idba →
1.1.1-3 →
armhf → 2014-06-26 06:13:42
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ idba 1.1.1-3 (armhf) 26 Jun 2014 05:48 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: idba
Version: 1.1.1-3
Source Version: 1.1.1-3
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/idba-wFf06n/idba-1.1.1' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/idba-wFf06n' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-f452128c-6cb2-4ef9-99e6-5e2c8c3a7ada' 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 [7343 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8268 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 15.6 MB in 28s (542 kB/s)
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 216 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main idba 1.1.1-3 (dsc) [1915 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main idba 1.1.1-3 (tar) [209 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main idba 1.1.1-3 (diff) [4428 B]
Fetched 216 kB in 0s (2661 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-wpPD9e/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 21 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 ... 11817 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-sqEoDY/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 21 not upgraded.
Need to get 8289 kB/8290 kB of archives.
After this operation, 22.8 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.3.0-1 [21.1 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 2.6.7.1-1 [964 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.2-2 [29.2 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.18-1 [229 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 3.1-2 [18.1 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.40.0-3 [2247 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 1:5.18-1 [57.2 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3.2-2 [112 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3.2-2 [1136 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 9.20140613 [692 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 8289 kB in 1s (4236 kB/s)
Selecting previously unselected package libpipeline1:armhf.
(Reading database ... 11817 files and directories currently installed.)
Preparing to unpack .../libpipeline1_1.3.0-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.3.0-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../groff-base_1.22.2-5_armhf.deb ...
Unpacking groff-base (1.22.2-5) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../bsdmainutils_9.0.5_armhf.deb ...
Unpacking bsdmainutils (9.0.5) ...
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Preparing to unpack .../man-db_2.6.7.1-1_armhf.deb ...
Unpacking man-db (2.6.7.1-1) ...
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Preparing to unpack .../libasprintf0c2_0.18.3.2-2_armhf.deb ...
Unpacking libasprintf0c2:armhf (0.18.3.2-2) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../libmagic1_1%3a5.18-1_armhf.deb ...
Unpacking libmagic1:armhf (1:5.18-1) ...
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Preparing to unpack .../libxml2_2.9.1+dfsg1-3_armhf.deb ...
Unpacking libxml2:armhf (2.9.1+dfsg1-3) ...
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Preparing to unpack .../libffi6_3.1-2_armhf.deb ...
Unpacking libffi6:armhf (3.1-2) ...
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Unpacking libglib2.0-0:armhf (2.40.0-3) ...
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Unpacking file (1:5.18-1) ...
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Unpacking gettext (0.18.3.2-2) ...
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Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.1) ...
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Unpacking debhelper (9.20140613) ...
Selecting previously unselected package sbuild-build-depends-idba-dummy.
Preparing to unpack .../sbuild-build-depends-idba-dummy.deb ...
Unpacking sbuild-build-depends-idba-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.3.0-1) ...
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 (2.6.7.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.18.3.2-2) ...
Setting up libmagic1:armhf (1:5.18-1) ...
Setting up libxml2:armhf (2.9.1+dfsg1-3) ...
Setting up libffi6:armhf (3.1-2) ...
Setting up libglib2.0-0:armhf (2.40.0-3) ...
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 (1:5.18-1) ...
Setting up gettext-base (0.18.3.2-2) ...
Setting up gettext (0.18.3.2-2) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20140613) ...
Setting up sbuild-build-depends-idba-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-1) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.14-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24.51.20140604-3 dpkg-dev_1.17.10 g++-4.9_4.9.0-6 gcc-4.8_4.8.3-3 gcc-4.9_4.9.0-6 libc6-dev_2.19-1 libstdc++-4.9-dev_4.9.0-6 libstdc++6_4.9.0-6 linux-libc-dev_3.14.4-1+rpi1
Package versions: apt_1.0.3 base-files_7.3+rpi1 base-passwd_3.5.28 bash_4.3-7 binutils_2.24.51.20140604-3 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.6 bzip2_1.0.6-5 coreutils_8.21-1.2 cpio_2.11+dfsg-2 cpp_4:4.9.0-3 cpp-4.8_4.8.3-3 cpp-4.9_4.9.0-6 dash_0.5.7-4 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-1.2 debhelper_9.20140613 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.10 dpkg-dev_1.17.10 e2fslibs_1.42.10-1 e2fsprogs_1.42.10-1 fakeroot_1.18.4-2 file_1:5.18-1 findutils_4.4.2-8 g++_4:4.9.0-3 g++-4.9_4.9.0-6 gcc_4:4.9.0-3 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8_4.8.3-3 gcc-4.8-base_4.8.3-3 gcc-4.9_4.9.0-6 gcc-4.9-base_4.9.0-6 gettext_0.18.3.2-2 gettext-base_0.18.3.2-2 gnupg_1.4.16-1.1 gpgv_1.4.16-1.1 grep_2.18-2 groff-base_1.22.2-5 gzip_1.6-3 hostname_3.15 init-system-helpers_1.18 initramfs-tools_0.115 initscripts_2.88dsf-53.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.3-1+rpi1 kmod_16-2 libacl1_2.2.52-1 libapt-pkg4.12_1.0.3 libasan0_4.8.3-3 libasan1_4.9.0-6 libasprintf0c2_0.18.3.2-2 libatomic1_4.9.0-6 libattr1_1:2.4.47-1 libaudit-common_1:2.3.6-1 libaudit1_1:2.3.6-1 libblkid1_2.20.1-5.8 libbz2-1.0_1.0.6-5 libc-bin_2.19-1 libc-dev-bin_2.19-1 libc6_2.19-1 libc6-dev_2.19-1 libcap2_1:2.22-1.2 libcloog-isl4_0.18.2-1 libcomerr2_1.42.10-1 libcroco3_0.6.8-2 libdb5.1_5.1.29-6 libdb5.3_5.3.28-3 libdbus-1-3_1.8.4-1 libdpkg-perl_1.17.10 libffi6_3.1-2 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.3-3 libgcc-4.9-dev_4.9.0-6 libgcc1_1:4.9.0-6 libgdbm3_1.8.3-12 libglib2.0-0_2.40.0-3 libgmp10_2:6.0.0+dfsg-4+rpi1 libgomp1_4.9.0-6 libisl10_0.12.2-1 libklibc_2.0.3-1+rpi1 libkmod2_16-2 liblocale-gettext-perl_1.05-8 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.18-1 libmount1_2.20.1-5.8 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libncursesw5_5.9+20140118-1 libpam-modules_1.1.8-3 libpam-modules-bin_1.1.8-3 libpam-runtime_1.1.8-3 libpam0g_1.1.8-3 libpcre3_1:8.31-5 libpipeline1_1.3.0-1 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-5 libreadline6_6.3-6 libselinux1_2.3-1 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-1 libslang2_2.2.4-16 libss2_1.42.10-1 libstdc++-4.9-dev_4.9.0-6 libstdc++6_4.9.0-6 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b3 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140118-1 libubsan0_4.9.0-6 libudev1_204-8 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.8 libxml2_2.9.1+dfsg1-3 linux-libc-dev_3.14.4-1+rpi1 login_1:4.2-2 lsb-base_4.1+Debian12+rpi1 make_4.0-8 makedev_2.3.1-93 man-db_2.6.7.1-1 mawk_1.3.3-17 mount_2.20.1-5.8 multiarch-support_2.19-1 nano_2.2.6-1.1 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 passwd_1:4.2-2 patch_2.7.1-5 perl_5.18.2-4 perl-base_5.18.2-4 perl-modules_5.18.2-4 plymouth_0.8.8-17 po-debconf_1.0.16+nmu2 procps_1:3.3.9-5 raspbian-archive-keyring_20120528.2 readline-common_6.3-6 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 startpar_0.59-3 sysv-rc_2.88dsf-53.2 sysvinit_2.88dsf-53.2 sysvinit-core_2.88dsf-53.2 sysvinit-utils_2.88dsf-53.2 tar_1.27.1-2 tzdata_2014e-1 udev_204-8 util-linux_2.20.1-5.8 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1+rpi1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Fri Jun 20 11:26:14 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_1.1.1-3.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_1.1.1-3.debian.tar.xz
dpkg-source: info: applying use-atomic-for-mips.patch
dpkg-source: info: applying clang.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
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/root
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-f452128c-6cb2-4ef9-99e6-5e2c8c3a7ada
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
SHLVL=1
SSH_CLIENT=172.17.0.6 46828 22
SSH_CONNECTION=172.17.0.6 46828 172.17.2.2 22
SSH_TTY=/dev/pts/0
TERM=xterm
USER=buildd
_=/etc/init.d/buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package idba
dpkg-buildpackage: source version 1.1.1-3
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
debian/rules override_dh_auto_configure
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_configure -- LDFLAGS="-Wl,-z,relro -Wl,--as-needed" LIBS=" -latomic"
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
make[1]: Leaving directory '/«PKGBUILDDIR»'
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 -Wl,--as-needed -o idba_hybrid idba_hybrid.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o sort_reads sort_reads.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o parallel_rna_blat parallel_rna_blat.o ../lib/libassembly.a -latomic
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
#include "graph/contig_graph.h";
^
../src/tools/test.cpp:7:31: warning: extra tokens at end of #include directive
#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 -Wl,--as-needed -o test test.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o print_graph print_graph.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o validate_rna validate_rna.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o scaffold scaffold.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o shuffle_reads shuffle_reads.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o fa2fq fa2fq.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o validate_contigs_mummer validate_contigs_mummer.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o filter_blat filter_blat.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o sort_psl sort_psl.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o validate_reads_blat validate_reads_blat.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o validate_component validate_component.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o filter_contigs filter_contigs.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o sample_reads sample_reads.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o split_fq split_fq.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o idba_tran_test idba_tran_test.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o split_fa split_fa.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o fq2fa fq2fa.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o raw_n50 raw_n50.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o parallel_blat parallel_blat.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o split_scaffold split_scaffold.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o validate_contigs_blat validate_contigs_blat.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o filterfa filterfa.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o sim_reads sim_reads.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o idba_ud idba_ud.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o sim_reads_tran sim_reads_tran.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o idba_tran idba_tran.o ../lib/libassembly.a -latomic
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 -Wl,--as-needed -o idba idba.o ../lib/libassembly.a -latomic
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
dpkg-shlibdeps: warning: debian/idba/usr/bin/idba_hybrid contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
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_1.1.1-3_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../idba_1.1.1-3_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 20140626-0613
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
idba_1.1.1-3_armhf.changes:
───────────────────────────
Format: 1.8
Date: Fri, 20 Jun 2014 13:20:09 +0200
Source: idba
Binary: idba
Architecture: armhf
Version: 1.1.1-3
Distribution: jessie-staging
Urgency: medium
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: 752122
Changes:
idba (1.1.1-3) unstable; urgency=medium
.
* Enable build using clang (thanks for the patch to Alexander Ovchinnikov
<sanek23994@gmail.com>)
Closes: #752122
Checksums-Sha1:
967695590a7ea1c91921ac4b588a97dd55e4bc67 249252 idba_1.1.1-3_armhf.deb
Checksums-Sha256:
5af184ddeba929b58b22dd09bd15fd5a105f39083e36e111212c786988214b01 249252 idba_1.1.1-3_armhf.deb
Files:
c66b99b988d4672d815b737af64241a2 249252 science optional idba_1.1.1-3_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
idba_1.1.1-3_armhf.deb
──────────────────────
new debian package, version 2.0.
size 249252 bytes: control archive=920 bytes.
946 bytes, 18 lines control
260 bytes, 4 lines md5sums
Package: idba
Version: 1.1.1-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 736
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libgomp1 (>= 4.9), libstdc++6 (>= 4.9), 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 2014-06-26 06:12 ./
drwxr-xr-x root/root 0 2014-06-26 06:12 ./usr/
drwxr-xr-x root/root 0 2014-06-26 06:12 ./usr/bin/
-rwxr-xr-x root/root 750712 2014-06-26 06:12 ./usr/bin/idba_hybrid
drwxr-xr-x root/root 0 2014-06-26 06:12 ./usr/share/
drwxr-xr-x root/root 0 2014-06-26 06:12 ./usr/share/doc/
drwxr-xr-x root/root 0 2014-06-26 06:12 ./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 364 2014-06-20 11:23 ./usr/share/doc/idba/changelog.Debian.gz
drwxr-xr-x root/root 0 2014-06-26 06:12 ./usr/share/man/
drwxr-xr-x root/root 0 2014-06-26 06:12 ./usr/share/man/man1/
-rw-r--r-- root/root 1071 2014-06-26 06:12 ./usr/share/man/man1/idba_hybrid.1.gz
lrwxrwxrwx root/root 0 2014-06-26 06:12 ./usr/bin/idba -> idba_hybrid
lrwxrwxrwx root/root 0 2014-06-26 06:12 ./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: 142416
Build-Time: 1298
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 152
Job: idba_1.1.1-3
Machine Architecture: armhf
Package: idba
Package-Time: 1501
Source-Version: 1.1.1-3
Space: 142416
Status: successful
Version: 1.1.1-3
────────────────────────────────────────────────────────────────────────────────
Finished at 20140626-0613
Build needed 00:25:01, 142416k disc space