discosnp →
1.0.1-3 →
armhf → 2014-02-17 06:46:46
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-03
╔══════════════════════════════════════════════════════════════════════════════╗
║ discosnp 1.0.1-3 (armhf) 17 Feb 2014 06:44 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: discosnp
Version: 1.0.1-3
Source Version: 1.0.1-3
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/discosnp-kVTwwP/discosnp-1.0.1' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/discosnp-kVTwwP' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-5c6540b1-cc22-412f-a004-0be6d5a03dc4' 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 [7261 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8390 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 15.7 MB in 36s (426 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: 'discosnp' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/discosnp/trunk/
Need to get 477 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main discosnp 1.0.1-3 (dsc) [1970 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main discosnp 1.0.1-3 (tar) [464 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main discosnp 1.0.1-3 (diff) [11.2 kB]
Fetched 477 kB in 0s (3669 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-1902bS/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 43 not upgraded.
Need to get 0 B/758 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 ... 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-discosnp-dummy' in `/«BUILDDIR»/resolver-vW6rnp/apt_archive/sbuild-build-depends-discosnp-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install discosnp 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-discosnp-dummy zlib1g-dev
0 upgraded, 22 newly installed, 0 to remove and 43 not upgraded.
Need to get 8529 kB/8530 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 1.2.6-2 [20.3 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 1.44.1 [94.9 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 8529 kB in 2s (4006 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_1.2.6-2_armhf.deb ...
Unpacking libpipeline1:armhf (1.2.6-2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../groff-base_1.22.2-5_armhf.deb ...
Unpacking groff-base (1.22.2-5) ...
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Preparing to unpack .../bsdmainutils_9.0.5_armhf.deb ...
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Preparing to unpack .../man-db_2.6.6-1_armhf.deb ...
Unpacking man-db (2.6.6-1) ...
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Unpacking libasprintf0c2:armhf (0.18.3.2-1) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../libmagic1_1%3a5.14-2_armhf.deb ...
Unpacking libmagic1:armhf (1:5.14-2) ...
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Preparing to unpack .../libxml2_2.9.1+dfsg1-3_armhf.deb ...
Unpacking libxml2:armhf (2.9.1+dfsg1-3) ...
Selecting previously unselected package libffi6:armhf.
Preparing to unpack .../libffi6_3.0.13-12_armhf.deb ...
Unpacking libffi6:armhf (3.0.13-12) ...
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Preparing to unpack .../libglib2.0-0_2.36.4-1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.36.4-1) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../libcroco3_0.6.8-2_armhf.deb ...
Unpacking libcroco3:armhf (0.6.8-2) ...
Selecting previously unselected package libunistring0:armhf.
Preparing to unpack .../libunistring0_0.9.3-5_armhf.deb ...
Unpacking libunistring0:armhf (0.9.3-5) ...
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Unpacking gettext (0.18.3.2-1) ...
Selecting previously unselected package intltool-debian.
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Unpacking intltool-debian (0.35.0+20060710.1) ...
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Unpacking help2man (1.44.1) ...
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Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-1) ...
Selecting previously unselected package sbuild-build-depends-discosnp-dummy.
Preparing to unpack .../sbuild-build-depends-discosnp-dummy.deb ...
Unpacking sbuild-build-depends-discosnp-dummy (0.invalid.0) ...
Processing triggers for install-info (5.2.0.dfsg.1-2) ...
Setting up libpipeline1:armhf (1.2.6-2) ...
Setting up groff-base (1.22.2-5) ...
Setting up bsdmainutils (9.0.5) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.6-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.18.3.2-1) ...
Setting up libmagic1:armhf (1:5.14-2) ...
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 (1.44.1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1) ...
Setting up sbuild-build-depends-discosnp-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_1.44.1 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_1.2.6-2 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-discosnp-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 08:13:33 2014 UTC using RSA key ID 326D8438
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./discosnp_1.0.1-3.dsc
dpkg-source: info: extracting discosnp in discosnp-1.0.1
dpkg-source: info: unpacking discosnp_1.0.1.orig.tar.xz
dpkg-source: info: unpacking discosnp_1.0.1-3.debian.tar.xz
dpkg-source: info: applying fix_build
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-5c6540b1-cc22-412f-a004-0be6d5a03dc4
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
SHLVL=1
SSH_CLIENT=172.17.0.6 54878 22
SSH_CONNECTION=172.17.0.6 54878 172.17.2.3 22
SSH_TTY=/dev/pts/0
TERM=xterm
USER=buildd
_=/etc/init.d/buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package discosnp
dpkg-buildpackage: source version 1.0.1-3
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build discosnp-1.0.1
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
debian/rules:39: warning: overriding commands for target `get-orig-source'
debian/rules:12: warning: ignoring old commands for target `get-orig-source'
dh clean
dh_testdir
dh_auto_clean
debian/rules override_dh_clean
debian/rules:39: warning: overriding commands for target `get-orig-source'
debian/rules:12: warning: ignoring old commands for target `get-orig-source'
make[1]: Entering directory `/«PKGBUILDDIR»'
cd minia && make clean
make[2]: Entering directory `/«PKGBUILDDIR»/minia'
rm -rf *.o
make[2]: Leaving directory `/«PKGBUILDDIR»/minia'
cd kissnp2 && make clean
make[2]: Entering directory `/«PKGBUILDDIR»/kissnp2'
rm -rf *.o ../minia/*.o
make[2]: Leaving directory `/«PKGBUILDDIR»/kissnp2'
cd kissreads && make clean
make[2]: Entering directory `/«PKGBUILDDIR»/kissreads'
rm -rf ./src/*.o kissreads
make[2]: Leaving directory `/«PKGBUILDDIR»/kissreads'
rm -f output_analyses/discoSnp_to_genotypes
rm -f output_analyses/discoSnp_to_csv
rm -f kissnp2/kissnp2
rm -f kissreads/kissreads
rm -f kissreads.1
rm -f kissnp2.1
dh_clean
make[1]: Leaving directory `/«PKGBUILDDIR»'
debian/rules build-arch
debian/rules:39: warning: overriding commands for target `get-orig-source'
debian/rules:12: warning: ignoring old commands for target `get-orig-source'
dh build-arch
dh_testdir -a
dh_auto_configure -a
debian/rules override_dh_auto_build
debian/rules:39: warning: overriding commands for target `get-orig-source'make[1]: Entering directory `/«PKGBUILDDIR»'
debian/rules:12: warning: ignoring old commands for target `get-orig-source'
dh_auto_build
cd kissnp2 && make k=29
make[2]: Entering directory `/«PKGBUILDDIR»/kissnp2'
g++ -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 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -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 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Bank.cpp: In member function 'int KmersBuffer::readkmers()':
../minia/Bank.cpp:922:65: 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 sequences into the buffer
^
g++ -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 -O4 -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++ -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 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -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 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -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 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -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 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Traversal.cpp: In member function 'bool MonumentTraversal::find_starting_kmer(kmer_type, kmer_type&)':
../minia/Traversal.cpp:343:66: warning: format '%d' expects a matching 'int' argument [-Wformat=]
if (debug) printf("strand %d shouldnt continue\n");
^
../minia/Traversal.cpp:357:72: warning: format '%d' expects a matching 'int' argument [-Wformat=]
if (debug) printf("strand %d nothing more to explore\n");
^
g++ -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 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -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 -O4 -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++ -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 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Utils.cpp: In function 'uint64_t extrapolate_distinct_kmers_wrapped(long unsigned int, Bank*)':
../minia/Utils.cpp:434:96: 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:162:85: required from here
../minia/Utils.cpp:125:81: 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:182:42: 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:194:54: 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:220:45: 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++ -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 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/SortingCount.cpp: In function 'void sorting_count(Bank*, char*, int, int, bool, int, bool)':
../minia/SortingCount.cpp:52:50: 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:248:52: 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:469:56: 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++ -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 -O4 -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++ -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 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -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 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o SNP.o -c SNP.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
SNP.cpp: In member function 'void Bubble::find_bubbles(const char*, int, int)':
SNP.cpp:846:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
{printf("%c \t %llu %%",13,(nb*100)/nbel);
^
g++ -o filter.o -c filter.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o IterativeExtensions.o -c IterativeExtensions.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o commons.o -c commons.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o kissnp2 ../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 SNP.o filter.o IterativeExtensions.o commons.o kissnp2.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER -Wl,-z,relro
kissnp2.cpp:70:1: warning: this decimal constant is unsigned only in ISO C90 [enabled by default]
int64_t genome_size = 3000000000;
^
kissnp2.cpp: In function 'int main(int, char**)':
kissnp2.cpp:114:62: warning: too many arguments for format [-Wformat-extra-args]
printf("This is kissnp2, version 2.1.1.5\n", getVersion());
^
kissnp2.cpp:245:85: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'unsigned int' [-Wformat=]
printf("Max kmer size on this compiled version is %lu\n",sizeof(kmer_type)*2);
^
make[2]: Leaving directory `/«PKGBUILDDIR»/kissnp2'
cd kissreads && make k=29
make[2]: Entering directory `/«PKGBUILDDIR»/kissreads'
gcc -o src/coherent_algorithm.o -c src/coherent_algorithm.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
gcc -o src/commons.o -c src/commons.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
src/commons.c: In function 'print_rev_comp':
src/commons.c:119:2: warning: passing argument 1 of 'fprintf' from incompatible pointer type [enabled by default]
for(i=len-1;i>-1;i--)fprintf(out, "%c",comp[(int)s[i]]);
^
In file included from /usr/include/stdio.h:937:0,
from ./include/commons.h:47,
from src/commons.c:43:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:95:1: note: expected 'struct FILE * __restrict__' but argument is of type 'gzFile'
fprintf (FILE *__restrict __stream, const char *__restrict __fmt, ...)
^
gcc -o src/couple.o -c src/couple.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
gcc -o src/extension_algorithm.o -c src/extension_algorithm.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
src/extension_algorithm.c: In function 'read_coherence':
src/extension_algorithm.c:346:4: warning: passing argument 1 of 'get_next_sequence_for_fastq' from incompatible pointer type [enabled by default]
read_len = get_next_sequence_for_fastq(reads_file, read, quality,line);
^
In file included from src/extension_algorithm.c:47:0:
./include/commons.h:85:5: note: expected 'gzFile' but argument is of type 'struct FILE *'
int get_next_sequence_for_fastq (gzFile file, char * read, char * quality, char * line);
^
src/extension_algorithm.c:348:4: warning: passing argument 1 of 'get_next_fasta_sequence' from incompatible pointer type [enabled by default]
read_len = get_next_fasta_sequence(reads_file, read,line);
^
In file included from src/extension_algorithm.c:47:0:
./include/commons.h:83:5: note: expected 'gzFile' but argument is of type 'struct FILE *'
int get_next_fasta_sequence (gzFile file, char * read, char * line);
^
gcc -o src/fragment_index.o -c src/fragment_index.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
gcc -o src/kissReads.o -c src/kissReads.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
src/kissReads.c: In function 'main':
src/kissReads.c:359:19: warning: assignment makes pointer from integer without a cast [enabled by default]
found = strstr(reads_file_names[i],"fastq") || strstr(reads_file_names[i],"fq") || strstr(reads_file_names[i],"txt");
^
src/kissReads.c:364:19: warning: assignment makes pointer from integer without a cast [enabled by default]
found = strstr(reads_file_names[i],"fastq") || strstr(reads_file_names[i],"fq") || strstr(reads_file_names[i],"txt") || strstr(reads_file_names[i],"fa") || strstr(reads_file_names[i],"fasta") || strstr(reads_file_names[i],"fna");
^
src/kissReads.c:428:9: warning: passing argument 1 of 'read_coherence' from incompatible pointer type [enabled by default]
read_coherence(reads_files[i], reads_file_names[i], size_seeds, min_coverage, results_against_set, number_of_starters, i, quality, nb_events_per_set, number_paths_per_event, sam_out, max_substitutions, no_subsutitution_on_central_position);
^
In file included from src/kissReads.c:46:0:
./include/extension_algorithm.h:52:7: note: expected 'struct FILE *' but argument is of type 'gzFile'
float read_coherence (FILE * reads_file,
^
gcc -o src/list.o -c src/list.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
gcc -o src/outputs.o -c src/outputs.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
gcc -o src/interface_libchash.o -c src/interface_libchash.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
src/interface_libchash.c: In function 'hash_clear':
src/interface_libchash.c:136:16: warning: 'data' may be used uninitialized in this function [-Wmaybe-uninitialized]
specific_free(data);
^
src/interface_libchash.c: In function 'hash_delete':
src/interface_libchash.c:170:16: warning: 'data' may be used uninitialized in this function [-Wmaybe-uninitialized]
specific_free(data);
^
gcc -o src/libchash.o -c src/libchash.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
In file included from src/libchash.c:126:0:
src/libchash.c: In function 'EntriesUpto':
src/libchash.c:468:14: warning: comparison with string literal results in unspecified behavior [-Waddress]
assert("" == "word size is too big in EntriesUpto()");
^
src/libchash.c: In function 'Delete':
src/libchash.c:165:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if ( STORES_PTR(ht) && (ht)->fSaveKeys ) \
^
./include/libchash.h:165:40: note: in expansion of macro 'FREE_KEY'
FREE_KEY(ht, (bck)->key); } while ( 0 )
^
src/libchash.c:1119:4: note: in expansion of macro 'SET_BCK_DELETED'
SET_BCK_DELETED(ht, ht->posLastFind); /* find set this, how nice */
^
src/libchash.c: In function 'ClearHashTable':
src/libchash.c:165:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if ( STORES_PTR(ht) && (ht)->fSaveKeys ) \
^
src/libchash.c:1183:3: note: in expansion of macro 'FREE_KEY'
FREE_KEY(ht, bck->key);
^
src/libchash.c: In function 'HashFind':
src/libchash.c:1221:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL));
^
src/libchash.c:1221:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
src/libchash.c: In function 'HashFindOrInsert':
src/libchash.c:1244:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
return Insert(ht, KEY_TRUNC(ht, key), dataInsert, 0);
^
src/libchash.c: In function 'HashInsert':
src/libchash.c:1254:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
return Insert(ht, KEY_TRUNC(ht, key), data, SAMEKEY_OVERWRITE);
^
src/libchash.c: In function 'HashDelete':
src/libchash.c:1264:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
return Delete(ht, KEY_TRUNC(ht, key), !FAST_DELETE, 0);
^
src/libchash.c: In function 'HashFirstBucket':
src/libchash.c:1289:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if ( !IS_BCK_DELETED(retval) )
^
src/libchash.c: In function 'HashNextBucket':
src/libchash.c:1299:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if ( !IS_BCK_DELETED(retval) )
^
src/libchash.c: In function 'HashDoLoad':
src/libchash.c:1431:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if ( dataRead != NULL ) /* if it's null, we're done */
^
src/libchash.c: At top level:
src/libchash.c:691:18: warning: 'DenseFree' defined but not used [-Wunused-function]
static DenseBin *DenseFree(DenseBin *bin, ulong cBuckets)
^
src/libchash.c:710:21: warning: 'DenseInsert' defined but not used [-Wunused-function]
static DenseBucket *DenseInsert(DenseBin *bin, DenseBucket *bckInsert,
^
src/libchash.c:739:21: warning: 'DenseFirstBucket' defined but not used [-Wunused-function]
static DenseBucket *DenseFirstBucket(DenseIterator *iter,
^
src/libchash.c:748:13: warning: 'DenseWrite' defined but not used [-Wunused-function]
static void DenseWrite(FILE *fp, DenseBin *bin, ulong cBuckets)
^
src/libchash.c:767:14: warning: 'DenseRead' defined but not used [-Wunused-function]
static ulong DenseRead(FILE *fp, DenseBin **pbin)
^
src/libchash.c:789:14: warning: 'DenseMemory' defined but not used [-Wunused-function]
static ulong DenseMemory(ulong cBuckets, ulong cOccupied)
^
src/libchash.c: In function 'HashFind':
src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
src/libchash.c:220:7: note: in expansion of macro 'READ_UL'
READ_UL((ht)->fpData, cchData); \
^
src/libchash.c:1221:4: note: in expansion of macro 'LOAD_AND_RETURN'
LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL));
^
src/libchash.c: In function 'HashFindLast':
src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
src/libchash.c:220:7: note: in expansion of macro 'READ_UL'
READ_UL((ht)->fpData, cchData); \
^
src/libchash.c:1226:4: note: in expansion of macro 'LOAD_AND_RETURN'
LOAD_AND_RETURN(ht, ht->posLastFind);
^
src/libchash.c: In function 'HashFirstBucket':
src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
src/libchash.c:220:7: note: in expansion of macro 'READ_UL'
READ_UL((ht)->fpData, cchData); \
^
src/libchash.c:1290:3: note: in expansion of macro 'LOAD_AND_RETURN'
LOAD_AND_RETURN(ht, retval);
^
src/libchash.c: In function 'HashNextBucket':
src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
src/libchash.c:220:7: note: in expansion of macro 'READ_UL'
READ_UL((ht)->fpData, cchData); \
^
src/libchash.c:1300:3: note: in expansion of macro 'LOAD_AND_RETURN'
LOAD_AND_RETURN(ht, retval);
^
src/libchash.c: In function 'HashDoLoad':
src/libchash.c:1407:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(szMagicKey, 1, 4, fp);
^
src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
src/libchash.c:1416:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, ht->cchKey);
^
src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
src/libchash.c:1417:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, ht->cItems);
^
src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
src/libchash.c:1418:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, ht->cDeletedItems);
^
src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
src/libchash.c:1421:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, cchKey);
^
src/libchash.c:1423:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(rgchKeys, 1, cchKey, fp);
^
src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
src/libchash.c:1428:7: note: in expansion of macro 'READ_UL'
READ_UL(fp, bck->data); /* all we need if dataRead is NULL */
^
src/libchash.c: In function 'SparseRead':
src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
src/libchash.c:622:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, cBuckets); /* actually, cBuckets is stored */
^
src/libchash.c:193:12: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^
src/libchash.c:627:3: note: in expansion of macro 'READ_UL'
READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]);
^
gcc -o src/tree.o -c src/tree.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
gcc -o kissreads src/coherent_algorithm.o src/commons.o src/couple.o src/extension_algorithm.o src/fragment_index.o src/kissReads.o src/list.o src/outputs.o src/interface_libchash.o src/libchash.o src/tree.o -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -Wl,-z,relro -Wall -lm -O3 -lz
#################
# Compilation OK#
#################
make[2]: Leaving directory `/«PKGBUILDDIR»/kissreads'
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_test -a
fakeroot debian/rules binary-arch
debian/rules:39: warning: overriding commands for target `get-orig-source'
debian/rules:12: warning: ignoring old commands for target `get-orig-source'
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
debian/rules override_dh_install
make[1]: Entering directory `/«PKGBUILDDIR»'
debian/rules:39: warning: overriding commands for target `get-orig-source'
debian/rules:12: warning: ignoring old commands for target `get-orig-source'
cp output_analyses/discoSnp_to_genotypes.py output_analyses/discoSnp_to_genotypes
cp output_analyses/discoSnp_to_csv.py output_analyses/discoSnp_to_csv
help2man --help-option=-h --no-discard-stderr --version-string=1.0.1 kissnp2/kissnp2 > kissnp2.1
help2man --help-option=-h --no-discard-stderr --version-string=1.0.1 kissreads/kissreads > kissreads.1
dh_install
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package `discosnp' in `../discosnp_1.0.1-3_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../discosnp_1.0.1-3_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 discosnp-1.0.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140217-0650
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
discosnp_1.0.1-3_armhf.changes:
───────────────────────────────
Format: 1.8
Date: Thu, 06 Feb 2014 09:10:12 +0100
Source: discosnp
Binary: discosnp
Architecture: armhf
Version: 1.0.1-3
Distribution: jessie-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Olivier Sallou <osallou@debian.org>
Description:
discosnp - discovering Single Nucleotide Polymorphism from raw set(s) of rea
Changes:
discosnp (1.0.1-3) unstable; urgency=low
.
* d/rules: FTBS fix help2man command
Checksums-Sha1:
3b1d03bbb98d245d299f1f4137846dbb0ae1e827 123210 discosnp_1.0.1-3_armhf.deb
Checksums-Sha256:
f89eac3e5ffc83478a046ae9e9f25ae563650c323533bd8051e17f9449eeb505 123210 discosnp_1.0.1-3_armhf.deb
Files:
d17a9b086be0507dccae381255d04520 123210 science optional discosnp_1.0.1-3_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
discosnp_1.0.1-3_armhf.deb
──────────────────────────
new debian package, version 2.0.
size 123210 bytes: control archive=1181 bytes.
1048 bytes, 23 lines control
850 bytes, 12 lines md5sums
Package: discosnp
Version: 1.0.1-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 259
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.2.3.4), bc, python
Section: science
Priority: optional
Homepage: http://colibread.inria.fr/discosnp/
Description: discovering Single Nucleotide Polymorphism from raw set(s) of reads
Software discoSnp is designed for discovering Single Nucleotide
Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation
Sequencers (NGS).
.
Note that number of input read sets is not constrained, it can be one, two,
or more. Note also that no other data as reference genome or annotations
are needed.
.
The software is composed by two modules. First module, kissnp2, detects SNPs
from read sets. A second module, kissreads, enhance the kissnp2 results by
computing per read set and for each found SNP:
1) its mean read coverage
2) the (phred) quality of reads generating the polymorphism.
drwxr-xr-x root/root 0 2014-02-17 06:50 ./
drwxr-xr-x root/root 0 2014-02-17 06:50 ./usr/
drwxr-xr-x root/root 0 2014-02-17 06:50 ./usr/bin/
-rwxr-xr-x root/root 1612 2014-02-17 06:50 ./usr/bin/discoSnp_to_csv
-rwxr-xr-x root/root 2099 2014-02-17 06:50 ./usr/bin/discoSnp_to_genotypes
-rwxr-xr-x root/root 145360 2014-02-17 06:50 ./usr/bin/kissnp2
-rwxr-xr-x root/root 54864 2014-02-17 06:50 ./usr/bin/kissreads
drwxr-xr-x root/root 0 2014-02-17 06:50 ./usr/share/
drwxr-xr-x root/root 0 2014-02-17 06:50 ./usr/share/doc/
drwxr-xr-x root/root 0 2014-02-17 06:50 ./usr/share/doc/discosnp/
drwxr-xr-x root/root 0 2014-02-17 06:50 ./usr/share/doc/discosnp/examples/
drwxr-xr-x root/root 0 2014-02-17 06:50 ./usr/share/doc/discosnp/examples/data_sample/
-rw-r--r-- root/root 13449 2013-10-14 18:51 ./usr/share/doc/discosnp/examples/data_sample/reads_sequence2.fasta.gz
-rw-r--r-- root/root 12531 2013-10-14 18:51 ./usr/share/doc/discosnp/examples/data_sample/reads_sequence1.fasta.gz
-rw-r--r-- root/root 300 2014-02-01 11:13 ./usr/share/doc/discosnp/README.Debian
-rw-r--r-- root/root 26823 2014-02-05 07:29 ./usr/share/doc/discosnp/copyright
-rw-r--r-- root/root 4672 2013-10-14 19:07 ./usr/share/doc/discosnp/README.txt.gz
-rw-r--r-- root/root 248 2014-02-06 08:10 ./usr/share/doc/discosnp/changelog.Debian.gz
drwxr-xr-x root/root 0 2014-02-17 06:50 ./usr/share/man/
drwxr-xr-x root/root 0 2014-02-17 06:50 ./usr/share/man/man1/
-rw-r--r-- root/root 1131 2014-02-17 06:50 ./usr/share/man/man1/kissnp2.1.gz
-rw-r--r-- root/root 1381 2014-02-17 06:50 ./usr/share/man/man1/kissreads.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 5972
Build-Time: 176
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 153
Job: discosnp_1.0.1-3
Machine Architecture: armhf
Package: discosnp
Package-Time: 385
Source-Version: 1.0.1-3
Space: 5972
Status: successful
Version: 1.0.1-3
────────────────────────────────────────────────────────────────────────────────
Finished at 20140217-0650
Build needed 00:06:25, 5972k disc space