mapsembler2 →
2.0.5+dfsg-2 →
armhf → 2014-02-11 10:28:43
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-01
╔══════════════════════════════════════════════════════════════════════════════╗
║ mapsembler2 2.0.5+dfsg-2 (armhf) 11 Feb 2014 10:24 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: mapsembler2
Version: 2.0.5+dfsg-2
Source Version: 2.0.5+dfsg-2
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/mapsembler2-MJz8zA/mapsembler2-2.0.5+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/mapsembler2-MJz8zA' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-8a005455-1501-4f76-9e67-173c7dcdb5c5' 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 [7254 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8367 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 15.6 MB in 36s (429 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: 'mapsembler2' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/mapsembler2/trunk/
Need to get 246 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main mapsembler2 2.0.5+dfsg-2 (dsc) [2041 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main mapsembler2 2.0.5+dfsg-2 (tar) [233 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main mapsembler2 2.0.5+dfsg-2 (diff) [11.4 kB]
Fetched 246 kB in 0s (2883 kB/s)
Download complete and in download only mode
Check arch
──────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-aDf_mG/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 25 not upgraded.
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After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11477 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), bc, zlib1g-dev, help2man
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), bc, zlib1g-dev, help2man
dpkg-deb: building package `sbuild-build-depends-mapsembler2-dummy' in `/«BUILDDIR»/resolver-ms8LxU/apt_archive/sbuild-build-depends-mapsembler2-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install mapsembler2 build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bc bsdmainutils debhelper file gettext gettext-base groff-base help2man
install-info intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0
libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bc bsdmainutils debhelper file gettext gettext-base groff-base help2man
install-info intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0
libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf
sbuild-build-depends-mapsembler2-dummy zlib1g-dev
0 upgraded, 22 newly installed, 0 to remove and 25 not upgraded.
Need to get 8543 kB/8544 kB of archives.
After this operation, 23.3 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main install-info armhf 5.2.0.dfsg.1-2 [194 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.2.6-1 [24.4 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-5 [962 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.6-1 [961 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.2-1 [29.0 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.14-2 [213 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-3 [836 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.0.13-12 [17.4 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.36.4-1 [1907 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main bc armhf 1.06.95-8 [106 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.14-2 [53.8 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3.2-1 [112 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3.2-1 [1137 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20131227 [687 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main help2man armhf 1.43.3 [104 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1 [212 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 8543 kB in 2s (4013 kB/s)
Selecting previously unselected package install-info.
(Reading database ... 11477 files and directories currently installed.)
Preparing to unpack .../install-info_5.2.0.dfsg.1-2_armhf.deb ...
Unpacking install-info (5.2.0.dfsg.1-2) ...
Setting up install-info (5.2.0.dfsg.1-2) ...
Selecting previously unselected package libpipeline1:armhf.
(Reading database ... 11491 files and directories currently installed.)
Preparing to unpack .../libpipeline1_1.2.6-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.2.6-1) ...
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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 libcroco3:armhf (0.6.8-2) ...
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Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-1) ...
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Preparing to unpack .../sbuild-build-depends-mapsembler2-dummy.deb ...
Unpacking sbuild-build-depends-mapsembler2-dummy (0.invalid.0) ...
Processing triggers for install-info (5.2.0.dfsg.1-2) ...
Setting up libpipeline1:armhf (1.2.6-1) ...
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 (2.6.6-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.18.3.2-1) ...
Setting up libmagic1:armhf (1:5.14-2) ...
Setting up libxml2:armhf (2.9.1+dfsg1-3) ...
Setting up libffi6:armhf (3.0.13-12) ...
Setting up libglib2.0-0:armhf (2.36.4-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-2) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up bc (1.06.95-8) ...
Setting up file (1:5.14-2) ...
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 (9.20131227) ...
Setting up help2man (1.43.3) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1) ...
Setting up sbuild-build-depends-mapsembler2-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.17-97) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.13-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24-2 dpkg-dev_1.17.5+rpi1 g++-4.8_4.8.2-14 gcc-4.8_4.8.2-14 libc6-dev_2.17-97 libstdc++-4.8-dev_4.8.2-14 libstdc++6_4.8.2-14 linux-libc-dev_3.12.6-2+rpi1
Package versions: apt_0.9.14.2 base-files_7.2+rpi1 base-passwd_3.5.28 bash_4.2+dfsg-1 bc_1.06.95-8 binutils_2.24-2 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.5 build-essential_11.6 bzip2_1.0.6-5 coreutils_8.21-1 cpio_2.11+dfsg-1 cpp_4:4.8.2-1 cpp-4.8_4.8.2-14 dash_0.5.7-4 debconf_1.5.52 debconf-i18n_1.5.52 debfoster_2.7-1.2 debhelper_9.20131227 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.5+rpi1 dpkg-dev_1.17.5+rpi1 e2fslibs_1.42.9-2 e2fsprogs_1.42.9-2 fakeroot_1.18.4-2 file_1:5.14-2 findutils_4.4.2-7 g++_4:4.8.2-1 g++-4.8_4.8.2-14 gcc_4:4.8.2-1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-9+rpi1 gcc-4.8_4.8.2-14 gcc-4.8-base_4.8.2-14 gettext_0.18.3.2-1 gettext-base_0.18.3.2-1 gnupg_1.4.16-1 gpgv_1.4.16-1 grep_2.15-2 groff-base_1.22.2-5 gzip_1.6-3 help2man_1.43.3 hostname_3.15 initramfs-tools_0.115 initscripts_2.88dsf-45 insserv_1.14.0-5 install-info_5.2.0.dfsg.1-2 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_0.9.14.2 libasan0_4.8.2-14 libasprintf0c2_0.18.3.2-1 libatomic1_4.8.2-14 libattr1_1:2.4.47-1 libaudit-common_1:2.3.2-3 libaudit1_1:2.3.2-3 libblkid1_2.20.1-5.5 libbz2-1.0_1.0.6-5 libc-bin_2.17-97 libc-dev-bin_2.17-97 libc6_2.17-97 libc6-dev_2.17-97 libcap2_1:2.22-1.2 libcloog-isl4_0.18.1-3 libcomerr2_1.42.9-2 libcroco3_0.6.8-2 libdb5.1_5.1.29-6 libdbus-1-3_1.7.10-2 libdpkg-perl_1.17.5+rpi1 libffi6_3.0.13-12 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.2-14 libgcc1_1:4.8.2-14 libgdbm3_1.8.3-12 libglib2.0-0_2.36.4-1 libgmp10_2:5.1.3+dfsg-1 libgomp1_4.8.2-14 libisl10_0.12.1-2 libklibc_2.0.2-1+rpi1 libkmod2_16-2 liblocale-gettext-perl_1.05-7+b3 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.14-2 libmount1_2.20.1-5.5 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20130608-1 libncursesw5_5.9+20130608-1 libnih-dbus1_1.0.3-4.2 libnih1_1.0.3-4.2 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.6-1 libprocps0_1:3.3.4-2 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_1.42.9-2 libstdc++-4.8-dev_4.8.2-14 libstdc++6_4.8.2-14 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+20130608-1 libudev1_204-6 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.5 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_2.20.1-5.5 mountall_2.52 multiarch-support_2.17-97 ncurses-base_5.9+20130608-1 ncurses-bin_5.9+20130608-1 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_1:3.3.4-2 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-mapsembler2-dummy_0.invalid.0 sed_4.2.2-3 sensible-utils_0.0.9 sysv-rc_2.88dsf-45 sysvinit_2.88dsf-45 sysvinit-core_2.88dsf-45 sysvinit-utils_2.88dsf-45 tar_1.26+dfsg-8 tzdata_2013i-1 udev_204-6 util-linux_2.20.1-5.5 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1 zlib1g-dev_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 6 07:09:49 2014 UTC using RSA key ID 326D8438
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./mapsembler2_2.0.5+dfsg-2.dsc
dpkg-source: info: extracting mapsembler2 in mapsembler2-2.0.5+dfsg
dpkg-source: info: unpacking mapsembler2_2.0.5+dfsg.orig.tar.xz
dpkg-source: info: unpacking mapsembler2_2.0.5+dfsg-2.debian.tar.xz
dpkg-source: info: applying fix_build
dpkg-source: info: applying fix_path
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-8a005455-1501-4f76-9e67-173c7dcdb5c5
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
SHLVL=1
SSH_CLIENT=172.17.0.6 53834 22
SSH_CONNECTION=172.17.0.6 53834 172.17.2.1 22
SSH_TTY=/dev/pts/0
TERM=xterm
USER=buildd
_=/etc/init.d/buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package mapsembler2
dpkg-buildpackage: source version 2.0.5+dfsg-2
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build mapsembler2-2.0.5+dfsg
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
debian/rules override_dh_clean
make[1]: Entering directory `/«BUILDDIR»/mapsembler2-2.0.5+dfsg'
cd minia && make clean
make[2]: Entering directory `/«BUILDDIR»/mapsembler2-2.0.5+dfsg/minia'
rm -rf *.o
make[2]: Leaving directory `/«BUILDDIR»/mapsembler2-2.0.5+dfsg/minia'
cd kissreads_g && make clean
make[2]: Entering directory `/«BUILDDIR»/mapsembler2-2.0.5+dfsg/kissreads_g'
rm -rf kissreads_graph *.o read_coherence_mapsembler/*.o ../minia/*.o
make[2]: Leaving directory `/«BUILDDIR»/mapsembler2-2.0.5+dfsg/kissreads_g'
cd maps && make clean
make[2]: Entering directory `/«BUILDDIR»/mapsembler2-2.0.5+dfsg/maps'
rm -rf *.o ../minia/*.o read_coherence_mapsembler/*.o
make[2]: Leaving directory `/«BUILDDIR»/mapsembler2-2.0.5+dfsg/maps'
rm -f maps/mapsembler
rm -f kissreads_g/kissreads_graph
rm -f run_mapsembler_and_phaser
rm -f run_mapsembler_and_phaser.1
rm -f mapsembler.1
rm -f kissreads_graph.1
dh_clean
make[1]: Leaving directory `/«BUILDDIR»/mapsembler2-2.0.5+dfsg'
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory `/«BUILDDIR»/mapsembler2-2.0.5+dfsg'
dh_auto_build
cd maps && make k=29
make[2]: Entering directory `/«BUILDDIR»/mapsembler2-2.0.5+dfsg/maps'
g++ -lz -o ../minia/Pool.o -c ../minia/Pool.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o ../minia/Bank.o -c ../minia/Bank.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Bank.cpp: In member function 'int KmersBuffer::readkmers()':
../minia/Bank.cpp:911:65: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(buffer,sizeof( char),block_size, binary_read_file); // read a block of reads into the buffer
^
g++ -lz -o ../minia/Bloom.o -c ../minia/Bloom.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Bloom.cpp: In member function 'void Bloom::load(char*)':
../minia/Bloom.cpp:257:56: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(blooma, sizeof(unsigned char), nchar, file_data);
^
g++ -lz -o ../minia/Hash16.o -c ../minia/Hash16.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o ../minia/Terminator.o -c ../minia/Terminator.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o ../minia/Kmer.o -c ../minia/Kmer.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o ../minia/Traversal.o -c ../minia/Traversal.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o ../minia/LinearCounter.o -c ../minia/LinearCounter.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o ../minia/Set.o -c ../minia/Set.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Set.cpp: In member function 'void AssocSet::print_total_size()':
../minia/Set.cpp:132:48: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
printf("Assoc set size: %li\n",liste.size());
^
../minia/Set.cpp:133:103: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
printf("Assoc set capacity: listekmer %li liste val%li\n",liste.capacity(),liste_value.capacity());
^
../minia/Set.cpp:133:103: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'std::vector<short unsigned int>::size_type {aka unsigned int}' [-Wformat=]
../minia/Set.cpp:136:11: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
);
^
../minia/Set.cpp:136:11: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
../minia/Set.cpp:136:11: warning: format '%li' expects argument of type 'long int', but argument 4 has type 'std::vector<short unsigned int>::size_type {aka unsigned int}' [-Wformat=]
../minia/Set.cpp:136:11: warning: format '%li' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=]
../minia/Set.cpp:136:11: warning: format '%li' expects argument of type 'long int', but argument 6 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
../minia/Set.cpp: In member function 'void AssocPairedSet::print_total_size()':
../minia/Set.cpp:296:55: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
printf("Assoc paired set size: %li\n",liste.size());
^
../minia/Set.cpp:297:110: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
printf("Assoc paired set capacity: listekmer %li liste val%li\n",liste.capacity(),liste_value.capacity());
^
../minia/Set.cpp:297:110: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'std::vector<pair_nt_kmer>::size_type {aka unsigned int}' [-Wformat=]
../minia/Set.cpp:300:12: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
);
^
../minia/Set.cpp:300:12: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
../minia/Set.cpp:300:12: warning: format '%li' expects argument of type 'long int', but argument 4 has type 'std::vector<pair_nt_kmer>::size_type {aka unsigned int}' [-Wformat=]
../minia/Set.cpp:300:12: warning: format '%li' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=]
../minia/Set.cpp:300:12: warning: format '%li' expects argument of type 'long int', but argument 6 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
../minia/Set.cpp: In member function 'void AssocPairedSet::load(char*)':
../minia/Set.cpp:288:82: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&liste_value[0], sizeof(pair_nt_kmer_t), liste_value.size(), file_data);
^
g++ -lz -o ../minia/Utils.o -c ../minia/Utils.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Utils.cpp: In function 'uint64_t extrapolate_distinct_kmers_wrapped(long unsigned int, Bank*)':
../minia/Utils.cpp:431:96: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
printf("Inaccurate estimation, restarting with %d MB RAM\n",(2*nbytes_memory)/1024/1024);
^
../minia/Utils.cpp: In instantiation of 'Bloom* bloom_create_bloo1(T*, bool) [with T = BloomCpt]':
../minia/Utils.cpp:159:85: required from here
../minia/Utils.cpp:124:81: warning: format '%lli' expects argument of type 'long long int', but argument 2 has type 'off_t {aka long int}' [-Wformat=]
printf("nelem %lli nbits %g \n",SolidKmers->nb_elements(),NBITS_PER_KMER);
^
../minia/Utils.cpp: In function 'void end_kmer_count_partition(bool, Hash16*)':
../minia/Utils.cpp:179:42: warning: ignoring return value of 'int ftruncate(int, __off_t)', declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(F_kmercpt_write), 0); //erase previous file
^
../minia/Utils.cpp:191:54: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&cptk, sizeof(cptk), 1, F_kmercpt_read);
^
../minia/Utils.cpp:217:45: warning: ignoring return value of 'int ftruncate(int, __off_t)', declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(F_kmercpt_read), 0); //erase previous file
^
g++ -lz -o ../minia/SortingCount.o -c ../minia/SortingCount.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/SortingCount.cpp: In function 'void sorting_count(Bank*, char*, int, int, bool, int)':
../minia/SortingCount.cpp:51:50: warning: ignoring return value of 'char* getcwd(char*, size_t)', declared with attribute warn_unused_result [-Wunused-result]
getcwd(current_path,sizeof(current_path));
^
../minia/SortingCount.cpp:231:52: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system("echo 3 > /proc/sys/vm/drop_caches");
^
../minia/SortingCount.cpp:452:56: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system("echo 3 > /proc/sys/vm/drop_caches");
^
g++ -lz -o ../minia/Debloom.o -c ../minia/Debloom.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Debloom.cpp: In function 'Set* load_false_positives_cascading4()':
../minia/Debloom.cpp:369:89: warning: format '%lld' expects argument of type 'long long int', but argument 2 has type 'int' [-Wformat=]
printf("\nInserted %lld (estimated, %llu) kmers in B3.\n", addKmers, estimated_T2_size);
^
../minia/Debloom.cpp:393:89: warning: format '%lld' expects argument of type 'long long int', but argument 2 has type 'int' [-Wformat=]
printf("\nInserted %lld (estimated, %lld) kmers in B4.\n", addKmers, estimated_T3_size);
^
../minia/Debloom.cpp:423:115: warning: format '%lld' expects argument of type 'long long int', but argument 2 has type 'int' [-Wformat=]
printf("\nInserted %lld (estimated, %lld) kmers in T4.\n\n", addKmers, (uint64_t)fp->false_positives->capacity());
^
../minia/Debloom.cpp: In function 'void end_debloom_partition(bool)':
../minia/Debloom.cpp:30:39: warning: ignoring return value of 'int ftruncate(int, __off_t)', declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(F_debloom_write), 0); //erase previous file
^
g++ -lz -o ../minia/OAHash.o -c ../minia/OAHash.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o Kmer_for_kissnp2.o -c Kmer_for_kissnp2.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o Extension.o -c Extension.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o Extension_Bank.o -c Extension_Bank.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o Starter.o -c Starter.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
Starter.cpp: In member function 'std::id_els Starter::starter_output_graph(Extension_Bank*, GraphOutput, std::id_els)':
Starter.cpp:183:165: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
sprintf (data, "\"length\":%d, \"extremGraphRight\":\"k%d\", \"extremGraphLeft\":\"k%d\"",strlen(substarters_sequences[i]), extremKmerRightId, extremKmerLeftId);
^
Starter.cpp:183:165: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long int' [-Wformat=]
g++ -lz -o commons.o -c commons.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o read_coherence_mapsembler/libchash.o -c read_coherence_mapsembler/libchash.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
read_coherence_mapsembler/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)':
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:226:7: note: in expansion of macro 'READ_UL'
READ_UL((ht)->fpData, cchData); \
^
read_coherence_mapsembler/libchash.cpp:1227:3: note: in expansion of macro 'LOAD_AND_RETURN'
LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL));
^
read_coherence_mapsembler/libchash.cpp: In function 'HTItem* HashFindLast(HashTable*)':
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:226:7: note: in expansion of macro 'READ_UL'
READ_UL((ht)->fpData, cchData); \
^
read_coherence_mapsembler/libchash.cpp:1232:4: note: in expansion of macro 'LOAD_AND_RETURN'
LOAD_AND_RETURN(ht, ht->posLastFind);
^
read_coherence_mapsembler/libchash.cpp: In function 'HTItem* HashFirstBucket(HashTable*)':
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:226:7: note: in expansion of macro 'READ_UL'
READ_UL((ht)->fpData, cchData); \
^
read_coherence_mapsembler/libchash.cpp:1296:3: note: in expansion of macro 'LOAD_AND_RETURN'
LOAD_AND_RETURN(ht, retval);
^
read_coherence_mapsembler/libchash.cpp: In function 'HTItem* HashNextBucket(HashTable*)':
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:226:7: note: in expansion of macro 'READ_UL'
READ_UL((ht)->fpData, cchData); \
^
read_coherence_mapsembler/libchash.cpp:1306:3: note: in expansion of macro 'LOAD_AND_RETURN'
LOAD_AND_RETURN(ht, retval);
^
read_coherence_mapsembler/libchash.cpp: In function 'HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)':
read_coherence_mapsembler/libchash.cpp:1413:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(szMagicKey, 1, 4, fp);
^
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:1422:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, ht->cchKey);
^
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:1423:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, ht->cItems);
^
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:1424:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, ht->cDeletedItems);
^
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:1427:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, cchKey);
^
read_coherence_mapsembler/libchash.cpp:1429:34: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(rgchKeys, 1, cchKey, fp);
^
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:1434:7: note: in expansion of macro 'READ_UL'
READ_UL(fp, bck->data); /* all we need if dataRead is NULL */
^
read_coherence_mapsembler/libchash.cpp: In function 'u_long SparseRead(FILE*, SparseBin**)':
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:628:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, cBuckets); /* actually, cBuckets is stored */
^
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:633:3: note: in expansion of macro 'READ_UL'
READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]);
^
g++ -lz -o read_coherence_mapsembler/couple.o -c read_coherence_mapsembler/couple.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o read_coherence_mapsembler/misc_tools.o -c read_coherence_mapsembler/misc_tools.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o read_coherence_mapsembler/read_groups.o -c read_coherence_mapsembler/read_groups.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o read_coherence_mapsembler/consensus_common.o -c read_coherence_mapsembler/consensus_common.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o read_coherence_mapsembler/list.o -c read_coherence_mapsembler/list.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o read_coherence_mapsembler/read_coherence.o -c read_coherence_mapsembler/read_coherence.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
read_coherence_mapsembler/read_coherence.cpp: In function 'char** read_coherent_homologs(hash_t, const char*, int, int, int, int, int*)':
read_coherence_mapsembler/read_coherence.cpp:991:53: warning: format '%X' expects argument of type 'unsigned int', but argument 3 has type 'group_t {aka list_*}' [-Wformat=]
substarters[*nb_consensuses]);
^
read_coherence_mapsembler/read_coherence.cpp:1004:69: warning: format '%X' expects argument of type 'unsigned int', but argument 3 has type 'group_t {aka list_*}' [-Wformat=]
current_read_group_info->consensus, fragment);
^
g++ -lz -o read_coherence_mapsembler/interface_libchash.o -c read_coherence_mapsembler/interface_libchash.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o BooleanVector.o -c BooleanVector.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o Starter_Bank.o -c Starter_Bank.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o IterativeExtensions.o -c IterativeExtensions.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o Fragment_Bank.o -c Fragment_Bank.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o Fragment.o -c Fragment.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o GraphOutput.o -c GraphOutput.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
GraphOutput.cpp: In constructor 'GraphOutput::GraphOutput(std::string, int, std::id_els)':
GraphOutput.cpp:64:117: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
printf("graph_format=%d first_id_nodes=%d first_id_edges=%d\n", graph_format, first_id_els.node, first_id_els.edge);
^
GraphOutput.cpp:64:117: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
GraphOutput.cpp: In member function 'std::id_els GraphOutput::construct_graph(std::string)':
GraphOutput.cpp:544:141: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long int' [-Wformat=]
fprintf(nodes_file, "\"sequence\":\"%s\", \"direction\":\"%s\", \"firstNodeId\":\"n%d\",\n ", kmerSequence.c_str(),direction,nb_els.node);
^
g++ -o mapsembler ../minia/Pool.o ../minia/Bank.o ../minia/Bloom.o ../minia/Hash16.o ../minia/Terminator.o ../minia/Kmer.o ../minia/Traversal.o ../minia/LinearCounter.o ../minia/Set.o ../minia/Utils.o ../minia/SortingCount.o ../minia/Debloom.o ../minia/OAHash.o Kmer_for_kissnp2.o Extension.o Extension_Bank.o Starter.o commons.o read_coherence_mapsembler/libchash.o read_coherence_mapsembler/couple.o read_coherence_mapsembler/misc_tools.o read_coherence_mapsembler/read_groups.o read_coherence_mapsembler/consensus_common.o read_coherence_mapsembler/list.o read_coherence_mapsembler/read_coherence.o read_coherence_mapsembler/interface_libchash.o BooleanVector.o Starter_Bank.o IterativeExtensions.o Fragment_Bank.o Fragment.o GraphOutput.o mapsembler.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER -Wl,-z,relro
mapsembler.cpp:100:5: warning: this decimal constant is unsigned only in ISO C90 [enabled by default]
genome_size=3000000000;
^
mapsembler.cpp: In function 'int main(int, char**)':
mapsembler.cpp:137:142: warning: too many arguments for format [-Wformat-extra-args]
printf(" Mapsembler will extend the starters, not checking their read-coherency nor generating substarters\n", extension_type);
^
mapsembler.cpp:379:101: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
command = string("rm -f ")+prefix_trashable.c_str()+string("*"); system((char *)command.c_str());
^
make[2]: Leaving directory `/«BUILDDIR»/mapsembler2-2.0.5+dfsg/maps'
cd kissreads_g && make k=29
make[2]: Entering directory `/«BUILDDIR»/mapsembler2-2.0.5+dfsg/kissreads_g'
g++ -lz -o block_allocator.o -c block_allocator.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o DeBruijnGraph.o -c DeBruijnGraph.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o Fragment.o -c Fragment.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o json.o -c json.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o read_coherence_mapsembler/libchash.o -c read_coherence_mapsembler/libchash.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
read_coherence_mapsembler/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)':
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:226:7: note: in expansion of macro 'READ_UL'
READ_UL((ht)->fpData, cchData); \
^
read_coherence_mapsembler/libchash.cpp:1227:3: note: in expansion of macro 'LOAD_AND_RETURN'
LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL));
^
read_coherence_mapsembler/libchash.cpp: In function 'HTItem* HashFindLast(HashTable*)':
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:226:7: note: in expansion of macro 'READ_UL'
READ_UL((ht)->fpData, cchData); \
^
read_coherence_mapsembler/libchash.cpp:1232:4: note: in expansion of macro 'LOAD_AND_RETURN'
LOAD_AND_RETURN(ht, ht->posLastFind);
^
read_coherence_mapsembler/libchash.cpp: In function 'HTItem* HashFirstBucket(HashTable*)':
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:226:7: note: in expansion of macro 'READ_UL'
READ_UL((ht)->fpData, cchData); \
^
read_coherence_mapsembler/libchash.cpp:1296:3: note: in expansion of macro 'LOAD_AND_RETURN'
LOAD_AND_RETURN(ht, retval);
^
read_coherence_mapsembler/libchash.cpp: In function 'HTItem* HashNextBucket(HashTable*)':
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:226:7: note: in expansion of macro 'READ_UL'
READ_UL((ht)->fpData, cchData); \
^
read_coherence_mapsembler/libchash.cpp:1306:3: note: in expansion of macro 'LOAD_AND_RETURN'
LOAD_AND_RETURN(ht, retval);
^
read_coherence_mapsembler/libchash.cpp: In function 'HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)':
read_coherence_mapsembler/libchash.cpp:1413:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(szMagicKey, 1, 4, fp);
^
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:1422:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, ht->cchKey);
^
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:1423:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, ht->cItems);
^
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:1424:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, ht->cDeletedItems);
^
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:1427:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, cchKey);
^
read_coherence_mapsembler/libchash.cpp:1429:34: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(rgchKeys, 1, cchKey, fp);
^
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:1434:7: note: in expansion of macro 'READ_UL'
READ_UL(fp, bck->data); /* all we need if dataRead is NULL */
^
read_coherence_mapsembler/libchash.cpp: In function 'u_long SparseRead(FILE*, SparseBin**)':
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:628:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, cBuckets); /* actually, cBuckets is stored */
^
read_coherence_mapsembler/libchash.cpp:199:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
read_coherence_mapsembler/libchash.cpp:633:3: note: in expansion of macro 'READ_UL'
READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]);
^
g++ -lz -o read_coherence_mapsembler/couple.o -c read_coherence_mapsembler/couple.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o read_coherence_mapsembler/misc_tools.o -c read_coherence_mapsembler/misc_tools.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o read_coherence_mapsembler/read_groups.o -c read_coherence_mapsembler/read_groups.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o read_coherence_mapsembler/consensus_common.o -c read_coherence_mapsembler/consensus_common.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o read_coherence_mapsembler/list.o -c read_coherence_mapsembler/list.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o read_coherence_mapsembler/read_coherence.o -c read_coherence_mapsembler/read_coherence.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
read_coherence_mapsembler/read_coherence.cpp: In function 'char** read_coherent_homologs(hash_t, const char*, int, int, int, int, int*)':
read_coherence_mapsembler/read_coherence.cpp:991:53: warning: format '%X' expects argument of type 'unsigned int', but argument 3 has type 'group_t {aka list_*}' [-Wformat=]
substarters[*nb_consensuses]);
^
read_coherence_mapsembler/read_coherence.cpp:1004:69: warning: format '%X' expects argument of type 'unsigned int', but argument 3 has type 'group_t {aka list_*}' [-Wformat=]
current_read_group_info->consensus, fragment);
^
g++ -lz -o read_coherence_mapsembler/interface_libchash.o -c read_coherence_mapsembler/interface_libchash.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o commons.o -c commons.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o Loader.o -c Loader.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o BooleanVector.o -c BooleanVector.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -lz -o ReadMapper.o -c ReadMapper.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER
ReadMapper.cpp: In function 'uint64_t map_reads(Bank*, DBG*)':
ReadMapper.cpp:25:60: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'uint64_t {aka long long unsigned int}' [-Wformat=]
printf("\r %ld reads mapped", number_mapped);
^
g++ -o kissreads_graph block_allocator.o DeBruijnGraph.o Fragment.o json.o read_coherence_mapsembler/libchash.o read_coherence_mapsembler/couple.o read_coherence_mapsembler/misc_tools.o read_coherence_mapsembler/read_groups.o read_coherence_mapsembler/consensus_common.o read_coherence_mapsembler/list.o read_coherence_mapsembler/read_coherence.o read_coherence_mapsembler/interface_libchash.o commons.o ../minia/Kmer.o ../minia/Bank.o Loader.o BooleanVector.o ReadMapper.o KissReadsGraph.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -lz -DMINIA_IS_IN_PARENT_FOLDER -Wl,-z,relro
make[2]: Leaving directory `/«BUILDDIR»/mapsembler2-2.0.5+dfsg/kissreads_g'
make[1]: Leaving directory `/«BUILDDIR»/mapsembler2-2.0.5+dfsg'
dh_auto_test -a
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
debian/rules override_dh_install
make[1]: Entering directory `/«BUILDDIR»/mapsembler2-2.0.5+dfsg'
cp run_mapsembler_and_phaser.sh run_mapsembler_and_phaser
help2man --help-option=-h --version-string=2.0.5+dfsg ./run_mapsembler_and_phaser > run_mapsembler_and_phaser.1
help2man --help-option=-h --no-discard-stderr --version-string=2.0.5+dfsg ./maps/mapsembler > mapsembler.1
help2man --help-option=-h --no-discard-stderr --version-string=2.0.5+dfsg ./kissreads_g/kissreads_graph > kissreads_graph.1
dh_install
make[1]: Leaving directory `/«BUILDDIR»/mapsembler2-2.0.5+dfsg'
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 `mapsembler2' in `../mapsembler2_2.0.5+dfsg-2_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../mapsembler2_2.0.5+dfsg-2_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 mapsembler2-2.0.5+dfsg
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140211-1032
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
mapsembler2_2.0.5+dfsg-2_armhf.changes:
───────────────────────────────────────
Format: 1.8
Date: Thu, 06 Feb 2014 08:06:55 +0100
Source: mapsembler2
Binary: mapsembler2
Architecture: armhf
Version: 2.0.5+dfsg-2
Distribution: jessie-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Olivier Sallou <osallou@debian.org>
Description:
mapsembler2 - bioinformatics targeted assembly software
Changes:
mapsembler2 (2.0.5+dfsg-2) unstable; urgency=low
.
* d/control: Add missing build dep
Checksums-Sha1:
f58177895c863908dec030e42513f6ecc9301439 291166 mapsembler2_2.0.5+dfsg-2_armhf.deb
Checksums-Sha256:
41246970cf6a31dc98c054e06054db2708059870ef7ffad79c9a2b606c3004dd 291166 mapsembler2_2.0.5+dfsg-2_armhf.deb
Files:
579f7431ad3c4f781d847fbb256cdaac 291166 science optional mapsembler2_2.0.5+dfsg-2_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
mapsembler2_2.0.5+dfsg-2_armhf.deb
──────────────────────────────────
new debian package, version 2.0.
size 291166 bytes: control archive=1290 bytes.
1378 bytes, 27 lines control
805 bytes, 11 lines md5sums
Package: mapsembler2
Version: 2.0.5+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 479
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.2.3.4), bc
Section: science
Priority: optional
Homepage: http://colibread.inria.fr/mapsembler2/
Description: bioinformatics targeted assembly software
Mapsembler2 is a targeted assembly software.
It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not)
and a set of input sequences (starters).
.
It first determines if each starter is read-coherent, e.g. whether reads
confirm the presence of each starter in the original sequence.
Then for each read-coherent starter, Mapsembler2 outputs its sequence
neighborhood as a linear sequence or as a graph, depending on the user choice.
.
Mapsembler2 may be used for (not limited to):
- Validate an assembled sequence (input as starter), e.g. from a de
Bruijn graph assembly where read-coherence was not enforced.
- Checks if a gene (input as starter) has an homolog in a set of reads
- Checks if a known enzyme is present in a metagenomic NGS read set.
- Enrich unmappable reads by extending them, possibly making them mappable
- Checks what happens at the extremities of a contig
- Remove contaminants or symbiont reads from a read set
drwxr-xr-x root/root 0 2014-02-11 10:32 ./
drwxr-xr-x root/root 0 2014-02-11 10:32 ./usr/
drwxr-xr-x root/root 0 2014-02-11 10:32 ./usr/bin/
-rwxr-xr-x root/root 6679 2014-02-11 10:32 ./usr/bin/run_mapsembler_and_phaser
-rwxr-xr-x root/root 91880 2014-02-11 10:32 ./usr/bin/kissreads_graph
-rwxr-xr-x root/root 182300 2014-02-11 10:32 ./usr/bin/mapsembler
drwxr-xr-x root/root 0 2014-02-11 10:32 ./usr/share/
drwxr-xr-x root/root 0 2014-02-11 10:32 ./usr/share/doc/
drwxr-xr-x root/root 0 2014-02-11 10:32 ./usr/share/doc/mapsembler2/
drwxr-xr-x root/root 0 2014-02-11 10:32 ./usr/share/doc/mapsembler2/sample_example/
-rw-r--r-- root/root 113 2013-08-02 15:57 ./usr/share/doc/mapsembler2/sample_example/fragments.fa
-rw-r--r-- root/root 179834 2013-08-02 15:57 ./usr/share/doc/mapsembler2/sample_example/reads.fa.gz
-rw-r--r-- root/root 219 2014-02-01 14:13 ./usr/share/doc/mapsembler2/README.Debian
-rw-r--r-- root/root 25350 2014-02-05 07:37 ./usr/share/doc/mapsembler2/copyright
-rw-r--r-- root/root 223 2014-02-06 07:07 ./usr/share/doc/mapsembler2/changelog.Debian.gz
drwxr-xr-x root/root 0 2014-02-11 10:32 ./usr/share/man/
drwxr-xr-x root/root 0 2014-02-11 10:32 ./usr/share/man/man1/
-rw-r--r-- root/root 1009 2014-02-11 10:32 ./usr/share/man/man1/run_mapsembler_and_phaser.1.gz
-rw-r--r-- root/root 1401 2014-02-11 10:32 ./usr/share/man/man1/mapsembler.1.gz
-rw-r--r-- root/root 1017 2014-02-11 10:32 ./usr/share/man/man1/kissreads_graph.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 10840
Build-Time: 255
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 152
Job: mapsembler2_2.0.5+dfsg-2
Machine Architecture: armhf
Package: mapsembler2
Package-Time: 464
Source-Version: 2.0.5+dfsg-2
Space: 10840
Status: successful
Version: 2.0.5+dfsg-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20140211-1032
Build needed 00:07:44, 10840k disc space