idba →
1.1.1-1 →
armhf → 2014-03-09 07:14:09
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ idba 1.1.1-1 (armhf) 09 Mar 2014 06:54 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: idba
Version: 1.1.1-1
Source Version: 1.1.1-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/idba-0rc7ry/idba-1.1.1' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/idba-0rc7ry' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-0f5e3d57-9d59-4bb4-8d04-9a735008b53c' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7301 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8461 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
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Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
─────────
Checking available source versions...
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'idba' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/idba/trunk/
Need to get 214 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main idba 1.1.1-1 (dsc) [1910 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main idba 1.1.1-1 (tar) [209 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main idba 1.1.1-1 (diff) [3116 B]
Fetched 214 kB in 0s (2670 kB/s)
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-eULgqp/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...
Reading state information...
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 5 not upgraded.
Need to get 0 B/816 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11599 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9)
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9)
dpkg-deb: building package `sbuild-build-depends-idba-dummy' in `/«BUILDDIR»/resolver-gr95FD/apt_archive/sbuild-build-depends-idba-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install idba 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 intltool-debian
libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1 libpipeline1
libunistring0 libxml2 man-db po-debconf
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 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils debhelper file gettext gettext-base groff-base intltool-debian
libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libmagic1 libpipeline1
libunistring0 libxml2 man-db po-debconf sbuild-build-depends-idba-dummy
0 upgraded, 18 newly installed, 0 to remove and 5 not upgraded.
Need to get 8104 kB/8105 kB of archives.
After this operation, 22.5 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.2.6-2 [20.3 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-5 [962 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.6-1 [961 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.2-1 [29.0 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.17-0.1 [224 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-3 [836 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.0.13-12 [17.4 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.38.2-5 [2073 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.17-0.1 [54.8 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3.2-1 [112 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3.2-1 [1137 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20140228 [691 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 8104 kB in 1s (4171 kB/s)
Selecting previously unselected package libpipeline1:armhf.
(Reading database ... 11599 files and directories currently installed.)
Preparing to unpack .../libpipeline1_1.2.6-2_armhf.deb ...
Unpacking libpipeline1:armhf (1.2.6-2) ...
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Preparing to unpack .../groff-base_1.22.2-5_armhf.deb ...
Unpacking groff-base (1.22.2-5) ...
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Unpacking man-db (2.6.6-1) ...
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Unpacking libasprintf0c2:armhf (0.18.3.2-1) ...
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Preparing to unpack .../libxml2_2.9.1+dfsg1-3_armhf.deb ...
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Preparing to unpack .../sbuild-build-depends-idba-dummy.deb ...
Unpacking sbuild-build-depends-idba-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.2.6-2) ...
Setting up groff-base (1.22.2-5) ...
Setting up bsdmainutils (9.0.5) ...
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 (2.6.6-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.18.3.2-1) ...
Setting up libmagic1:armhf (1:5.17-0.1) ...
Setting up libxml2:armhf (2.9.1+dfsg1-3) ...
Setting up libffi6:armhf (3.0.13-12) ...
Setting up libglib2.0-0:armhf (2.38.2-5) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-2) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up file (1:5.17-0.1) ...
Setting up gettext-base (0.18.3.2-1) ...
Setting up gettext (0.18.3.2-1) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20140228) ...
Setting up sbuild-build-depends-idba-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.18-4) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.13-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24-3 dpkg-dev_1.17.6+rpi1 g++-4.8_4.8.2-16 gcc-4.8_4.8.2-16 libc6-dev_2.18-4 libstdc++-4.8-dev_4.8.2-16 libstdc++6_4.8.2-16 linux-libc-dev_3.12.6-2+rpi1
Package versions: apt_0.9.15.4 base-files_7.2+rpi1 base-passwd_3.5.28 bash_4.2+dfsg-1 binutils_2.24-3 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.6 build-essential_11.6 bzip2_1.0.6-5 coreutils_8.21-1 cpio_2.11+dfsg-1 cpp_4:4.8.2-2 cpp-4.8_4.8.2-16 dash_0.5.7-4 debconf_1.5.52 debconf-i18n_1.5.52 debfoster_2.7-1.2 debhelper_9.20140228 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.6+rpi1 dpkg-dev_1.17.6+rpi1 e2fslibs_1.42.9-3 e2fsprogs_1.42.9-3 fakeroot_1.18.4-2 file_1:5.17-0.1 findutils_4.4.2-7 g++_4:4.8.2-2 g++-4.8_4.8.2-16 gcc_4:4.8.2-2 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-10+rpi1 gcc-4.8_4.8.2-16 gcc-4.8-base_4.8.2-16 gettext_0.18.3.2-1 gettext-base_0.18.3.2-1 gnupg_1.4.16-1.1 gpgv_1.4.16-1.1 grep_2.16-1 groff-base_1.22.2-5 gzip_1.6-3 hostname_3.15 initramfs-tools_0.115 initscripts_2.88dsf-51 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.2-1+rpi1 kmod_16-2 libacl1_2.2.52-1 libapt-pkg4.12_0.9.15.4 libasan0_4.8.2-16 libasprintf0c2_0.18.3.2-1 libatomic1_4.8.2-16 libattr1_1:2.4.47-1 libaudit-common_1:2.3.3-4 libaudit1_1:2.3.3-4 libblkid1_2.20.1-5.6 libbz2-1.0_1.0.6-5 libc-bin_2.18-4 libc-dev-bin_2.18-4 libc6_2.18-4 libc6-dev_2.18-4 libcap2_1:2.22-1.2 libcloog-isl4_0.18.2-1 libcomerr2_1.42.9-3 libcroco3_0.6.8-2 libdb5.1_5.1.29-6 libdb5.3_5.3.28-3 libdbus-1-3_1.8.0-1 libdpkg-perl_1.17.6+rpi1 libffi6_3.0.13-12 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.2-16 libgcc1_1:4.8.2-16 libgdbm3_1.8.3-12 libglib2.0-0_2.38.2-5 libgmp10_2:5.1.3+dfsg-1 libgomp1_4.8.2-16 libisl10_0.12.2-1 libklibc_2.0.2-1+rpi1 libkmod2_16-2 liblocale-gettext-perl_1.05-7+b3 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.17-0.1 libmount1_2.20.1-5.6 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libncursesw5_5.9+20140118-1 libpam-modules_1.1.8-2 libpam-modules-bin_1.1.8-2 libpam-runtime_1.1.8-2 libpam0g_1.1.8-2 libpcre3_1:8.31-2 libpipeline1_1.2.6-2 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-2 libreadline6_6.2+dfsg-0.1 libselinux1_2.2.2-1 libsemanage-common_2.2-1 libsemanage1_2.2-1 libsepol1_2.2-1 libslang2_2.2.4-16 libss2_1.42.9-3 libstdc++-4.8-dev_4.8.2-16 libstdc++6_4.8.2-16 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b3 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-1 libtinfo5_5.9+20140118-1 libudev1_204-7 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.6 libxml2_2.9.1+dfsg1-3 linux-libc-dev_3.12.6-2+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian12+rpi1 make_3.81-8.3 makedev_2.3.1-93 man-db_2.6.6-1 mawk_1.3.3-17 mount_2.20.1-5.6 multiarch-support_2.18-4 nano_2.2.6-1 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 passwd_1:4.1.5.1-1 patch_2.7.1-4 perl_5.18.2-2 perl-base_5.18.2-2 perl-modules_5.18.2-2 plymouth_0.8.8-6+deb8u3 po-debconf_1.0.16+nmu2 procps_1:3.3.9-2 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-idba-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 sysv-rc_2.88dsf-51 sysvinit_2.88dsf-51 sysvinit-core_2.88dsf-51 sysvinit-utils_2.88dsf-51 tar_1.27.1-1 tzdata_2013i-1 udev_204-7 util-linux_2.20.1-5.6 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Thu Feb 13 16:58:56 2014 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./idba_1.1.1-1.dsc
dpkg-source: info: extracting idba in idba-1.1.1
dpkg-source: info: unpacking idba_1.1.1.orig.tar.gz
dpkg-source: info: unpacking idba_1.1.1-1.debian.tar.xz
Check disc space
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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
PWD=/build/buildd
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-0f5e3d57-9d59-4bb4-8d04-9a735008b53c
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package idba
dpkg-buildpackage: source version 1.1.1-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build idba-1.1.1
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_auto_configure -a
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... none
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... none
checking for ranlib... ranlib
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for working memcmp... yes
checking for vprintf... yes
checking for _doprnt... no
checking for sqrt... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bin/Makefile
config.status: creating lib/Makefile
config.status: creating test/Makefile
config.status: creating script/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
dh_auto_build -a
make[1]: Entering directory `/«PKGBUILDDIR»'
make all-recursive
make[2]: Entering directory `/«PKGBUILDDIR»'
Making all in lib
make[3]: Entering directory `/«PKGBUILDDIR»/lib'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o math.o `test -f '../src/basic/math.cpp' || echo './'`../src/basic/math.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o utils.o `test -f '../src/misc/utils.cpp' || echo './'`../src/misc/utils.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o hash_aligner.o `test -f '../src/misc/hash_aligner.cpp' || echo './'`../src/misc/hash_aligner.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o blat_record.o `test -f '../src/misc/blat_record.cpp' || echo './'`../src/misc/blat_record.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o options_description.o `test -f '../src/misc/options_description.cpp' || echo './'`../src/misc/options_description.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o log.o `test -f '../src/misc/log.cpp' || echo './'`../src/misc/log.cpp
../src/misc/log.cpp: In static member function 'static void* LogThread::LogThreadFunc(void*)':
../src/misc/log.cpp:121:44: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result]
write(log_thread.out_fd, line, len);
^
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o compact_sequence.o `test -f '../src/sequence/compact_sequence.cpp' || echo './'`../src/sequence/compact_sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o sequence_writer.o `test -f '../src/sequence/sequence_writer.cpp' || echo './'`../src/sequence/sequence_writer.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o sequence.o `test -f '../src/sequence/sequence.cpp' || echo './'`../src/sequence/sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o sequence_io.o `test -f '../src/sequence/sequence_io.cpp' || echo './'`../src/sequence/sequence_io.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o short_sequence.o `test -f '../src/sequence/short_sequence.cpp' || echo './'`../src/sequence/short_sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o sequence_reader.o `test -f '../src/sequence/sequence_reader.cpp' || echo './'`../src/sequence/sequence_reader.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o hash_graph_branch_group.o `test -f '../src/graph/hash_graph_branch_group.cpp' || echo './'`../src/graph/hash_graph_branch_group.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o hash_graph.o `test -f '../src/graph/hash_graph.cpp' || echo './'`../src/graph/hash_graph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o scaffold_graph.o `test -f '../src/graph/scaffold_graph.cpp' || echo './'`../src/graph/scaffold_graph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o contig_graph_branch_group.o `test -f '../src/graph/contig_graph_branch_group.cpp' || echo './'`../src/graph/contig_graph_branch_group.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o contig_graph.o `test -f '../src/graph/contig_graph.cpp' || echo './'`../src/graph/contig_graph.cpp
../src/graph/contig_graph.cpp: In member function 'void ContigGraph::TopSort(std::deque<ContigGraphVertexAdaptor>&, std::deque<ContigGraphVertexAdaptor>&)':
../src/graph/contig_graph.cpp:1385:30: warning: variable 'end' set but not used [-Wunused-but-set-variable]
ContigGraphVertexAdaptor end = GetEndVertexAdaptor(component);
^
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o contig_info.o `test -f '../src/graph/contig_info.cpp' || echo './'`../src/graph/contig_info.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o local_assembler.o `test -f '../src/assembly/local_assembler.cpp' || echo './'`../src/assembly/local_assembler.cpp
../src/assembly/local_assembler.cpp: In static member function 'static void* LocalAssemblerWithReference::LocalAssembleThread(void*)':
../src/assembly/local_assembler.cpp:488:22: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
bool flag = false;
^
../src/assembly/local_assembler.cpp:489:21: warning: variable 'aligned' set but not used [-Wunused-but-set-variable]
int aligned[2] = {0};
^
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o assembly_utility.o `test -f '../src/assembly/assembly_utility.cpp' || echo './'`../src/assembly/assembly_utility.cpp
rm -f libassembly.a
ar cru libassembly.a math.o utils.o hash_aligner.o blat_record.o options_description.o log.o compact_sequence.o sequence_writer.o sequence.o sequence_io.o short_sequence.o sequence_reader.o hash_graph_branch_group.o hash_graph.o scaffold_graph.o contig_graph_branch_group.o contig_graph.o contig_info.o local_assembler.o assembly_utility.o
ranlib libassembly.a
make[3]: Leaving directory `/«PKGBUILDDIR»/lib'
Making all in bin
make[3]: Entering directory `/«PKGBUILDDIR»/bin'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o idba_hybrid.o `test -f '../src/release/idba_hybrid.cpp' || echo './'`../src/release/idba_hybrid.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o idba_hybrid idba_hybrid.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o sort_reads.o `test -f '../src/tools/sort_reads.cpp' || echo './'`../src/tools/sort_reads.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o sort_reads sort_reads.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o parallel_rna_blat.o `test -f '../src/tools/parallel_rna_blat.cpp' || echo './'`../src/tools/parallel_rna_blat.cpp
../src/tools/parallel_rna_blat.cpp: In function 'void CreateFile(const string&)':
../src/tools/parallel_rna_blat.cpp:47:24: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
^
../src/tools/parallel_rna_blat.cpp: In function 'void RemoveFile(const string&)':
../src/tools/parallel_rna_blat.cpp:53:24: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
^
../src/tools/parallel_rna_blat.cpp: In function 'void Append(const string&, const string&)':
../src/tools/parallel_rna_blat.cpp:59:24: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
^
../src/tools/parallel_rna_blat.cpp: In function 'void RunBlat(const string&)':
../src/tools/parallel_rna_blat.cpp:96:32: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
^
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o parallel_rna_blat parallel_rna_blat.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o test.o `test -f '../src/tools/test.cpp' || echo './'`../src/tools/test.cpp
../src/tools/test.cpp:6:32: warning: extra tokens at end of #include directive [enabled by default]
#include "graph/contig_graph.h";
^
../src/tools/test.cpp:7:31: warning: extra tokens at end of #include directive [enabled by default]
#include "sequence/sequence.h";
^
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o test test.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o print_graph.o `test -f '../src/tools/print_graph.cpp' || echo './'`../src/tools/print_graph.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o print_graph print_graph.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o validate_rna.o `test -f '../src/tools/validate_rna.cpp' || echo './'`../src/tools/validate_rna.cpp
../src/tools/validate_rna.cpp: In function 'int main(int, char**)':
../src/tools/validate_rna.cpp:396:55: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
fscanf(flist, "%s %lf", buf, &coverage[i]);
^
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o validate_rna validate_rna.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o scaffold.o `test -f '../src/tools/scaffold.cpp' || echo './'`../src/tools/scaffold.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o scaffold scaffold.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o shuffle_reads.o `test -f '../src/tools/shuffle_reads.cpp' || echo './'`../src/tools/shuffle_reads.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o shuffle_reads shuffle_reads.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o fa2fq.o `test -f '../src/tools/fa2fq.cpp' || echo './'`../src/tools/fa2fq.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o fa2fq fa2fq.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o validate_contigs_mummer.o `test -f '../src/tools/validate_contigs_mummer.cpp' || echo './'`../src/tools/validate_contigs_mummer.cpp
../src/tools/validate_contigs_mummer.cpp: In function 'int main(int, char**)':
../src/tools/validate_contigs_mummer.cpp:218:33: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MaxLine, fcoord);
^
../src/tools/validate_contigs_mummer.cpp:219:33: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MaxLine, fcoord);
^
../src/tools/validate_contigs_mummer.cpp:220:33: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MaxLine, fcoord);
^
../src/tools/validate_contigs_mummer.cpp:221:33: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MaxLine, fcoord);
^
../src/tools/validate_contigs_mummer.cpp:222:33: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MaxLine, fcoord);
^
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o validate_contigs_mummer validate_contigs_mummer.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o filter_blat.o `test -f '../src/tools/filter_blat.cpp' || echo './'`../src/tools/filter_blat.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o filter_blat filter_blat.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o sort_psl.o `test -f '../src/tools/sort_psl.cpp' || echo './'`../src/tools/sort_psl.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o sort_psl sort_psl.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o validate_reads_blat.o `test -f '../src/tools/validate_reads_blat.cpp' || echo './'`../src/tools/validate_reads_blat.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o validate_reads_blat validate_reads_blat.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o validate_component.o `test -f '../src/tools/validate_component.cpp' || echo './'`../src/tools/validate_component.cpp
../src/tools/validate_component.cpp: In function 'int main(int, char**)':
../src/tools/validate_component.cpp:141:13: warning: unused variable 'ref_id' [-Wunused-variable]
int ref_id = dict[record.ref_name];
^
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o validate_component validate_component.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o filter_contigs.o `test -f '../src/tools/filter_contigs.cpp' || echo './'`../src/tools/filter_contigs.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o filter_contigs filter_contigs.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o sample_reads.o `test -f '../src/tools/sample_reads.cpp' || echo './'`../src/tools/sample_reads.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o sample_reads sample_reads.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o split_fq.o `test -f '../src/tools/split_fq.cpp' || echo './'`../src/tools/split_fq.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o split_fq split_fq.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o idba_tran_test.o `test -f '../src/tools/idba_tran_test.cpp' || echo './'`../src/tools/idba_tran_test.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o idba_tran_test idba_tran_test.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o split_fa.o `test -f '../src/tools/split_fa.cpp' || echo './'`../src/tools/split_fa.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o split_fa split_fa.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o fq2fa.o `test -f '../src/release/fq2fa.cpp' || echo './'`../src/release/fq2fa.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o fq2fa fq2fa.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o raw_n50.o `test -f '../src/release/raw_n50.cpp' || echo './'`../src/release/raw_n50.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o raw_n50 raw_n50.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o parallel_blat.o `test -f '../src/release/parallel_blat.cpp' || echo './'`../src/release/parallel_blat.cpp
../src/release/parallel_blat.cpp: In function 'void CreateFile(const string&)':
../src/release/parallel_blat.cpp:47:24: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
^
../src/release/parallel_blat.cpp: In function 'void RemoveFile(const string&)':
../src/release/parallel_blat.cpp:53:24: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
^
../src/release/parallel_blat.cpp: In function 'void Append(const string&, const string&)':
../src/release/parallel_blat.cpp:59:24: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
^
../src/release/parallel_blat.cpp: In function 'void RunBlat(const string&)':
../src/release/parallel_blat.cpp:96:32: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
^
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o parallel_blat parallel_blat.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o split_scaffold.o `test -f '../src/release/split_scaffold.cpp' || echo './'`../src/release/split_scaffold.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o split_scaffold split_scaffold.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o validate_contigs_blat.o `test -f '../src/release/validate_contigs_blat.cpp' || echo './'`../src/release/validate_contigs_blat.cpp
../src/release/validate_contigs_blat.cpp: In function 'int main(int, char**)':
../src/release/validate_contigs_blat.cpp:388:55: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
fscanf(flist, "%s %lf", buf, &coverage[i]);
^
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o validate_contigs_blat validate_contigs_blat.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o filterfa.o `test -f '../src/release/filterfa.cpp' || echo './'`../src/release/filterfa.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o filterfa filterfa.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o sim_reads.o `test -f '../src/release/sim_reads.cpp' || echo './'`../src/release/sim_reads.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o sim_reads sim_reads.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o idba_ud.o `test -f '../src/release/idba_ud.cpp' || echo './'`../src/release/idba_ud.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o idba_ud idba_ud.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o sim_reads_tran.o `test -f '../src/release/sim_reads_tran.cpp' || echo './'`../src/release/sim_reads_tran.cpp
../src/release/sim_reads_tran.cpp: In function 'int main(int, char**)':
../src/release/sim_reads_tran.cpp:89:49: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
fscanf(flist, "%s %lf", buf, &weight[i]);
^
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o sim_reads_tran sim_reads_tran.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o idba_tran.o `test -f '../src/release/idba_tran.cpp' || echo './'`../src/release/idba_tran.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o idba_tran idba_tran.o ../lib/libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o idba.o `test -f '../src/release/idba.cpp' || echo './'`../src/release/idba.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -o idba idba.o ../lib/libassembly.a
make[3]: Leaving directory `/«PKGBUILDDIR»/bin'
Making all in test
make[3]: Entering directory `/«PKGBUILDDIR»/test'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/«PKGBUILDDIR»/test'
Making all in script
make[3]: Entering directory `/«PKGBUILDDIR»/script'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/«PKGBUILDDIR»/script'
make[3]: Entering directory `/«PKGBUILDDIR»'
make[3]: Leaving directory `/«PKGBUILDDIR»'
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_test -a
make[1]: Entering directory `/«PKGBUILDDIR»'
Making check in lib
make[2]: Entering directory `/«PKGBUILDDIR»/lib'
make[2]: Nothing to be done for `check'.
make[2]: Leaving directory `/«PKGBUILDDIR»/lib'
Making check in bin
make[2]: Entering directory `/«PKGBUILDDIR»/bin'
make[2]: Nothing to be done for `check'.
make[2]: Leaving directory `/«PKGBUILDDIR»/bin'
Making check in test
make[2]: Entering directory `/«PKGBUILDDIR»/test'
make[2]: Nothing to be done for `check'.
make[2]: Leaving directory `/«PKGBUILDDIR»/test'
Making check in script
make[2]: Entering directory `/«PKGBUILDDIR»/script'
make[2]: Nothing to be done for `check'.
make[2]: Leaving directory `/«PKGBUILDDIR»/script'
make[2]: Entering directory `/«PKGBUILDDIR»'
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
make[1]: Entering directory `/«PKGBUILDDIR»'
Making install in lib
make[2]: Entering directory `/«PKGBUILDDIR»/lib'
make[3]: Entering directory `/«PKGBUILDDIR»/lib'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/«PKGBUILDDIR»/lib'
make[2]: Leaving directory `/«PKGBUILDDIR»/lib'
Making install in bin
make[2]: Entering directory `/«PKGBUILDDIR»/bin'
make[3]: Entering directory `/«PKGBUILDDIR»/bin'
/bin/mkdir -p '/«PKGBUILDDIR»/debian/idba/usr/bin'
/usr/bin/install -c idba_hybrid '/«PKGBUILDDIR»/debian/idba/usr/bin'
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/«PKGBUILDDIR»/bin'
make[2]: Leaving directory `/«PKGBUILDDIR»/bin'
Making install in test
make[2]: Entering directory `/«PKGBUILDDIR»/test'
make[3]: Entering directory `/«PKGBUILDDIR»/test'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/«PKGBUILDDIR»/test'
make[2]: Leaving directory `/«PKGBUILDDIR»/test'
Making install in script
make[2]: Entering directory `/«PKGBUILDDIR»/script'
make[3]: Entering directory `/«PKGBUILDDIR»/script'
/bin/mkdir -p '/«PKGBUILDDIR»/debian/idba/usr/bin'
/usr/bin/install -c scan.py run-unittest.py validate_blat validate_blat_parallel '/«PKGBUILDDIR»/debian/idba/usr/bin'
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/«PKGBUILDDIR»/script'
make[2]: Leaving directory `/«PKGBUILDDIR»/script'
make[2]: Entering directory `/«PKGBUILDDIR»'
make[3]: Entering directory `/«PKGBUILDDIR»'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/«PKGBUILDDIR»'
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
debian/rules override_dh_install
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_install
# for the moment the role of these scripts is totally unknown but they do not seem to be necessary
rm -f debian/idba/usr/bin/*.py
rm -f debian/idba/usr/bin/validate_blat*
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package `idba' in `../idba_1.1.1-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../idba_1.1.1-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build idba-1.1.1
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140309-0717
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
idba_1.1.1-1_armhf.changes:
───────────────────────────
Format: 1.8
Date: Thu, 13 Feb 2014 13:57:55 +0100
Source: idba
Binary: idba
Architecture: armhf
Version: 1.1.1-1
Distribution: jessie-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
idba - iterative De Bruijn Graph De Novo short read assembler for transc
Closes: 738860
Changes:
idba (1.1.1-1) unstable; urgency=low
.
* Initial release (Closes: #738860)
Checksums-Sha1:
0bdef7ac36997a78b49fec50aa05de4738554b18 259290 idba_1.1.1-1_armhf.deb
Checksums-Sha256:
89c6b3cc48ab633187ef703bbbcab1574307d95c75bd4c8ee6750ec130e4e2a7 259290 idba_1.1.1-1_armhf.deb
Files:
4db8bbec053004b942f0aab621bee601 259290 science optional idba_1.1.1-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
idba_1.1.1-1_armhf.deb
──────────────────────
new debian package, version 2.0.
size 259290 bytes: control archive=921 bytes.
948 bytes, 18 lines control
260 bytes, 4 lines md5sums
Package: idba
Version: 1.1.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 740
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libgomp1 (>= 4.4), libstdc++6 (>= 4.4.0), python
Section: science
Priority: optional
Homepage: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_tran/
Description: iterative De Bruijn Graph De Novo short read assembler for transcriptome
IDBA-Tran is an iterative De Bruijn Graph De Novo short read assembler
for transcriptome. It is purely de novo assembler based on only RNA
sequencing reads. IDBA-Tran uses local assembly to reconstructing
missing k-mers in low-expressed transcripts and then employs progressive
cutoff on contigs to separate the graph into components. Each component
corresponds to one gene in most cases and contains not many transcripts.
A heuristic algorithm based on pair-end reads is then used to find the
isoforms.
drwxr-xr-x root/root 0 2014-03-09 07:17 ./
drwxr-xr-x root/root 0 2014-03-09 07:17 ./usr/
drwxr-xr-x root/root 0 2014-03-09 07:17 ./usr/bin/
-rwxr-xr-x root/root 754816 2014-03-09 07:17 ./usr/bin/idba_hybrid
drwxr-xr-x root/root 0 2014-03-09 07:17 ./usr/share/
drwxr-xr-x root/root 0 2014-03-09 07:17 ./usr/share/doc/
drwxr-xr-x root/root 0 2014-03-09 07:17 ./usr/share/doc/idba/
-rw-r--r-- root/root 938 2014-02-13 13:58 ./usr/share/doc/idba/copyright
-rw-r--r-- root/root 151 2014-02-13 16:55 ./usr/share/doc/idba/changelog.Debian.gz
drwxr-xr-x root/root 0 2014-03-09 07:17 ./usr/share/man/
drwxr-xr-x root/root 0 2014-03-09 07:17 ./usr/share/man/man1/
-rw-r--r-- root/root 1071 2014-03-09 07:17 ./usr/share/man/man1/idba_hybrid.1.gz
lrwxrwxrwx root/root 0 2014-03-09 07:17 ./usr/bin/idba -> idba_hybrid
lrwxrwxrwx root/root 0 2014-03-09 07:17 ./usr/share/man/man1/idba.1.gz -> idba_hybrid.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 133460
Build-Time: 1235
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 125
Job: idba_1.1.1-1
Machine Architecture: armhf
Package: idba
Package-Time: 1417
Source-Version: 1.1.1-1
Space: 133460
Status: successful
Version: 1.1.1-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20140309-0717
Build needed 00:23:37, 133460k disc space