samtools →
0.1.19-1 →
armhf → 2013-05-27 07:45:19
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on debian-armhf
╔══════════════════════════════════════════════════════════════════════════════╗
║ samtools 0.1.19-1 (armhf) 27 May 2013 07:37 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
Version: 0.1.19-1
Source Version: 0.1.19-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/samtools-mfzGS4/samtools-0.1.19' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/samtools-mfzGS4' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-494b21d4-f01b-4add-8840-36dcc61101f1' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging Release.gpg [490 B]
Get:2 http://172.17.0.1 jessie-staging Release [10.8 kB]
Get:3 http://172.17.0.1 jessie-staging/main Sources [6585 kB]
Get:4 http://172.17.0.1 jessie-staging/main armhf Packages [7570 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 14.2 MB in 43s (329 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: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
Need to get 570 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main samtools 0.1.19-1 (dsc) [2078 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main samtools 0.1.19-1 (tar) [558 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main samtools 0.1.19-1 (diff) [10.2 kB]
Fetched 570 kB in 0s (590 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-1P1iW5/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 24 not upgraded.
Need to get 0 B/704 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 ... 11288 files and directories currently installed.)
Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-eoXyBl/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install samtools build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bash-completion bsdmainutils cdbs debhelper diffstat file gettext
gettext-base groff-base html2text intltool-debian libasprintf-dev
libasprintf0c2 libcroco3 libffi6 libgettextpo-dev libgettextpo0 libglib2.0-0
libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
libxml2 man-db po-debconf quilt zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bash-completion bsdmainutils cdbs debhelper diffstat file gettext
gettext-base groff-base html2text intltool-debian libasprintf-dev
libasprintf0c2 libcroco3 libffi6 libgettextpo-dev libgettextpo0 libglib2.0-0
libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
libxml2 man-db po-debconf quilt sbuild-build-depends-samtools-dummy
zlib1g-dev
0 upgraded, 30 newly installed, 0 to remove and 24 not upgraded.
Need to get 9976 kB/9977 kB of archives.
After this operation, 26.3 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpcre3 armhf 1:8.31-2 [248 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.2.3-1 [35.8 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-2 [666 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.4 [206 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.3-3 [867 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main bash-completion all 1:2.0-1 [193 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.1.1-10 [26.8 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.11-3 [199 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.8.0+dfsg1-7+nmu1 [822 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.0.13-4 [19.8 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.36.1-2build1 [1895 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.6-2 [119 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main libgettextpo0 armhf 0.18.1.1-10 [131 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.11-3 [51.6 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.1.1-10 [130 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main cdbs all 0.4.121 [80.5 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main html2text armhf 1.3.2a-15 [98.5 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main libasprintf-dev armhf 0.18.1.1-10 [26.7 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main libgettextpo-dev armhf 0.18.1.1-10 [160 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.1.1-10 [1721 kB]
Get:22 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:24 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20120909 [705 kB]
Get:25 http://172.17.0.1/private/ jessie-staging/main diffstat armhf 1.55-3 [28.6 kB]
Get:26 http://172.17.0.1/private/ jessie-staging/main libtinfo-dev armhf 5.9-10 [89.6 kB]
Get:27 http://172.17.0.1/private/ jessie-staging/main libncurses5-dev armhf 5.9-10 [202 kB]
Get:28 http://172.17.0.1/private/ jessie-staging/main quilt all 0.60-8 [381 kB]
Get:29 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.7.dfsg-13 [212 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 9976 kB in 10s (989 kB/s)
Selecting previously unselected package libpcre3:armhf.
(Reading database ... 11288 files and directories currently installed.)
Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.31-2_armhf.deb) ...
Selecting previously unselected package libpipeline1:armhf.
Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.3-1_armhf.deb) ...
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Unpacking groff-base (from .../groff-base_1.22.2-2_armhf.deb) ...
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Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_armhf.deb) ...
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Unpacking libffi6:armhf (from .../libffi6_3.0.13-4_armhf.deb) ...
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Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.36.1-2build1_armhf.deb) ...
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Selecting previously unselected package libgettextpo-dev:armhf.
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Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-10_armhf.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
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Selecting previously unselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_armhf.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
Selecting previously unselected package zlib1g-dev:armhf.
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Selecting previously unselected package sbuild-build-depends-samtools-dummy.
Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
Setting up libpcre3:armhf (1:8.31-2) ...
Setting up libpipeline1:armhf (1.2.3-1) ...
Setting up groff-base (1.22.2-2) ...
Setting up bsdmainutils (9.0.4) ...
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 (2.6.3-3) ...
Building database of manual pages ...
Setting up bash-completion (1:2.0-1) ...
Setting up libasprintf0c2:armhf (0.18.1.1-10) ...
Setting up libmagic1:armhf (1:5.11-3) ...
Setting up libxml2:armhf (2.8.0+dfsg1-7+nmu1) ...
Setting up libffi6:armhf (3.0.13-4) ...
Setting up libglib2.0-0:armhf (2.36.1-2build1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.6-2) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up libgettextpo0:armhf (0.18.1.1-10) ...
Setting up file (1:5.11-3) ...
Setting up gettext-base (0.18.1.1-10) ...
Setting up cdbs (0.4.121) ...
Setting up html2text (1.3.2a-15) ...
Setting up libasprintf-dev:armhf (0.18.1.1-10) ...
Setting up libgettextpo-dev:armhf (0.18.1.1-10) ...
Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:armhf (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
Setting up quilt (0.60-8) ...
Setting up zlib1g-dev:armhf (1:1.2.7.dfsg-13) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.9.1-imx4 armhf (armv7l)
Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.3-14+rpi1 gcc-4.6_4.6.3-14+rpi1 libc6-dev_2.13-38+rpi2 libstdc++6_4.7.2-5+rpi1 libstdc++6-4.6-dev_4.6.3-14+rpi1 linux-libc-dev_3.2.41-2+rpi1
Package versions: apt_0.9.7.8+rpi1 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.5+b1 bzip2_1.0.6-4 cdbs_0.4.121 coreutils_8.13-3.5 cpio_2.11+dfsg-0.1 cpp_4:4.6.3-8 cpp-4.6_4.6.3-14+rpi1 dash_0.5.7-3 debconf_1.5.50 debconf-i18n_1.5.50 debfoster_2.7-1.2 debhelper_9.20120909 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 fakeroot_1.18.4-2 file_1:5.11-3 findutils_4.4.2-4 g++_4:4.6.3-8 g++-4.6_4.6.3-14+rpi1 gcc_4:4.6.3-8 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-14+rpi1 gcc-4.6-base_4.6.3-14+rpi1 gcc-4.7-base_4.7.2-5+rpi1 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.12-2 groff-base_1.22.2-2 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initramfs-tools_0.112 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.1-3.1+rpi1 kmod_9-3 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.8+rpi1 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-38+rpi2 libc-dev-bin_2.13-38+rpi2 libc6_2.13-38+rpi2 libc6-dev_2.13-38+rpi2 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1.1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdbus-1-3_1.6.8-1 libdpkg-perl_1.16.10 libffi6_3.0.13-4 libgc1c2_1:7.1-9.1 libgcc1_1:4.7.2-5+rpi1 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.36.1-2build1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-5+rpi1 libklibc_2.0.1-3.1+rpi1 libkmod2_9-3 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.11-3 libmount1_2.20.1-5.3 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libncursesw5_5.9-10 libnih-dbus1_1.0.3-4.1 libnih1_1.0.3-4.1 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-9 libpam0g_1.1.3-7.1 libpcre3_1:8.31-2 libpipeline1_1.2.3-1 libprocps0_1:3.3.3-3 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1.1 libstdc++6_4.7.2-5+rpi1 libstdc++6-4.6-dev_4.6.3-14+rpi1 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libudev0_175-7.2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7+nmu1 linux-libc-dev_3.2.41-2+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian8+rpi1 make_3.81-8.2 makedev_2.3.1-92 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.3 mountall_2.46 multiarch-support_2.13-38+rpi2 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-21+rpi1 perl-base_5.14.2-21+rpi1 perl-modules_5.14.2-21+rpi1 plymouth_0.8.5.1-5 po-debconf_1.0.16+nmu2 procps_1:3.3.3-3 quilt_0.60-8 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-0.1 tzdata_2013b-2 udev_175-7.2 util-linux_2.20.1-5.3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
dpkg-source: info: extracting samtools in samtools-0.1.19
dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=POSIX
LOGNAME=root
LS_OPTIONS=--color=auto
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=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-494b21d4-f01b-4add-8840-36dcc61101f1
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
SHLVL=1
SSH_CLIENT=192.168.1.2 53109 22
SSH_CONNECTION=192.168.1.2 53109 192.168.1.45 22
SSH_TTY=/dev/pts/1
TERM=xterm
USER=root
XDG_SESSION_COOKIE=106ef489ba27ee071ab233f6518d3bce-1369081280.146676-2082782793
_=/etc/init.d/buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
dpkg-buildpackage: source version 0.1.19-1
dpkg-buildpackage: source changed by Charles Plessy <plessy@debian.org>
dpkg-source --before-build samtools-0.1.19
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
make[1]: Entering directory `/«PKGBUILDDIR»'
make[2]: Entering directory `/«PKGBUILDDIR»'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[2]: Entering directory `/«PKGBUILDDIR»/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
make[2]: Leaving directory `/«PKGBUILDDIR»/bcftools'
make[2]: Entering directory `/«PKGBUILDDIR»/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
make[1]: Leaving directory `/«PKGBUILDDIR»'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
make[1]: Entering directory `/«PKGBUILDDIR»'
make[1]: Nothing to be done for `reverse-config'.
make[1]: Leaving directory `/«PKGBUILDDIR»'
if [ -d "." ]; then \
cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
Removing patch fix_segfault_with_small_ref.patch
Restoring bam_plcmd.c
Removing patch fix_example_makefile.patch
Restoring examples/Makefile
No patches applied
rm -rf ./.pc
rm -f debian/stamp-patch*
rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
make[1]: Entering directory `/«PKGBUILDDIR»'
make[1]: Nothing to be done for `reverse-config'.
make[1]: Leaving directory `/«PKGBUILDDIR»'
cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch fix_example_makefile.patch
patching file examples/Makefile
Applying patch fix_segfault_with_small_ref.patch
patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
Now at patch fix_coverage_cap.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
make[1]: Entering directory `/«PKGBUILDDIR»'
make[1]: Nothing to be done for `update-config'.
make[1]: Leaving directory `/«PKGBUILDDIR»'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
make[1]: Entering directory `/«PKGBUILDDIR»'
make[2]: Entering directory `/«PKGBUILDDIR»'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
bgzf.c: In function 'worker_aux':
bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
bgzf.c: In function 'bgzf_close':
bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
bam_import.c: In function 'append_text':
bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
bam_index.c: In function 'bam_index_load_core':
bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
bam_pileup.c: In function 'resolve_cigar2':
bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
razf.c: In function 'razf_close':
razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
razf.c: In function 'razf_end_flush':
razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
razf.c: In function '_razf_write':
razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
razf.c: In function 'save_zindex':
razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
razf.c: In function 'razf_flush':
razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
knetfile.c: In function 'khttp_connect_file':
knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
knetfile.c: In function 'kftp_send_cmd':
knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
bam_reheader.c: In function 'bam_reheader':
bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[2]: Entering directory `/«PKGBUILDDIR»/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
bcf.c: In function 'bcf_fmt_core':
bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
bcfutils.c: In function 'bcf_fit_alt':
bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
make[2]: Leaving directory `/«PKGBUILDDIR»/bcftools'
make[2]: Entering directory `/«PKGBUILDDIR»/misc'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
padding.c: In function 'bam_pad2unpad':
padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
make[2]: Entering directory `/«PKGBUILDDIR»'
make[3]: Entering directory `/«PKGBUILDDIR»'
make[3]: Nothing to be done for `lib'.
make[3]: Leaving directory `/«PKGBUILDDIR»'
make[3]: Entering directory `/«PKGBUILDDIR»/bcftools'
make[3]: Nothing to be done for `lib'.
make[3]: Leaving directory `/«PKGBUILDDIR»/bcftools'
make[3]: Entering directory `/«PKGBUILDDIR»/misc'
make[3]: Nothing to be done for `lib'.
make[3]: Leaving directory `/«PKGBUILDDIR»/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[2]: Entering directory `/«PKGBUILDDIR»/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
make[2]: Leaving directory `/«PKGBUILDDIR»/bcftools'
make[2]: Entering directory `/«PKGBUILDDIR»/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
ace2sam.c: In function 'main':
ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
razip.c: In function 'main':
razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
razip.c: In function 'write_open':
razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/«PKGBUILDDIR»'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
make[1]: Entering directory `/«PKGBUILDDIR»/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
../samtools index ex1.bam
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
[samopen] SAM header is present: 2 sequences.
(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
../samtools rmdup ex1f.bam ex1f-rmduppe.bam
[bam_rmdup_core] processing reference seq1...
[bam_rmdup_core] processing reference seq2...
[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
make[1]: Leaving directory `/«PKGBUILDDIR»/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
Adding cdbs dependencies to debian/libbam-dev.substvars
dh_installdirs -plibbam-dev
dh_installdocs -psamtools ./NEWS ./AUTHORS
dh_installexamples -psamtools
dh_installman -psamtools
dh_installinfo -psamtools
dh_installmenu -psamtools
dh_installcron -psamtools
dh_installinit -psamtools
dh_installdebconf -psamtools
dh_installemacsen -psamtools
dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
dh_installchangelogs -psamtools NEWS
dh_installudev -psamtools
dh_lintian -psamtools
dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
install -m 644 bcftools/README /«PKGBUILDDIR»/debian/samtools/usr/share/doc/samtools/README.bcftools
ln -s samtools.1.gz /«PKGBUILDDIR»/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_bash-completion
dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
dh_installinfo -plibbam-dev
dh_installmenu -plibbam-dev
dh_installcron -plibbam-dev
dh_installinit -plibbam-dev
dh_installdebconf -plibbam-dev
dh_installemacsen -plibbam-dev
dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
dh_installchangelogs -plibbam-dev NEWS
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
dh_installgsettings -plibbam-dev
dh_strip -psamtools
dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /«PKGBUILDDIR»/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
dh_makeshlibs -plibbam-dev
dh_installdeb -psamtools
dh_perl -psamtools
dh_shlibdeps -psamtools
dh_installdeb -plibbam-dev
dh_perl -plibbam-dev
dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_armhf.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_armhf.deb'.
dpkg-genchanges -B >../samtools_0.1.19-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build samtools-0.1.19
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20130527-0745
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
samtools_0.1.19-1_armhf.changes:
────────────────────────────────
Format: 1.8
Date: Sat, 30 Mar 2013 17:31:47 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: armhf
Version: 0.1.19-1
Distribution: jessie-staging
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy@debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
samtools (0.1.19-1) unstable; urgency=low
.
cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
e194f9e Removed fix_float_tag.patch, corrected upstream.
9c0e543 Refreshed patches.
3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
8d8550e example/Makefile: pass -lpthread when compiling calDepth.
fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
6f75b48 debian/control: normalised with cme.
e13bb5e debian/control: normalised VCS URLs.
a1b1b00 debian/control: deleted DM-Upload-Allowed field.
ddcd54e Use NEWS as upstream changelog.
81ad760 Conforms to Policy version 3.9.4.
Checksums-Sha1:
b1b2168a944a7cf4aac082f7743c3c142276b0ea 522580 samtools_0.1.19-1_armhf.deb
4c11176e8e4b363d54d8a8a2efbc1179b6507e02 110418 libbam-dev_0.1.19-1_armhf.deb
Checksums-Sha256:
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73ff14aa2d5559c4a797038a20ee1c2aae9c0f2c1c87b4e7055b5caa856af46d 110418 libbam-dev_0.1.19-1_armhf.deb
Files:
9a7d1d71c6383b410e75c6e3a75429d9 522580 science optional samtools_0.1.19-1_armhf.deb
b02589cdb52be9d87354a5d3fff79d45 110418 libdevel optional libbam-dev_0.1.19-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
samtools_0.1.19-1_armhf.deb
───────────────────────────
new debian package, version 2.0.
size 522580 bytes: control archive=1948 bytes.
32 bytes, 1 lines conffiles
818 bytes, 16 lines control
2766 bytes, 42 lines md5sums
Package: samtools
Version: 0.1.19-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1168
Depends: libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
Priority: optional
Homepage: http://samtools.sourceforge.net
Description: processing sequence alignments in SAM and BAM formats
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format. It imports from and exports to the ascii SAM
(Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
drwxr-xr-x root/root 0 2013-05-27 07:44 ./
drwxr-xr-x root/root 0 2013-05-27 07:44 ./usr/
drwxr-xr-x root/root 0 2013-05-27 07:44 ./usr/share/
drwxr-xr-x root/root 0 2013-05-27 07:44 ./usr/share/doc/
drwxr-xr-x root/root 0 2013-05-27 07:44 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
-rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
-rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
drwxr-xr-x root/root 0 2013-05-27 07:44 ./usr/share/doc/samtools/examples/
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libbam-dev_0.1.19-1_armhf.deb
─────────────────────────────
new debian package, version 2.0.
size 110418 bytes: control archive=930 bytes.
712 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
Version: 0.1.19-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 320
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
Description: manipulates nucleotide sequence alignments in BAM or SAM format
The BAM library provides I/O and various operations on manipulating nucleotide
sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
Alignment/Map) format. It now supports importing from or exporting to SAM,
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
.
This library is part of SAMtools.
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-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
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Purging /«BUILDDIR»
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
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Build Architecture: armhf
Build-Space: 11232
Build-Time: 268
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 151
Job: samtools_0.1.19-1
Machine Architecture: armhf
Package: samtools
Package-Time: 484
Source-Version: 0.1.19-1
Space: 11232
Status: successful
Version: 0.1.19-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20130527-0745
Build needed 00:08:04, 11232k disc space