buildpackage died)
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 122040
Build-Time: 320
Distribution: stretch-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 155
Job: subread_1.4.6-p2+dfsg-2
Machine Architecture: armhf
Package: subread
Package-Time: 544
Source-Version: 1.4.6-p2+dfsg-2
Space: 122040
Status: attempted
Version: 1.4.6-p2+dfsg-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20150525-1526
Build needed 00:09:04, 122040k disc space