[med-svn] [SCM] Processing of sequence alignments in SAM and BAM formats. branch, meta, updated. meta/0.1.14-1-2-g014d9f4
Charles Plessy
plessy at debian.org
Sat May 7 09:11:03 UTC 2011
The following commit has been merged in the meta branch:
commit 014d9f4794f8b4895173e1f7d975ae2ddf15bd1f
Author: Charles Plessy <plessy at debian.org>
Date: Sat May 7 18:10:04 2011 +0900
Collected available build logs for version 0.1.15-1.
diff --git a/alpha.log b/alpha.log
deleted file mode 100644
index c953805..0000000
--- a/alpha.log
+++ /dev/null
@@ -1,738 +0,0 @@
-From buildd at goetz.debian.org Tue Mar 29 05:05:38 2011
-Return-path: <buildd at goetz.debian.org>
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-Date: Tue, 29 Mar 2011 05:05:27 +0000
-From: buildd on goetz <buildd at goetz.debian.org>
-To: kurt at roeckx.be,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.14-1 on alpha (dist=sid)
-Key-Id: C9E783F4
-Message-Id: <E1Q4R7P-0003oI-FF at goetz.debian.org>
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on goetz.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.14-1 (alpha) 29 Mar 2011 04:57 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.14-1
-Source Version: 0.1.14-1
-Architecture: alpha
-Get:1 http://ftp.uk.debian.org unstable InRelease [184 kB]
-Get:2 http://incoming.debian.org unstable InRelease [185 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [5169 kB]
-Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://ftp.uk.debian.org unstable/contrib Sources [47.0 kB]
-Get:6 http://ftp.uk.debian.org unstable/non-free Sources [99.0 kB]
-Get:7 http://incoming.debian.org unstable/main Sources [5142 kB]
-Get:8 http://ftp.uk.debian.org unstable/main alpha Packages [6845 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib alpha Packages [51.2 kB]
-Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2232 B]
-Ign http://ftp.uk.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [47.4 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
-Get:13 http://incoming.debian.org unstable/main alpha Packages [6854 kB]
-Get:14 http://incoming.debian.org unstable/contrib alpha Packages [51.1 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [30.5 kB]
-Get:18 http://incoming.debian.org Packages [608 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Ign http://incoming.debian.org Translation-en
-Fetched 25.4 MB in 31s (795 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://git.debian.org/debian-med/samtools.git
-Need to get 379 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (tar) [370 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (diff) [6869 B]
-Fetched 379 kB in 1s (326 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.5)
-fakeroot: already installed (1.14.5-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6.1-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (6.1)
-base-passwd: already installed (3.5.22)
-bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (3.4.4)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.15.8.10)
-e2fsprogs: already installed (1.41.12-2)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.6.3-3)
-gzip: already installed (1.3.12-9)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.8+20110307-1)
-ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-17)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.1)
-sysvinit: already installed (2.88dsf-13.1)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
-mount: already installed (2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
-libc6.1-dev: already installed (2.11.2-13)
-gcc: already installed (4:4.4.5-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-4 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8)
-dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 8.1.2
-cdbs: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
-Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff ncurses-doc less www-browser libmail-box-perl
-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:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 20 newly installed, 0 to remove and 16 not upgraded.
-Need to get 11.6 MB of archives.
-After this operation, 34.2 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils alpha 8.2.2 [215 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base alpha 1.21-5 [1183 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 alpha 1.2.0-1 [40.5 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db alpha 2.5.9-4 [1070 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 alpha 5.04-5 [243 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main file alpha 5.04-5 [50.2 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main gettext-base alpha 0.18.1.1-3 [160 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 alpha 8.12-3 [285 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 alpha 2.7.8.dfsg-2 [901 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main html2text alpha 1.3.2a-15 [111 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 alpha 2.28.2-1 [1676 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 alpha 0.6.2-1 [128 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 alpha 0.9.3-3 [447 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext alpha 0.18.1.1-3 [2218 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian alpha 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf alpha 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper alpha 8.1.2 [553 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs alpha 0.4.92 [1268 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev alpha 5.8+20110307-1 [573 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev alpha 1:1.2.3.4.dfsg-3 [206 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.6 MB in 1s (6632 kB/s)
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 10145 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_alpha.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-5_alpha.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_alpha.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.9-4_alpha.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_alpha.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../archives/file_5.04-5_alpha.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_alpha.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_alpha.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_alpha.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_alpha.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.2-1_alpha.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_alpha.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_alpha.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_alpha.deb) ...
-Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_alpha.deb) ...
-Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_alpha.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_alpha.deb) ...
-Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_alpha.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_alpha.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_alpha.deb) ...
-Setting up bsdmainutils (8.2.2) ...
-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 groff-base (1.21-5) ...
-Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.5.9-4) ...
-Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.2-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
-Setting up gettext (0.18.1.1-3) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
-Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8+20110307-1) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32-bpo.5-alpha-generic alpha (alpha)
-Toolchain package versions: binutils_2.21.0.20110302-2 dpkg-dev_1.15.8.10 g++-4.4_4.4.5-14 gcc-4.4_4.4.5-14 libc6.1-dev_2.11.2-13 libstdc++6_4.5.2-6 libstdc++6-4.4-dev_4.4.5-14 linux-libc-dev_2.6.37-2
-Package versions: apt_0.8.12 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110302-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-4 cpp-4.4_4.4.5-14 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-4 g++-4.4_4.4.5-14 gcc_4:4.4.5-4 gcc-4.4_4.4.5-14 gcc-4.4-base_4.4.5-14 gcc-4.5-base_4.5.2-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc6.1_2.11.2-13 libc6.1-dev_2.11.2-13 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:7.1-7 libgcc1_1:4.5.2-6 libgdbm3_1.8.3-9 libglib2.0-0_2.28.2-1 libgmp10_2:5.0.1+dfsg-6 libgomp1_4.5.2-6 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-6 libstdc++6-4.4-dev_4.4.5-14 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 netbase_4.45 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011d-1 util-linux_2.17.2-9.1 vim-common_2:7.3.035+hg~8fdc12103333-1 vim-tiny_2:7.3.035+hg~8fdc12103333-1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.14
-dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.14-1
- dpkg-source --before-build samtools-0.1.14
-dpkg-buildpackage: host architecture alpha
- fakeroot debian/rules clean
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/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 `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
-rm -f debian/stamp-makefile-check
-dh_clean
-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
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/bcftools'
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/misc'
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/misc'
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/bcftools'
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/misc'
-gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/misc'
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
-../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] 4666 / 6542 = 0.7132 in library 'ex1'
-[bam_rmdupse_core] 1395 / 3271 = 0.4265 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-sample depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/examples'
-touch debian/stamp-makefile-check
- fakeroot debian/rules binary-arch
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-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
-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 ./ChangeLog
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_bugfiles -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
-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 ./ChangeLog
-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_strip -psamtools
-dh_compress -psamtools
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev
-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: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_alpha.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_alpha.deb'.
- dpkg-genchanges -B -malpha Build Daemon (goetz) <buildd_alpha-goetz at buildd.debian.org> >../samtools_0.1.14-1_alpha.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-0.1.14
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110329-0505
-
-samtools_0.1.14-1_alpha.changes:
-Format: 1.8
-Date: Tue, 29 Mar 2011 13:13:54 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: alpha
-Version: 0.1.14-1
-Distribution: sid
-Urgency: low
-Maintainer: alpha Build Daemon (goetz) <buildd_alpha-goetz at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at 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 (0.1.14-1) unstable; urgency=low
- .
- * New upstream release.
-Checksums-Sha1:
- 2fb37a759d9625771e6f84b1abbd78a1d294d7b0 632344 samtools_0.1.14-1_alpha.deb
- e0b4d734c63ee323ab1e52e305c09f80f068289a 196904 libbam-dev_0.1.14-1_alpha.deb
-Checksums-Sha256:
- 34d3c69ddcd76b87aff55e72a9eec57b4dd9d02c6248de911627d9cd3c9d1c7c 632344 samtools_0.1.14-1_alpha.deb
- 71e5a6a05da867b22d2345e5d1cdf115391a620cb556b036838b342667c5c1c9 196904 libbam-dev_0.1.14-1_alpha.deb
-Files:
- 1674299f87a3c486a866d6beae55fd00 632344 science optional samtools_0.1.14-1_alpha.deb
- 5dfeffb84ad1be59b007dfd8edad7321 196904 libdevel optional libbam-dev_0.1.14-1_alpha.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.14-1_alpha.deb
-───────────────────────────
-
- new debian package, version 2.0.
- size 632344 bytes: control archive= 1782 bytes.
- 788 bytes, 16 lines control
- 2520 bytes, 38 lines md5sums
- Package: samtools
- Version: 0.1.14-1
- Architecture: alpha
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1224
- Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
- 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 2011-03-29 05:05 ./
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/lib/samtools/
--rwxr-xr-x root/root 22296 2011-03-29 05:05 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 11136 2011-03-29 05:05 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 15320 2011-03-29 05:05 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 9728 2011-03-29 05:05 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 9728 2011-03-29 05:05 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/bin/
--rwxr-xr-x root/root 31568 2011-03-29 05:05 ./usr/bin/razip
--rwxr-xr-x root/root 466408 2011-03-29 05:05 ./usr/bin/samtools
--rwxr-xr-x root/root 135704 2011-03-29 05:05 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-03-29 05:05 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 126609 2011-03-29 05:00 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-03-29 05:05 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 2005 2011-03-29 05:05 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 8393 2011-03-29 05:05 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/samtools/
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 5778 2011-03-29 05:05 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-
-
-libbam-dev_0.1.14-1_alpha.deb
-─────────────────────────────
-
- new debian package, version 2.0.
- size 196904 bytes: control archive= 895 bytes.
- 674 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.14-1
- Architecture: alpha
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 636
- 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.
-
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/include/
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
--rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
--rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/lib/
--rw-r--r-- root/root 488754 2011-03-29 05:05 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-alpha-sbuild-f18f663f-c406-41c6-a710-7390dff00879/build/buildd-samtools_0.1.14-1-alpha-wRNWnM
-Not cleaning session: cloned chroot in use
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: alpha
-Build-Space: 12244
-Build-Time: 366
-Distribution: sid
-Install-Time: 56
-Job: samtools_0.1.14-1
-Package: samtools
-Package-Time: 486
-Source-Version: 0.1.14-1
-Space: 12244
-Status: successful
-Version: 0.1.14-1
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20110329-0505
-Build needed 00:08:06, 12244k disc space
-Signature with key 'C9E783F4' requested:
diff --git a/armel.log b/armel.log
index 65fc57d..ece10e6 100644
--- a/armel.log
+++ b/armel.log
@@ -1,546 +1,68 @@
-From buildd at ancina.debian.org Wed Mar 30 06:50:59 2011
-Return-path: <buildd at ancina.debian.org>
+From buildd at antheil.debian.org Tue Apr 12 12:14:05 2011
+Return-path: <buildd at antheil.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at ancina.debian.org>)
- id 1Q4pF4-0002Rl-TO
- for logs at buildd.debian.org; Wed, 30 Mar 2011 06:50:59 +0000
-Received: from ancina.ugent.be ([157.193.39.13] helo=ancina.debian.org)
+ (Exim 4.69) (envelope-from <buildd at antheil.debian.org>)
+ id 1Q9cTt-0005mO-0T
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 12:14:05 +0000
+Received: from antheil.islands.arm.com ([217.140.96.60]
+ helo=antheil.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=ancina.debian.org, EMAIL=hostmaster at ancina.debian.org (verified)
+ CN=antheil.debian.org, EMAIL=hostmaster at antheil.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at ancina.debian.org>)
- id 1Q4pEz-0002Lq-3t
- for logs at buildd.debian.org; Wed, 30 Mar 2011 06:50:53 +0000
-Received: from buildd by ancina.debian.org with local (Exim 4.69)
- (envelope-from <buildd at ancina.debian.org>)
- id 1Q4pEt-0007o3-00; Wed, 30 Mar 2011 06:50:47 +0000
-MIME-Version: 1.0
-Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
-Date: Wed, 30 Mar 2011 06:50:46 +0000
-From: Build Daemon <buildd at ancina.debian.org>
-To: buildd-porters at ancina.debian.org,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_0.1.14-1 on armel (dist=sid)
-Key-Id: A1EAA0BB
-Message-Id: <E1Q4pEt-0007o3-00 at ancina.debian.org>
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ancina.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.14-1 (armel) 30 Mar 2011 06:45 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.14-1
-Source Version: 0.1.14-1
-Architecture: armel
-Hit http://ftp.de.debian.org sid InRelease
-Hit http://incoming.debian.org sid InRelease
-Ign http://incoming.debian.org InRelease
-Hit http://ftp.de.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org Release.gpg
-Hit http://ftp.de.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.de.debian.org sid/main armel Packages/DiffIndex
-Hit http://ftp.de.debian.org sid/contrib armel Packages/DiffIndex
-Ign http://ftp.de.debian.org sid/contrib TranslationIndex
-Hit http://ftp.de.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/main armel Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib armel Packages/DiffIndex
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org Release
-Ign http://ftp.de.debian.org sid/contrib Translation-en
-Get:1 http://incoming.debian.org Sources [47.6 kB]
-Get:2 http://incoming.debian.org Packages [546 kB]
-Ign http://incoming.debian.org sid/contrib Translation-en
-Ign http://incoming.debian.org Translation-en
-Fetched 594 kB in 9s (59.6 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://git.debian.org/debian-med/samtools.git
-Need to get 379 kB of source archives.
-Get:1 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.14-1 (dsc) [1939 B]
-Get:2 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.14-1 (tar) [370 kB]
-Get:3 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.14-1 (diff) [6869 B]
-Fetched 379 kB in 0s (1039 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.5)
-fakeroot: already installed (1.14.5-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (6.1)
-base-passwd: already installed (3.5.22)
-bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (3.4.4)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.15.8.10)
-e2fsprogs: already installed (1.41.12-2)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.6.3-3)
-gzip: already installed (1.3.12-9)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.8+20110307-1)
-ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-18)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.1)
-sysvinit: already installed (2.88dsf-13.1)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
-mount: already installed (2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.11.2-13)
-gcc: already installed (4:4.5.2-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.5.2-2 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8)
-dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 8.1.2
-cdbs: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- file gettext gettext-base groff-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf
-Suggested packages:
- devscripts doc-base dh-make gettext-doc groff ncurses-doc less www-browser
- libmail-box-perl
-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:
- cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
- libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 18 newly installed, 0 to remove and 8 not upgraded.
-Need to get 0 B/10.2 MB of archives.
-After this operation, 28.4 MB of additional disk space will be used.
-Selecting previously deselected package groff-base.
-(Reading database ... 10908 files and directories currently installed.)
-Unpacking groff-base (from .../groff-base_1.21-5_armel.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_armel.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.9-4_armel.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_armel.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../archives/file_5.04-5_armel.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_armel.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_armel.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_armel.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_armel.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_armel.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_armel.deb) ...
-Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_armel.deb) ...
-Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_armel.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_armel.deb) ...
-Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_armel.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_armel.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_armel.deb) ...
-Setting up groff-base (1.21-5) ...
-Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.5.9-4) ...
-Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libxml2 (2.7.8.dfsg-2) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.4-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
-Setting up gettext (0.18.1.1-3) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
-Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8+20110307-1) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.31-rc9 armel (armv5tel)
-Toolchain package versions: binutils_2.21.0.20110322-1 dpkg-dev_1.15.8.10 g++-4.5_4.5.2-6 gcc-4.5_4.5.2-6 libc6-dev_2.11.2-13 libstdc++6_4.5.2-6 libstdc++6-4.5-dev_4.5.2-6 linux-libc-dev_2.6.38-1
-Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110322-1 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.5.2-3 cpp-4.5_4.5.2-6 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.63-2 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-2 g++-4.5_4.5.2-6 gawk_1:3.1.7.dfsg-5 gcc_4:4.5.2-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.5-14 gcc-4.5_4.5.2-6 gcc-4.5-base_4.5.2-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc6_2.11.2-13 libc6-dev_2.11.2-13 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdevmapper1.02.1_2:1.02.63-2 libdpkg-perl_1.15.8.10 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.5.2-6 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1 libgomp1_4.5.2-6 libgpg-error0_1.10-0.3 libgpm2_1.20.4-3.3 libldap-2.4-2_2.4.23-7 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libncursesw5_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libpng12-0_1.2.44-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-8 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libssl0.9.8_0.9.8o-5 libstdc++6_4.5.2-6 libstdc++6-4.5-dev_4.5.2-6 libtasn1-3_2.9-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_166-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libvolume-id1_0.141-2 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 netbase_4.45 nullmailer_1:1.04-1.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011d-1 util-linux_2.17.2-9.1 wget_1.12-2.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
-gpgv: keyblock resource `~/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.14
-dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.14-1
- dpkg-source --before-build samtools-0.1.14
-dpkg-buildpackage: host architecture armel
- fakeroot debian/rules clean
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/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 `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
-rm -f debian/stamp-makefile-check
-dh_clean
-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
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/bcftools'
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/misc'
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/misc'
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/bcftools'
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/misc'
-gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/misc'
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-Parse error at line 2: CIGAR and sequence length are inconsistent
-make[1]: *** [ex1.bam] Aborted
-make[1]: *** Deleting file `ex1.bam'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/examples'
-make: *** [debian/stamp-makefile-check] Error 2
-dpkg-buildpackage: error: debian/rules build gave error exit status 2
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110330-0650
-FAILED [dpkg-buildpackage died]
-────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armel-sbuild-dcfb9a37-2d85-45f3-b333-4887e86a90e9/build/buildd-samtools_0.1.14-1-armel-rQGmWd
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- cdbs* debhelper* file* gettext* gettext-base* groff-base* html2text*
- intltool-debian* libcroco3* libglib2.0-0* libmagic1* libncurses5-dev*
- libpipeline1* libunistring0* libxml2* man-db* po-debconf* zlib1g-dev*
-0 upgraded, 0 newly installed, 18 to remove and 8 not upgraded.
-After this operation, 28.4 MB disk space will be freed.
-(Reading database ... 12222 files and directories currently installed.)
-Removing cdbs ...
-Removing debhelper ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libncurses5-dev ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing zlib1g-dev ...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: armel
-Build-Space: 5972
-Build-Time: 253
-Distribution: sid
-Fail-Stage: build
-Install-Time: 29
-Job: samtools_0.1.14-1
-Package: samtools
-Package-Time: 302
-Source-Version: 0.1.14-1
-Space: 5972
-Status: attempted
-Version: 0.1.14-1
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20110330-0650
-Build needed 00:05:02, 5972k disc space
-Signature with key 'A1EAA0BB' requested:
-From buildd at arnold.debian.org Sat Apr 02 02:07:08 2011
-Return-path: <buildd at arnold.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at arnold.debian.org>)
- id 1Q5qF2-0001iw-B0
- for logs at buildd.debian.org; Sat, 02 Apr 2011 02:07:08 +0000
-Received: from arnold.islands.arm.com ([217.140.96.57] helo=arnold.debian.org)
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=arnold.debian.org, EMAIL=hostmaster at arnold.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at arnold.debian.org>)
- id 1Q5qEt-0003Fn-En
- for logs at buildd.debian.org; Sat, 02 Apr 2011 02:06:59 +0000
-Received: from buildd by arnold.debian.org with local (Exim 4.69)
- (envelope-from <buildd at arnold.debian.org>)
- id 1Q5qEp-0005c1-Pi; Sat, 02 Apr 2011 02:06:55 +0000
-From: buildd on arnold <buildd at arnold.debian.org>
-To: buildd-porters at arnold.debian.org,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_0.1.14-1 on armel (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at antheil.debian.org>)
+ id 1Q9cTm-0007Ul-0Z
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 12:13:58 +0000
+Received: from buildd by antheil.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at antheil.debian.org>)
+ id 1Q9cTk-0004Tf-HY; Tue, 12 Apr 2011 12:13:56 +0000
+From: buildd on antheil <buildd at antheil.debian.org>
+To: buildd-porters at antheil.debian.org,logs at buildd.debian.org
+Subject: Log for attempted build of samtools_0.1.15-1 on armel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1Q5qEp-0005c1-Pi at arnold.debian.org>
-Date: Sat, 02 Apr 2011 02:06:55 +0000
+Message-Id: <E1Q9cTk-0004Tf-HY at antheil.debian.org>
+Date: Tue, 12 Apr 2011 12:13:56 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on arnold.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on antheil.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.14-1 (armel) 02 Apr 2011 01:59 ║
+║ samtools 0.1.15-1 (armel) 12 Apr 2011 12:05 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.14-1
-Source Version: 0.1.14-1
+Version: 0.1.15-1
+Source Version: 0.1.15-1
Architecture: armel
-Get:1 http://ftp.uk.debian.org unstable InRelease [186 kB]
-Get:2 http://incoming.debian.org unstable InRelease [186 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [5195 kB]
+Get:1 http://ftp.uk.debian.org unstable InRelease [151 kB]
+Get:2 http://incoming.debian.org unstable InRelease [151 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [5265 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org Release [1604 B]
-Get:6 http://incoming.debian.org unstable/main Sources [5195 kB]
-Get:7 http://ftp.uk.debian.org unstable/contrib Sources [48.7 kB]
-Get:8 http://ftp.uk.debian.org unstable/non-free Sources [98.4 kB]
-Get:9 http://ftp.uk.debian.org unstable/main armel Packages [6919 kB]
-Get:10 http://incoming.debian.org unstable/contrib Sources [48.7 kB]
-Get:11 http://incoming.debian.org unstable/non-free Sources [98.4 kB]
-Get:12 http://incoming.debian.org unstable/main armel Packages [6919 kB]
-Get:13 http://ftp.uk.debian.org unstable/contrib armel Packages [52.4 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5265 kB]
+Get:6 http://ftp.uk.debian.org unstable/contrib Sources [48.2 kB]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [97.4 kB]
+Get:8 http://ftp.uk.debian.org unstable/main armel Packages [6998 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [48.2 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [97.4 kB]
+Get:11 http://incoming.debian.org unstable/main armel Packages [6998 kB]
+Get:12 http://ftp.uk.debian.org unstable/contrib armel Packages [52.2 kB]
Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:14 http://ftp.uk.debian.org unstable/main TranslationIndex [2232 B]
+Get:13 http://ftp.uk.debian.org unstable/main TranslationIndex [2264 B]
Ign http://ftp.uk.debian.org unstable/contrib Translation-en
-Get:15 http://incoming.debian.org unstable/contrib armel Packages [52.4 kB]
+Get:14 http://incoming.debian.org unstable/contrib armel Packages [52.2 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:16 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
-Get:17 http://incoming.debian.org Sources [36.9 kB]
-Get:18 http://incoming.debian.org Packages [498 kB]
-Ign http://incoming.debian.org Translation-en
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Get:17 http://incoming.debian.org Sources [49.7 kB]
+Get:18 http://incoming.debian.org Packages [772 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 25.5 MB in 57s (446 kB/s)
+Ign http://incoming.debian.org Translation-en
+Fetched 26.1 MB in 57s (450 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -561,11 +83,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 379 kB of source archives.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main samtools 0.1.14-1 (dsc) [1939 B]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main samtools 0.1.14-1 (tar) [370 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main samtools 0.1.14-1 (diff) [6869 B]
-Fetched 379 kB in 0s (2305 kB/s)
+Need to get 383 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
+Fetched 383 kB in 1s (373 kB/s)
Download complete and in download only mode
Check arch
@@ -579,18 +101,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15-1)
+fakeroot: already installed (1.15.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -606,7 +128,7 @@ coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
debianutils: already installed (3.4.4)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.15.8.10)
+dpkg: already installed (1.16.0)
e2fsprogs: already installed (1.41.12-2)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.6.3-3)
@@ -614,7 +136,7 @@ gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.8+20110307-1)
ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-18)
+perl-base: already installed (5.10.1-19)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.1)
@@ -624,12 +146,12 @@ bsdutils: already installed (1:2.17.2-9.1)
mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
libc6-dev: already installed (2.11.2-13)
-gcc: already installed (4:4.5.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.5.2-4 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.5.2-5 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.5.2-5 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8)
-dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.0 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.2
+Using default version 8.1.3
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -640,43 +162,55 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ libcroco3 libglib2.0-0 libmagic1 libncurses5 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db ncurses-bin po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
groff ncurses-doc less www-browser libmail-box-perl
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 20 newly installed, 0 to remove and 8 not upgraded.
-Need to get 10.6 MB of archives.
-After this operation, 29.6 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.2.2 [205 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-5 [1077 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.0-1 [33.8 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.5.9-4 [976 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.04-5 [237 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.04-5 [49.4 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-3 [129 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.12-3 [258 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-2 [816 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.28.4-1 [1531 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.2-1 [113 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-3 [410 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-3 [1981 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian armel 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf armel 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper armel 8.1.2 [553 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs armel 0.4.92 [1268 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 5.8+20110307-1 [473 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.3.4.dfsg-3 [190 kB]
+The following packages will be upgraded:
+ libncurses5 ncurses-bin
+2 upgraded, 20 newly installed, 0 to remove and 14 not upgraded.
+Need to get 11.3 MB of archives.
+After this operation, 29.7 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main ncurses-bin armel 5.9-1 [328 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main libncurses5 armel 5.9-1 [357 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.2.2 [205 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-5 [1077 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.0-1 [33.8 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.0.1-1 [983 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.04-5 [237 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.04-5 [49.4 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-3 [129 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.12-3 [258 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-2 [816 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.28.4-1 [1531 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.2-1 [113 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-3 [410 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-3 [1981 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian armel 0.35.0+20060710.1 [30.8 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main po-debconf armel 1.0.16+nmu1 [223 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main debhelper armel 8.1.3 [554 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main cdbs armel 0.4.92 [1268 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 5.9-1 [474 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.3.4.dfsg-3 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.6 MB in 4s (2184 kB/s)
+Fetched 11.3 MB in 3s (2987 kB/s)
+(Reading database ... 10102 files and directories currently installed.)
+Preparing to replace ncurses-bin 5.8+20110307-1 (using .../ncurses-bin_5.9-1_armel.deb) ...
+Unpacking replacement ncurses-bin ...
+Setting up ncurses-bin (5.9-1) ...
+(Reading database ... 10102 files and directories currently installed.)
+Preparing to replace libncurses5 5.8+20110307-1 (using .../libncurses5_5.9-1_armel.deb) ...
+Unpacking replacement libncurses5 ...
+Setting up libncurses5 (5.9-1) ...
Selecting previously deselected package bsdmainutils.
(Reading database ... 10102 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_armel.deb) ...
@@ -685,7 +219,7 @@ Unpacking groff-base (from .../groff-base_1.21-5_armel.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_armel.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.9-4_armel.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.1-1_armel.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_armel.deb) ...
Selecting previously deselected package file.
@@ -711,11 +245,11 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_armel.deb)
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_armel.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_armel.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.3_armel.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.92_armel.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_armel.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_armel.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_armel.deb) ...
Setting up bsdmainutils (8.2.2) ...
@@ -723,7 +257,7 @@ update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write)
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.5.9-4) ...
+Setting up man-db (2.6.0.1-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
@@ -738,19 +272,19 @@ Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
+Setting up debhelper (8.1.3) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8+20110307-1) ...
+Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32 armel (armv5tel)
-Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.15.8.10 g++-4.5_4.5.2-6 gcc-4.5_4.5.2-6 libc6-dev_2.11.2-13 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-6 linux-libc-dev_2.6.38-1
-Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.5.2-4 cpp-4.5_4.5.2-6 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-4 g++-4.5_4.5.2-6 gcc_4:4.5.2-4 gcc-4.4-base_4.4.5-15 gcc-4.5_4.5.2-6 gcc-4.5-base_4.5.2-6 gcc-4.6-base_4.6.0-1 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc6_2.11.2-13 libc6-dev_2.11.2-13 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-1 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-6 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011d-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0 g++-4.5_4.5.2-8 gcc-4.5_4.5.2-8 libc6-dev_2.11.2-13 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-8 linux-libc-dev_2.6.38-1
+Package versions: apt_0.8.13.1 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.5.2-5 cpp-4.5_4.5.2-8 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0 dpkg-dev_1.16.0 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-5 g++-4.5_4.5.2-8 gcc_4:4.5.2-5 gcc-4.4-base_4.4.5-15 gcc-4.5_4.5.2-8 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-1 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc6_2.11.2-13 libc6-dev_2.11.2-13 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-1 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-8 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011e-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -762,12 +296,12 @@ Unpack source
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.14
-dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.15-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.15
+dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
Check disc space
────────────────
@@ -783,8 +317,8 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.14-1
- dpkg-source --before-build samtools-0.1.14
+dpkg-buildpackage: source version 0.1.15-1
+ dpkg-source --before-build samtools-0.1.15
dpkg-buildpackage: host architecture armel
fakeroot debian/rules clean
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -795,17 +329,17 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/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 `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -818,8 +352,8 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -833,15 +367,16 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/bcftools'
+ar -cru 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 glf.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 `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -852,10 +387,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -873,25 +408,26 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/misc'
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/misc'
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/misc'
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -901,28 +437,28 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
Parse error at line 2: CIGAR and sequence length are inconsistent
make[1]: *** [ex1.bam] Aborted
make[1]: *** Deleting file `ex1.bam'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110402-0206
+Build finished at 20110412-1213
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armel-sbuild-0e6c2ddd-c764-4d7f-b937-429869013d12/build/buildd-samtools_0.1.14-1-armel-wkCxdP
+Purging /var/lib/schroot/mount/sid-armel-sbuild-677e6a3f-1a1c-435d-b1ac-727b84d7df3a/build/buildd-samtools_0.1.15-1-armel-QMGIbq
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -930,19 +466,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armel
-Build-Space: 5972
-Build-Time: 260
+Build-Space: 6084
+Build-Time: 295
Distribution: sid
Fail-Stage: build
-Install-Time: 85
-Job: samtools_0.1.14-1
+Install-Time: 92
+Job: samtools_0.1.15-1
Package: samtools
-Package-Time: 437
-Source-Version: 0.1.14-1
-Space: 5972
+Package-Time: 479
+Source-Version: 0.1.15-1
+Space: 6084
Status: attempted
-Version: 0.1.14-1
+Version: 0.1.15-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110402-0206
-Build needed 00:07:17, 5972k disc space
+Finished at 20110412-1213
+Build needed 00:07:59, 6084k disc space
diff --git a/armhf.log b/armhf.log
deleted file mode 100644
index 133daf2..0000000
--- a/armhf.log
+++ /dev/null
@@ -1,676 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><title>File `log' in samtools_0.1.12a-1_armhf (Dec 3 16:39)</title><meta http-equiv="content-type" content="text/html;charset=utf-8"></head><body bgcolor="#ffffff">
-<table width="100%"><tr valign=top><td align=left><h2>File `log' in samtools_0.1.12a-1_armhf (Dec 3 16:39)</h2></td><td align=right><a href="build.php?&pkg=samtools&arch=armhf">samtools</a> >> <a href="build.php?&pkg=samtools&ver=0.1.12a-1&arch=armhf">0.1.12a-1</a> >> <a href="build.php?&pkg=samtools&ver=0.1.12a-1&arch=armhf&stamp=1291394381">Dec 3 16:39</a> >> log</td></tr></table><p><pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on efikamx04.lan
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (armhf) 03 Dec 2010 19:37 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.12a-1
-Architecture: armhf
-Chroot Build Dir: /var/lib/schroot/mount/sid-armhf-sbuild-bee06c27-7dcb-4954-ac4b-1e6de6af9d42/build/buildd-samtools_0.1.12a-1-armhf-bIURqR
-Start Time: 20101203-1937
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-Hit http://ftp.gr.debian.org unstable Release.gpg
-Hit http://ftp.gr.debian.org unstable Release
-Hit http://www.freevec.org unstable Release.gpg
-Hit http://incoming.debian-ports.org unstable Release.gpg
-Ign http://incoming.debian-ports.org/buildd/ unstable/main Translation-en
-Ign http://www.freevec.org/repository/ unstable/main Translation-en
-Hit http://ftp.debian-ports.org unreleased Release.gpg
-Ign http://ftp.debian-ports.org/debian/ unreleased/main Translation-en
-Hit http://ftp.debian-ports.org unstable Release.gpg
-Hit http://ftp.gr.debian.org unstable/main Sources/DiffIndex
-Ign http://ftp.debian-ports.org/debian/ unstable/main Translation-en
-Hit http://ftp.debian-ports.org unreleased Release
-Hit http://www.freevec.org unstable Release
-Hit http://incoming.debian-ports.org unstable Release
-Hit http://ftp.debian-ports.org unstable Release
-Ign http://www.freevec.org unstable/main armhf Packages
-Hit http://incoming.debian-ports.org unstable/main Sources
-Hit http://ftp.debian-ports.org unreleased/main armhf Packages
-Hit http://incoming.debian-ports.org unstable/main armhf Packages
-Hit http://ftp.debian-ports.org unstable/main armhf Packages
-Hit http://www.freevec.org unstable/main armhf Packages
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-
-Download source files with APT
-──────────────────────────────
-
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-Reading package lists...
-Building dependency tree...
-Reading state information...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 364 kB of source archives.
-Get:1 http://ftp.gr.debian.org/debian/ unstable/main samtools 0.1.12a-1 (dsc) [1946 B]
-Get:2 http://ftp.gr.debian.org/debian/ unstable/main samtools 0.1.12a-1 (tar) [356 kB]
-Get:3 http://ftp.gr.debian.org/debian/ unstable/main samtools 0.1.12a-1 (diff) [6337 B]
-Fetched 364 kB in 0s (812 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Checking for already installed source dependencies...
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-debhelper: already installed (8.0.0 >= 8 is satisfied)
-cdbs: missing
-libncurses5-dev: already installed (5.7+20100313-4)
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
-Checking for source dependency conflicts...
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-Installing positive dependencies: cdbs
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 ttf-dejavu-core mime-support x11proto-kb-dev whiptail
- libgpg-error-dev x11proto-xinerama-dev comerr-dev x11proto-render-dev
- texlive-common m4 python-minimal xtrans-dev udev x11proto-core-dev
- x11proto-scrnsaver-dev x11proto-randr-dev qt4-qmake x11proto-input-dev
- libtext-format-perl libgpg-error0 adduser tcl ucf x11proto-print-dev tcl-dev
- uuid-dev libnewt0.52 tsconf x11-common x11proto-xf86vidmode-dev sgml-data
- libstreams0 libgc1c2 texlive-doc-base wx2.8-headers libreadline5 tex-common
-Use 'apt-get autoremove' to remove them.
-Suggested packages:
- doc-base
-Recommended packages:
- autotools-dev
-The following NEW packages will be installed:
- cdbs
-debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 1 newly installed, 0 to remove and 12 not upgraded.
-Need to get 0 B/1240 kB of archives.
-After this operation, 1696 kB of additional disk space will be used.
-Selecting previously deselected package cdbs.
-(Reading database ... 16417 files and directories currently installed.)
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
-Processing triggers for man-db ...
-Setting up cdbs (0.4.89) ...
-Removing negative dependencies:
-Checking correctness of source dependencies...
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-Kernel: Linux 2.6.31.14-efikamx armhf (armv7l)
-Toolchain package versions: libc6-dev_2.11.2-7 dpkg-dev_1.15.8.4+armhf linux-libc-dev_2.6.35~rc6-1+armhf~experimental.2 gcc-4.4_4.4.5-9 g++-4.4_4.4.5-9 binutils_2.20.51.20101009-1+armhf libstdc++6-4.4-dev_4.4.5-9 libstdc++6_4.4.5-9
-Package versions: adduser_3.112+nmu2 apt_0.8.9 autotools-dev_20100122.1 base-files_5.10 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.51.20101009-1+armhf bsdmainutils_8.0.17 bsdutils_1:2.17.2-3.1+armhf build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 comerr-dev_2.1-1.41.12-2 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-9 dash_0.5.5.1-7.3 debconf_1.5.37 debconf-i18n_1.5.37 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2010.06.16 debianutils_3.4.2 devscripts_2.10.69 diffutils_1:3.0-1 dmsetup_2:1.02.48-4 dpkg_1.15.8.4+armhf dpkg-dev_1.15.8.4+armhf e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-2 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.5-1 g++-4.4_4.4.5-9 gcc_4:4.4.5-1 gcc-4.4_4.4.5-9 gcc-4.4-base_4.4.5-9 gettext_0.18.1.1-1+armhf gettext-base_0.18.1.1-1+armhf gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 lib
- acl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.1+armhf libbsd-dev_0.2.0-1 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libbz2-dev_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc6_2.11.2-7 libc6-dev_2.11.2-7 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-10 libdb4.8_4.8.30-3 libdevmapper1.02.1_2:1.02.48-4 libdpkg-perl_1.15.8.4+armhf libffi-dev_3.0.9-2+armhf libffi5_3.0.9-2+armhf libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-9 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-9 libgpg-error-dev_1.6-1 libgpg-error0_1.6-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libncursesw5-dev_5.7+20100313-4 libnewt0.52_0.52.11-2 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpopt0_1.16-1 libreadline5_5.2-7 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 l
- ibssl0.9.8_0.9.8o-3 libstdc++6_4.4.5-9 libstdc++6-4.4-dev_4.4.5-9 libstreams0_0.7.2-1 libtext-charwidth-perl_0.04-6 libtext-format-perl_0.52-21 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_164-2 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.1+armhf libxml2_2.7.8.dfsg-1 libzzip-0-13_0.13.56-1 libzzip-dev_0.13.56-1 linux-libc-dev_2.6.35~rc6-1+armhf~experimental.2 llvm-2.7-priv-dev_2.7-6 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 m4_1.4.14-3 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mime-support_3.51-1 mount_2.17.2-3.1+armhf nano_2.2.5-1 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 netbase_4.43 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 patchutils_0.3.1-2 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 pkg-kde-tools_0.9.3 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 python-minimal_2.6.6-3+squeeze2 python2.6-minimal_2.6.6-7 qt4-qmake_4:4.6.3-3+armhf readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sgm
- l-base_1.26+nmu1 sgml-data_2.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-13 sysvinit_2.88dsf-13 sysvinit-utils_2.88dsf-13 tar_1.25-2 tcl_8.4.16-2 tcl-dev_8.4.16-2 tcl8.4_8.4.19-4 tcl8.4-dev_8.4.19-4 tcl8.5_8.5.8-2 tcl8.5-dev_8.5.8-2 tex-common_2.08 texinfo_4.13a.dfsg.1-6 texlive-common_2009-11 texlive-doc-base_2009-2 tsconf_1.0-7 ttf-dejavu-core_2.31-1 tzdata_2010o-1 ucf_3.0025+nmu1 udev_164-2 unzip_6.0-4 util-linux_2.17.2-3.1+armhf uuid-dev_2.17.2-3.1+armhf whiptail_0.52.11-2 wx2.8-headers_2.8.10.1-3 x11-common_1:7.5+8+armhf x11proto-core-dev_7.0.19-1 x11proto-input-dev_2.0.1-1 x11proto-kb-dev_1.0.5-1 x11proto-print-dev_1.0.3.xsf1-1 x11proto-randr-dev_1.3.2-1 x11proto-render-dev_2:0.11.1-1 x11proto-scrnsaver-dev_1.2.1-1 x11proto-xf86vidmode-dev_2.3-2 x11proto-xinerama-dev_1.2-2 xml-core_0.13 xtrans-dev_1.2.6-1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Dec 3 06:37:23 2010 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.12a
-dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.12a-1
- dpkg-source --before-build samtools-0.1.12a
-dpkg-buildpackage: host architecture armhf
- /usr/bin/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 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/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 `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
-rm -f debian/stamp-makefile-check
-dh_clean
-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
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -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: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
-bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
-bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 4 has type 'size_t'
-bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 5 has type 'size_t'
-bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 6 has type 'size_t'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/bcftools'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/misc'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/bcftools'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/misc'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/misc'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
-../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 glfview ex1.glf | gzip > ex1.glfview.gz
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-sample depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/examples'
-touch debian/stamp-makefile-check
- /usr/bin/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:104: WARNING: DEB_DH_BUILDDEB_ARGS 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 ./ChangeLog
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
-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 ./ChangeLog
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev
-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: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1_armhf.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1_armhf.deb'.
-dpkg-genchanges -B
-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-0.1.12a
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-1942
-
-samtools_0.1.12a-1_armhf.changes:
-Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: armhf
-Version: 0.1.12a-1
-Distribution: unstable
-Urgency: low
-Maintainer: armhf Build Daemon (efikamx04) <buildd_armhf-efikamx04 at debian-ports...>
-Changed-By: Charles Plessy <plessy at debian...>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
- samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.12a-1) unstable; urgency=low
- .
- * New upstream release.
- * Use bzip2 compression for the binary packages (debian/rules).
- * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
- available in earlier versions (debian/compat, debian/control).
-Checksums-Sha1:
- 76d314c62b90686808137f9226997b31f8546a1f 585164 samtools_0.1.12a-1_armhf.deb
- 5cda0c9d27be475906b6a2b722d74a0676d9627c 168644 libbam-dev_0.1.12a-1_armhf.deb
-Checksums-Sha256:
- e971e4844cd355f0d49db34d6104a19ee0c168feb9529fd47f08f94dc23779dc 585164 samtools_0.1.12a-1_armhf.deb
- 1807791a96b5502d0ed9939288c27c3c72948c63f3db5bb9301d714719916023 168644 libbam-dev_0.1.12a-1_armhf.deb
-Files:
- f9a15338d032e195e5056ad4edf9f6da 585164 science optional samtools_0.1.12a-1_armhf.deb
- c8fee737c0e6f9642b1c0ecb9618dff8 168644 libdevel optional libbam-dev_0.1.12a-1_armhf.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.12a-1_armhf.deb
-────────────────────────────
-
- new debian package, version 2.0.
- size 585164 bytes: control archive= 1793 bytes.
- 792 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
- Package: samtools
- Version: 0.1.12a-1
- Architecture: armhf
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 888
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
- 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 2010-12-03 19:42 ./
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/bin/
--rwxr-xr-x root/root 68536 2010-12-03 19:42 ./usr/bin/bcftools
--rwxr-xr-x root/root 20364 2010-12-03 19:42 ./usr/bin/razip
--rwxr-xr-x root/root 259436 2010-12-03 19:42 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/samtools/
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
--rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 5778 2010-12-03 19:42 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/doc/samtools/
--rw-r--r-- root/root 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 126609 2010-12-03 19:41 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1966 2010-12-03 19:42 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/man/man1/
--rw-r--r-- root/root 7546 2010-12-03 19:42 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2010-12-03 19:42 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/lib/
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/lib/samtools/
--rwxr-xr-x root/root 5828 2010-12-03 19:42 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 5828 2010-12-03 19:42 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7052 2010-12-03 19:42 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 15356 2010-12-03 19:42 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 10132 2010-12-03 19:42 ./usr/lib/samtools/md5fa
-lrwxrwxrwx root/root 0 2010-12-03 19:42 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.12a-1_armhf.deb
-──────────────────────────────
-
- new debian package, version 2.0.
- size 168644 bytes: control archive= 896 bytes.
- 675 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.12a-1
- Architecture: armhf
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 348
- 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.
-
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/include/
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
--rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
--rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
-drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/lib/
--rw-r--r-- root/root 205838 2010-12-03 19:42 ./usr/lib/libbam.a
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armhf-sbuild-bee06c27-7dcb-4954-ac4b-1e6de6af9d42/build/buildd-samtools_0.1.12a-1-armhf-bIURqR
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
-I: This option will be removed in the future; please update your configuration
-W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-(Reading database ... 16473 files and directories currently installed.)
-Removing cdbs ...
-Processing triggers for man-db ...
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-1942
-Build needed 00:04:49, 8256k disc space
-
-</pre>
-<p>
-
-<!-- Footer menu bar -->
-
-<table width="100%">
-<tr valign=top>
- <td align=left>
- <address>
-
- These scripts were derived from the buildd.debian.org, thanks to Ryan Murray.<br>
- Contact address: <<a href="mailto:admin at debian-ports.org">admin at debian-ports.org</a>>
- </address>
- </td>
- <td align=right>
- <font size=-1>(
- <a href="index.php">index</a> |
- <a href="build.php">build logs</a>
- )</font>
- </td>
-</tr>
-</table>
-<br>
-</body>
diff --git a/hppa.log b/hppa.log
deleted file mode 100644
index 23b184b..0000000
--- a/hppa.log
+++ /dev/null
@@ -1,770 +0,0 @@
-From buildd at peri.debian.org Tue Mar 29 09:19:05 2011
-Return-path: <buildd at peri.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at peri.debian.org>)
- id 1Q4V4r-0001Zl-61
- for logs at buildd.debian.org; Tue, 29 Mar 2011 09:19:05 +0000
-Received: from peri.debian.org ([192.25.206.15])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=peri.debian.org, EMAIL=hostmaster at peri.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at peri.debian.org>)
- id 1Q4V4n-0002w2-7c; Tue, 29 Mar 2011 09:19:01 +0000
-Received: from buildd by peri.debian.org with local (Exim 4.69)
- (envelope-from <buildd at peri.debian.org>)
- id 1Q4V4j-00049P-54; Tue, 29 Mar 2011 09:18:57 +0000
-From: buildd on peri <buildd at peri.debian.org>
-To: dannf+buildd at dannf.org,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.14-1 on hppa (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-Message-Id: <E1Q4V4j-00049P-54 at peri.debian.org>
-Date: Tue, 29 Mar 2011 09:18:57 +0000
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on peri.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.14-1 (hppa) 29 Mar 2011 09:14 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.14-1
-Source Version: 0.1.14-1
-Architecture: hppa
-Get:1 http://spohr.debian.org sid InRelease [186 kB]
-Get:2 http://spohr.debian.org sid/main Sources/DiffIndex [2038 B]
-Get:3 http://incoming.debian.org sid InRelease [186 kB]
-Ign http://incoming.debian.org InRelease
-Hit http://spohr.debian.org sid/contrib Sources/DiffIndex
-Get:4 http://spohr.debian.org sid/main hppa Packages/DiffIndex [2038 B]
-Get:5 http://spohr.debian.org sid/contrib hppa Packages/DiffIndex [2023 B]
-Ign http://spohr.debian.org sid/contrib TranslationIndex
-Hit http://spohr.debian.org sid/main TranslationIndex
-Get:6 http://spohr.debian.org sid/main 2011-03-29-0818.12.pdiff [2203 B]
-Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://spohr.debian.org sid/main hppa 2011-03-29-0818.12.pdiff [4027 B]
-Get:9 http://spohr.debian.org sid/contrib hppa 2011-03-29-0818.12.pdiff [361 B]
-Ign http://spohr.debian.org sid/contrib Translation-en
-Get:10 http://spohr.debian.org sid/main 2011-03-29-0818.12.pdiff [2203 B]
-Get:11 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Get:12 http://incoming.debian.org sid/main hppa Packages/DiffIndex [2038 B]
-Get:13 http://incoming.debian.org sid/contrib hppa Packages/DiffIndex [2023 B]
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Get:14 http://incoming.debian.org Release [1604 B]
-Get:15 http://incoming.debian.org sid/main 2011-03-29-0818.12.pdiff [2203 B]
-Get:16 http://incoming.debian.org sid/main hppa 2011-03-29-0818.12.pdiff [4027 B]
-Get:17 http://incoming.debian.org sid/contrib hppa 2011-03-29-0818.12.pdiff [361 B]
-Get:18 http://spohr.debian.org sid/main hppa 2011-03-29-0818.12.pdiff [4027 B]
-Get:19 http://incoming.debian.org Sources [31.2 kB]
-Get:20 http://incoming.debian.org Packages [637 kB]
-Ign http://incoming.debian.org sid/contrib Translation-en
-Ign http://incoming.debian.org Translation-en
-Get:21 http://spohr.debian.org sid/contrib hppa 2011-03-29-0818.12.pdiff [361 B]
-Get:22 http://incoming.debian.org sid/main 2011-03-29-0818.12.pdiff [2203 B]
-Get:23 http://incoming.debian.org sid/main hppa 2011-03-29-0818.12.pdiff [4027 B]
-Get:24 http://incoming.debian.org sid/contrib hppa 2011-03-29-0818.12.pdiff [361 B]
-Fetched 1067 kB in 26s (40.1 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://git.debian.org/debian-med/samtools.git
-Need to get 379 kB of source archives.
-Get:1 http://spohr.debian.org/debian/ sid/main samtools 0.1.14-1 (dsc) [1939 B]
-Get:2 http://spohr.debian.org/debian/ sid/main samtools 0.1.14-1 (tar) [370 kB]
-Get:3 http://spohr.debian.org/debian/ sid/main samtools 0.1.14-1 (diff) [6869 B]
-Fetched 379 kB in 0s (5127 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.5)
-fakeroot: already installed (1.15-1)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (6.1)
-base-passwd: already installed (3.5.22)
-bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (3.4.4)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.15.8.10)
-e2fsprogs: already installed (1.41.12-2)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.6.3-3)
-gzip: already installed (1.3.12-9)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.8+20110307-1)
-ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-18)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.1)
-sysvinit: already installed (2.88dsf-13.1)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
-mount: already installed (2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.11.2-10)
-gcc: already installed (4:4.5.2-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.5.2-3 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8)
-dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 8.1.2
-cdbs: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
-Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff ncurses-doc less www-browser libmail-box-perl
-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:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/11.4 MB of archives.
-After this operation, 31.6 MB of additional disk space will be used.
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 10143 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_hppa.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-5_hppa.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_hppa.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.9-4_hppa.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_hppa.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../archives/file_5.04-5_hppa.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_hppa.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_hppa.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_hppa.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_hppa.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_hppa.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_hppa.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_hppa.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_hppa.deb) ...
-Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_hppa.deb) ...
-Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_hppa.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_hppa.deb) ...
-Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_hppa.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hppa.deb) ...
-Setting up bsdmainutils (8.2.2) ...
-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 groff-base (1.21-5) ...
-Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.5.9-4) ...
-Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.4-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
-Setting up gettext (0.18.1.1-3) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
-Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8+20110307-1) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-parisc hppa (parisc)
-Toolchain package versions: binutils_2.21.0.20110327-1 dpkg-dev_1.15.8.10 g++-4.5_4.5.2-7 gcc-4.5_4.5.2-7 libc6-dev_2.11.2-10 libstdc++6_4.5.2-7 libstdc++6-4.5-dev_4.5.2-7 linux-libc-dev_2.6.37-2
-Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-1 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.5.2-3 cpp-4.5_4.5.2-7 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-3 g++-4.5_4.5.2-7 gcc_4:4.5.2-3 gcc-4.5_4.5.2-7 gcc-4.5-base_4.5.2-7 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-10 libc-dev-bin_2.11.2-10 libc6_2.11.2-10 libc6-dev_2.11.2-10 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libelfg0_0.8.13-1 libgcc4_4.5.2-7 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.5.2-7 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-2 libppl9_0.11.2-2 libpwl5_0.11.2-2 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4+b1 libss2_1.41.12-2 libstdc++6_4.5.2-7 libstdc++6-4.5-dev_4.5.2-7 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011d-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
-gpgv: keyblock resource `~/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.14
-dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.14-1
- dpkg-source --before-build samtools-0.1.14
-dpkg-buildpackage: host architecture hppa
- fakeroot debian/rules clean
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/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 `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
-rm -f debian/stamp-makefile-check
-dh_clean
-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
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/bcftools'
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/misc'
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/misc'
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/bcftools'
-gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/misc'
-gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/misc'
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
-../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 glfview ex1.glf | gzip > ex1.glfview.gz
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-sample depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/examples'
-touch debian/stamp-makefile-check
- fakeroot debian/rules binary-arch
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-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
-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 ./ChangeLog
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_bugfiles -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
-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 ./ChangeLog
-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_strip -psamtools
-dh_compress -psamtools
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev
-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: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_hppa.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_hppa.deb'.
- dpkg-genchanges -B -mhppa Build Daemon (peri) <buildd_hppa-peri at buildd.debian.org> >../samtools_0.1.14-1_hppa.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-0.1.14
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110329-0918
-
-samtools_0.1.14-1_hppa.changes:
-Format: 1.8
-Date: Tue, 29 Mar 2011 13:13:54 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: hppa
-Version: 0.1.14-1
-Distribution: sid
-Urgency: low
-Maintainer: hppa Build Daemon (peri) <buildd_hppa-peri at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at 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 (0.1.14-1) unstable; urgency=low
- .
- * New upstream release.
-Checksums-Sha1:
- 124dd3e62f424d74082f970406e253d42366db4d 610592 samtools_0.1.14-1_hppa.deb
- c4bacf0729abff07775a5cc8cc4d2d5a8ac8c952 176994 libbam-dev_0.1.14-1_hppa.deb
-Checksums-Sha256:
- b50a3deb9524928b432f67f947204c2054e157f41225dd6479e3712fafa695bb 610592 samtools_0.1.14-1_hppa.deb
- e9cbfc41cc47f3a4bb943b300b656f4c12bb08c37d6309cb212fd3829e08fc65 176994 libbam-dev_0.1.14-1_hppa.deb
-Files:
- af9de90faf88c403f44d59ba1404ec3b 610592 science optional samtools_0.1.14-1_hppa.deb
- 49146b2f8ac2ea23a7390c154de5ae6a 176994 libdevel optional libbam-dev_0.1.14-1_hppa.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.14-1_hppa.deb
-──────────────────────────
-
- new debian package, version 2.0.
- size 610592 bytes: control archive= 1789 bytes.
- 786 bytes, 16 lines control
- 2520 bytes, 38 lines md5sums
- Package: samtools
- Version: 0.1.14-1
- Architecture: hppa
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1132
- Depends: libc6 (>= 2.11), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
- 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 2011-03-29 09:18 ./
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/samtools/
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 5778 2011-03-29 09:18 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/man/man1/
--rw-r--r-- root/root 2005 2011-03-29 09:18 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 8393 2011-03-29 09:18 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-03-29 09:18 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/doc/samtools/
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 126609 2011-03-29 09:17 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 1966 2011-03-29 09:18 ./usr/share/doc/samtools/README.bcftools
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/bin/
--rwxr-xr-x root/root 398484 2011-03-29 09:18 ./usr/bin/samtools
--rwxr-xr-x root/root 114496 2011-03-29 09:18 ./usr/bin/bcftools
--rwxr-xr-x root/root 26928 2011-03-29 09:18 ./usr/bin/razip
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/lib/samtools/
--rwxr-xr-x root/root 22684 2011-03-29 09:18 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 9932 2011-03-29 09:18 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 10072 2011-03-29 09:18 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 10072 2011-03-29 09:18 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 14100 2011-03-29 09:18 ./usr/lib/samtools/md5fa
-
-
-libbam-dev_0.1.14-1_hppa.deb
-────────────────────────────
-
- new debian package, version 2.0.
- size 176994 bytes: control archive= 899 bytes.
- 673 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.14-1
- Architecture: hppa
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 436
- 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.
-
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/include/
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
--rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
--rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
-drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/lib/
--rw-r--r-- root/root 286382 2011-03-29 09:18 ./usr/lib/libbam.a
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-hppa-sbuild-03c9b932-c06f-434d-911e-297794d47a06/build/buildd-samtools_0.1.14-1-hppa-LuAVpm
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- bsdmainutils* cdbs* debhelper* file* gettext* gettext-base* groff-base*
- html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
- libncurses5-dev* libpcre3* libpipeline1* libunistring0* libxml2* man-db*
- po-debconf* zlib1g-dev*
-0 upgraded, 0 newly installed, 20 to remove and 0 not upgraded.
-After this operation, 31.6 MB disk space will be freed.
-(Reading database ... 11580 files and directories currently installed.)
-Removing cdbs ...
-Removing debhelper ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libncurses5-dev ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing zlib1g-dev ...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: hppa
-Build-Space: 10284
-Build-Time: 171
-Distribution: sid
-Install-Time: 46
-Job: samtools_0.1.14-1
-Package: samtools
-Package-Time: 265
-Source-Version: 0.1.14-1
-Space: 10284
-Status: successful
-Version: 0.1.14-1
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20110329-0918
-Build needed 00:04:25, 10284k disc space
-
diff --git a/hurd-i386.log b/hurd-i386.log
index 215e39f..6e4ba54 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,67 +1,64 @@
-From buildd at mozart.debian.net Tue Mar 29 12:10:36 2011
-Return-path: <buildd at mozart.debian.net>
-Received: from callisto.debian.net ([80.87.129.151])
+From buildd at rossini.debian.net Tue Apr 12 11:41:20 2011
+Return-path: <buildd at rossini.debian.net>
+Received: from io.ethz.ch ([129.132.80.17] helo=io.debian.net)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at mozart.debian.net>)
- id 1Q4Xko-0006zs-I2
- for logs at buildd.debian.org; Tue, 29 Mar 2011 12:10:35 +0000
-Received: from mozart.debian.net ([10.1.0.1])
- by callisto.debian.net with esmtp (Exim 4.69)
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-Date: Tue, 29 Mar 2011 12:10:28 +0000
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-To: samuel.thibault at labri.fr, mbanck at gmx.net, logs at debian-ports.org,
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+Date: Tue, 12 Apr 2011 11:41:09 +0000
+Message-Id: <E1Q9by1-0006BB-88 at rossini.debian.net>
+From: Build Daemon <buildd at rossini.debian.net>
+To: samuel.thibault at labri.fr, mbanck at debian.org, logs at debian-ports.org,
logs at buildd.debian.org, debian-hurd-build-logs at lists.alioth.debian.org
-Subject: Log for successful build of samtools_0.1.14-1 on hurd-i386 (dist=sid)
+Subject: Log for successful build of samtools_0.1.15-1 on hurd-i386 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.59.1 (31 Jan 2010) on mozart.debian.net
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on rossini.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.14-1 (hurd-i386) 29 mars 2011 12:05 ║
+║ samtools 0.1.15-1 (hurd-i386) 12 Apr 2011 11:30 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.14-1
+Version: 0.1.15-1
Architecture: hurd-i386
-Chroot Build Dir: /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE
-Start Time: 20110329-1205
+Chroot Build Dir: /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe
+Start Time: 20110412-1130
Ign file: ./ InRelease
Ign file: ./ Release.gpg
Ign file: ./ Release
Ign file: ./ Translation-en
Ign http://ftp.debian-ports.org unreleased InRelease
+Hit http://ftp.uk.debian.org unstable InRelease
+Hit http://ftp.uk.debian.org experimental InRelease
Hit http://ftp.debian-ports.org unreleased Release.gpg
-Hit http://ftp.debian-ports.org unreleased Release
-Hit http://ftp.uk.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:1 http://incoming.debian.org Release.gpg [836 B]
-Get:2 http://incoming.debian.org Release [1604 B]
-Hit http://ftp.uk.debian.org sid/main Sources/DiffIndex
+Hit http://ftp.debian-ports.org unreleased Release
+Hit http://incoming.debian.org Release.gpg
+Hit http://incoming.debian.org Release
+Hit http://ftp.uk.debian.org unstable/main Sources/DiffIndex
+Hit http://ftp.uk.debian.org unstable/contrib Sources/DiffIndex
+Hit http://ftp.uk.debian.org unstable/non-free Sources/DiffIndex
+Hit http://ftp.uk.debian.org unstable/main hurd-i386 Packages/DiffIndex
+Hit http://ftp.uk.debian.org unstable/main TranslationIndex
+Hit http://ftp.uk.debian.org experimental/main Sources/DiffIndex
+Hit http://ftp.uk.debian.org experimental/contrib Sources/DiffIndex
+Hit http://ftp.uk.debian.org experimental/non-free Sources/DiffIndex
Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
-Hit http://ftp.uk.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.uk.debian.org sid/non-free Sources/DiffIndex
-Hit http://ftp.uk.debian.org sid/main hurd-i386 Packages/DiffIndex
-Hit http://ftp.uk.debian.org sid/contrib hurd-i386 Packages/DiffIndex
-Hit http://ftp.uk.debian.org sid/non-free hurd-i386 Packages/DiffIndex
-Ign http://ftp.uk.debian.org sid/contrib TranslationIndex
-Hit http://ftp.uk.debian.org sid/main TranslationIndex
-Ign http://ftp.uk.debian.org sid/non-free TranslationIndex
Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
-Get:3 http://incoming.debian.org Sources [35.0 kB]
Ign http://ftp.debian-ports.org unreleased/main Translation-en
-Get:4 http://incoming.debian.org Packages [643 kB]
-Ign http://ftp.uk.debian.org sid/contrib Translation-en
-Ign http://ftp.uk.debian.org sid/non-free Translation-en
+Hit http://incoming.debian.org Sources
+Hit http://incoming.debian.org Packages
Ign http://incoming.debian.org Translation-en
-Fetched 680 kB in 47s (14.3 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +79,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 379 kB of source archives.
-Get:1 http://ftp.uk.debian.org/debian/ sid/main samtools 0.1.14-1 (dsc) [1939 B]
-Get:2 http://ftp.uk.debian.org/debian/ sid/main samtools 0.1.14-1 (tar) [370 kB]
-Get:3 http://ftp.uk.debian.org/debian/ sid/main samtools 0.1.14-1 (diff) [6869 B]
-Fetched 379 kB in 0s (1051 kB/s)
+Need to get 383 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
+Fetched 383 kB in 2s (166 kB/s)
Download complete and in download only mode
Check arch
@@ -100,43 +97,113 @@ Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
└──────────────────────────────────────────────────────────────────────────────┘
Checking for already installed source dependencies...
-debhelper: already installed (8.1.2 >= 8 is satisfied)
+debhelper: missing
+Using default version 8.1.3
cdbs: missing
libncurses5-dev: missing
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
+zlib1g-dev: missing
Checking for source dependency conflicts...
-Installing positive dependencies: cdbs libncurses5-dev
+Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libboost-iostreams1.42.0 libusb-0.1-4p
+ libboost-iostreams1.42.0 libssl1.0.0
Use 'apt-get autoremove' to remove them.
+The following extra packages will be installed:
+ file gettext gettext-base html2text intltool-debian libcroco3 libexpat1
+ libglib2.0-0 libmagic1 libncurses5 libunistring0 libxml2 ncurses-bin
+ po-debconf
Suggested packages:
- devscripts doc-base ncurses-doc
+ devscripts doc-base dh-make gettext-doc ncurses-doc libmail-box-perl
Recommended packages:
- autotools-dev
+ autotools-dev autopoint libglib2.0-data shared-mime-info xml-core
+ libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs libncurses5-dev
-0 upgraded, 2 newly installed, 0 to remove and 67 not upgraded.
-Need to get 0 B/1733 kB of archives.
-After this operation, 3084 kB of additional disk space will be used.
+ cdbs debhelper file gettext gettext-base html2text intltool-debian libcroco3
+ libexpat1 libglib2.0-0 libmagic1 libncurses5-dev libunistring0 libxml2
+ po-debconf zlib1g-dev
+The following packages will be upgraded:
+ libncurses5 ncurses-bin
+2 upgraded, 16 newly installed, 0 to remove and 40 not upgraded.
+Need to get 1151 kB/9042 kB of archives.
+After this operation, 23.5 MB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
- cdbs libncurses5-dev
+ ncurses-bin libncurses5 libmagic1 file gettext-base libxml2 html2text
+ libglib2.0-0 libcroco3 libexpat1 libunistring0 gettext intltool-debian
+ po-debconf debhelper cdbs libncurses5-dev zlib1g-dev
Authentication warning overridden.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main ncurses-bin hurd-i386 5.9-1 [326 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main libncurses5 hurd-i386 5.9-1 [359 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev hurd-i386 5.9-1 [466 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 1151 kB in 1s (592 kB/s)
+(Reading database ... 11575 files and directories currently installed.)
+Preparing to replace ncurses-bin 5.8+20110307-1 (using .../ncurses-bin_5.9-1_hurd-i386.deb) ...
+Unpacking replacement ncurses-bin ...
+Processing triggers for man-db ...
+Setting up ncurses-bin (5.9-1) ...
+(Reading database ... 11575 files and directories currently installed.)
+Preparing to replace libncurses5 5.8+20110307-1 (using .../libncurses5_5.9-1_hurd-i386.deb) ...
+Unpacking replacement libncurses5 ...
+Setting up libncurses5 (5.9-1) ...
+Selecting previously deselected package libmagic1.
+(Reading database ... 11575 files and directories currently installed.)
+Unpacking libmagic1 (from .../libmagic1_5.03-5+b1_hurd-i386.deb) ...
+Selecting previously deselected package file.
+Unpacking file (from .../file_5.03-5+b1_hurd-i386.deb) ...
+Selecting previously deselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_hurd-i386.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_hurd-i386.deb) ...
+Selecting previously deselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15+b1_hurd-i386.deb) ...
+Selecting previously deselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_hurd-i386.deb) ...
+Selecting previously deselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-1_hurd-i386.deb) ...
+Selecting previously deselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7_hurd-i386.deb) ...
+Selecting previously deselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-3_hurd-i386.deb) ...
+Selecting previously deselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-3_hurd-i386.deb) ...
+Selecting previously deselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously deselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously deselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.1.3_all.deb) ...
Selecting previously deselected package cdbs.
-(Reading database ... 14520 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_hurd-i386.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_hurd-i386.deb) ...
+Selecting previously deselected package zlib1g-dev.
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hurd-i386.deb) ...
Processing triggers for man-db ...
+Processing triggers for install-info ...
+Setting up libmagic1 (5.03-5+b1) ...
+Setting up file (5.03-5+b1) ...
+Setting up gettext-base (0.18.1.1-3) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up html2text (1.3.2a-15+b1) ...
+Setting up libglib2.0-0 (2.28.4-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3 (0.6.2-1) ...
+Setting up libexpat1 (2.0.1-7) ...
+Setting up libunistring0 (0.9.3-3) ...
+Setting up gettext (0.18.1.1-3) ...
+Setting up intltool-debian (0.35.0+20060710.1) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.1.3) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8+20110307-1) ...
+Setting up libncurses5-dev (5.9-1) ...
+Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: libc0.3-dev_2.11.2-13 dpkg-dev_1.15.8.10 hurd-dev_20110303-1~1 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.21.0.20110302-2 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.5.2-4
-Package versions: adduser_3.112+nmu1 apt_0.8.11.5+b1 apt-utils_0.8.11.5+b1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3+hurd.1 binutils_2.21.0.20110302-2 bsdmainutils_8.0.13 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-4 cpp-4.4_4.4.5-10 cron_3.0pl1-115 dash_0.5.5.1-7 debconf_1.5.35 debconf-english_1.5.35 debfoster_2.6-2 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_3.4.1 deborphan_1.7.28 dialog_1.1-20100428-1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.12.4 file_5.03-5+b1 findutils_4.4.2-1 fontconfig_2.8.0-2.1 fontconfig-config_2.8.0-2.1 g++_4:4.4.4-2 g++-4.4_4.4.5-10 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-4 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gfortran-4.4_4.4.5-10 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15+b1 hurd_20110319-2 hurd-dev_20110303-1~1 initscripts_2.88dsf-12 insserv_1.14.0-2 install-info_4.13a.dfsg.1-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libapt-pkg-dev_0.8.11.5+b1 libattr1_1:2.4.44-2 libblkid1_2.16.2-0 libboost-iostreams1.42.0_1.42.0-4+b1 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc0.3_2.11.2-13 libc0.3-dev_2.11.2-13 libc0.3-xen_2.11.2-13 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdigest-sha1-perl_2.13-1 libdpkg-perl_1.15.8.10 libept-dev_1.0.3+b2 libept1_1.0.3+b2 libexpat1_2.0.1-7 libfontconfig1_2.8.0-2.1 libfreetype6_2.4.4-1 libgcc1_1:4.4.5-10 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgfortran3_4.4.5-10 libglib2.0-0_2.28.2-1 libglib2.0-data_2.28.0-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-1+b1 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.4-2 libgomp1_4.4.5-10 libgpg-error0_1.10-0.3 libidn11_1.20-1 libldap-2.4-2_2.4.17-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.03-5+b1 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libncursesw5_5.8+20110307-1 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.2-2 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-3+b1 libpng12-0_1.2.44-2 libpopt0_1.16-1 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-8 libsasl2-modules_2.1.23.dfsg1-8 libslang2_2.1.4-3 libss2_1.41.12-2 libssl0.9.8_0.9.8o-5 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-10 libtagcoll2-dev_2.0.11-1.1 libtasn1-3_2.9-2 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.16.2-0 libwibble-dev_0.1.26-1 libwrap0_7.6.dbs-8 libxapian-dev_1.2.3-2 libxapian22_1.2.3-2 libxml2_2.7.8.dfsg-2 lsb-base_3.2-25 lynx-cur_2.8.8dev.8-1 make_3.81-8 man-db_2.5.7-4 mawk_1.3.3-15 mime-support_3.48-1 ncurses-base_5.7+20100313-4 ncurses-bin_5.8+20110307-1 netbase_4.42 netcat-traditional_1.10-38 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 pkg-config_0.25-1 po-debconf_1.0.16 procps_1:3.2.7-11 psmisc_22.3-1 random-egd_0.5-0+hurd.1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sgml-base_1.26+nmu1 shared-mime-info_0.71-3 sudo_1.7.2p7-1 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 ttf-dejavu-core_2.31-1 type-handling_0.2.23 tzdata_2010m-1 ucf_3.0025+nmu1 util-linux_2.16.2-0 xml-core_0.13 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc0.3-dev_2.11.2-13 dpkg-dev_1.16.0.1 hurd-dev_20110303-1~1 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.21.0.20110327-2 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.5.2-4
+Package versions: adduser_3.112+nmu2 apt_0.8.13.2 base-files_6.1 base-passwd_3.5.22 bash_4.1-3+hurd.1 binutils_2.21.0.20110327-2 bsdmainutils_8.2.2 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 ca-certificates_20090814+nmu2 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-7 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.6-2 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_3.4.3 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.12.4 file_5.03-5+b1 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-4 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gfortran_4:4.4.5-4 gfortran-4.4_4.4.5-10 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gnupg_1.4.10-4 gnupg-curl_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15+b1 hurd_20110319-2 hurd-dev_20110303-1~1 ifupdown_0.6.9+hurd.1 inetutils-tools_2:1.8-3 initscripts_2.88dsf-13.1 insserv_1.14.0-2 install-info_4.13a.dfsg.1-6 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libattr1_1:2.4.44-2 libblkid1_2.16.2-0 libboost-iostreams1.42.0_1.42.0-4 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc0.3_2.11.2-13 libc0.3-dev_2.11.2-13 libc0.3-xen_2.11.2-13 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcurl3-gnutls_7.21.4-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0.1 libexpat1_2.0.1-7 libfribidi0_0.19.2-1 libgcc1_1:4.4.5-10 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgfortran3_4.4.5-10 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-1 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.4-2 libgomp1_4.4.5-10 libgpg-error0_1.10-0.3 libident_0.22-3 libidn11_1.20-1 libldap-2.4-2_2.4.17-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 liblzo2-2_2.04-1 libmagic1_5.03-5+b1 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.8+20110307-1 libnewt0.52_0.52.11-2 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.2-2 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-3+b1 libpipeline1_1.2.0-1 libpng12-0_1.2.44-2 libpopt0_1.16-1 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-8 libsasl2-modules_2.1.23.dfsg1-8 libslang2_2.2.3-3 libss2_1.41.12-2 libssl0.9.8_0.9.8o-5 libssl1.0.0_1.0.0d-1 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-10 libsysfs2_2.1.0+repack-1 libtasn1-3_2.9-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.16.2-0 libwrap0_7.6.dbs-8 libxml2_2.7.8.dfsg-2 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 ncurses-base_5.7+20100313-5 ncurses-bin_5.9-1 netbase_4.45 netcat-traditional_1.10-39 openssl_0.9.8o-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.3-1 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-2 tzdata_2011a-1 util-linux_2.16.2-0 wget_1.11.4-4 whiptail_0.52.11-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -148,12 +215,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.14
-dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.15-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.15
+dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
Check disc space
────────────────
@@ -165,38 +232,38 @@ dpkg-buildpackage
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
+ dpkg-source --before-build samtools-0.1.15
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.14-1
- dpkg-source --before-build samtools-0.1.14
+dpkg-buildpackage: source version 0.1.15-1
dpkg-buildpackage: host architecture hurd-i386
/usr/bin/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 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/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 `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
rm -f debian/stamp-makefile-check
dh_clean
- debian/rules build
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
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -210,15 +277,16 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/bcftools'
+ar -cru 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 glf.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 `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -229,10 +297,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -250,25 +318,26 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/misc'
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/misc'
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/misc'
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -278,27 +347,27 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
[sam_header_read2] 2 sequences loaded.
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
-[samopen] SAM header is present: 2 sequences.
../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.
+[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
+[bam_rmdup_core] processing reference seq1...
(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
-[bam_rmdup_core] processing reference seq1...
../samtools rmdup ex1f.bam ex1f-rmduppe.bam
[bam_rmdup_core] processing reference seq2...
[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
@@ -308,13 +377,13 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/sa
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
[mpileup] 1 samples in 1 input files
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
-<mpileup> Set max per-sample depth to 8000
+<mpileup> Set max per-file depth to 8000
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -348,7 +417,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -373,7 +442,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -388,65 +457,68 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_hurd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.15-1_hurd-i386.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_hurd-i386.deb'.
- dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org> >../samtools_0.1.14-1_hurd-i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.15-1_hurd-i386.deb'.
+ dpkg-genchanges -B -mhurd-i386 Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org> >../samtools_0.1.15-1_hurd-i386.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-0.1.14
+ dpkg-source --after-build samtools-0.1.15
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110329-1210
+Build finished at 20110412-1139
-samtools_0.1.14-1_hurd-i386.changes:
+samtools_0.1.15-1_hurd-i386.changes:
Format: 1.8
-Date: Tue, 29 Mar 2011 13:13:54 +0900
+Date: Tue, 12 Apr 2011 19:44:41 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: hurd-i386
-Version: 0.1.14-1
+Version: 0.1.15-1
Distribution: sid
Urgency: low
-Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org>
+Maintainer: hurd-i386 Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org>
Changed-By: Charles Plessy <plessy at 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 (0.1.14-1) unstable; urgency=low
+ samtools (0.1.15-1) unstable; urgency=low
.
* New upstream release.
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.2
+ (debian/control, no changes needed).
+ * debian/watch directly interrogates and downloads froms SourceForge.
Checksums-Sha1:
- 0d91d72190bf868ecec9648ba27c8e63ef9745ee 584046 samtools_0.1.14-1_hurd-i386.deb
- db3b2019d85c298a6a8c85e57a682d1f1b402843 165090 libbam-dev_0.1.14-1_hurd-i386.deb
+ 5a2b52e1a743e81dcdf4cd57a54b802246159028 588956 samtools_0.1.15-1_hurd-i386.deb
+ 709fc2c806a278672e608331c77b37c89afb6225 168354 libbam-dev_0.1.15-1_hurd-i386.deb
Checksums-Sha256:
- 2b87d92e9d3f06d6d1884bf62f56c7ee13f9e2a2c88882cc04c2bcf1c13c4f61 584046 samtools_0.1.14-1_hurd-i386.deb
- a247725321c5b88c1b5328fa2715ab8584de6cd479b70c4fe302751bce5ce6b8 165090 libbam-dev_0.1.14-1_hurd-i386.deb
+ d2eb106cfa417c51a00d174e2e800511a8b27efa0c8ff919c58ea5bea452f047 588956 samtools_0.1.15-1_hurd-i386.deb
+ 9b8f8cf412601848d6cccebd1e48c5599fd05b7619ad96f52072427f452b455e 168354 libbam-dev_0.1.15-1_hurd-i386.deb
Files:
- f88872b6051a468ca99bb0489daa19d6 584046 science optional samtools_0.1.14-1_hurd-i386.deb
- d0034d3677faf9a5afd7edab577ffd72 165090 libdevel optional libbam-dev_0.1.14-1_hurd-i386.deb
+ a131d11416146fe7efd8037643dd3420 588956 science optional samtools_0.1.15-1_hurd-i386.deb
+ cd846f388ba98037cd47cf6e3027df8a 168354 libdevel optional libbam-dev_0.1.15-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.14-1_hurd-i386.deb
+samtools_0.1.15-1_hurd-i386.deb
───────────────────────────────
new debian package, version 2.0.
- size 584046 bytes: control archive= 1793 bytes.
+ size 588956 bytes: control archive= 1797 bytes.
793 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1052
+ Installed-Size: 1068
Depends: libc0.3 (>= 2.11), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -459,32 +531,32 @@ samtools_0.1.14-1_hurd-i386.deb
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 2011-03-29 12:08 ./
-drwxr-xr-x root/root 0 2011-03-29 12:08 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 12:08 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 12:08 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-04-12 11:37 ./
+drwxr-xr-x root/root 0 2011-04-12 11:37 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 11:37 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 11:37 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-03-29 12:08 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-04-12 11:37 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-03-29 12:08 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-29 12:08 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-03-29 12:08 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8393 2011-03-29 12:08 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 2005 2011-03-29 12:08 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/share/samtools/
+-rw-r--r-- root/root 1966 2011-04-12 11:38 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-04-12 11:37 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-04-12 11:37 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8393 2011-04-12 11:37 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 2005 2011-04-12 11:37 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/share/samtools/
-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
@@ -497,33 +569,33 @@ drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-03-29 12:09 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/bin/
--rwxr-xr-x root/root 97540 2011-03-29 12:09 ./usr/bin/bcftools
--rwxr-xr-x root/root 23788 2011-03-29 12:09 ./usr/bin/razip
--rwxr-xr-x root/root 357868 2011-03-29 12:09 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-03-29 12:08 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/lib/samtools/
--rwxr-xr-x root/root 17488 2011-03-29 12:09 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6336 2011-03-29 12:09 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6320 2011-03-29 12:09 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10084 2011-03-29 12:09 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6920 2011-03-29 12:09 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.14-1_hurd-i386.deb
+-rwxr-xr-x root/root 5778 2011-04-12 11:38 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/bin/
+-rwxr-xr-x root/root 104676 2011-04-12 11:38 ./usr/bin/bcftools
+-rwxr-xr-x root/root 23788 2011-04-12 11:38 ./usr/bin/razip
+-rwxr-xr-x root/root 366060 2011-04-12 11:38 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-04-12 11:37 ./usr/lib/
+drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17488 2011-04-12 11:38 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6336 2011-04-12 11:38 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6320 2011-04-12 11:38 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10084 2011-04-12 11:38 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6920 2011-04-12 11:38 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.15-1_hurd-i386.deb
─────────────────────────────────
new debian package, version 2.0.
- size 165090 bytes: control archive= 904 bytes.
+ size 168354 bytes: control archive= 903 bytes.
678 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 404
+ Installed-Size: 408
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -534,21 +606,21 @@ libbam-dev_0.1.14-1_hurd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-29 12:09 ./
-drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 12:08 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 12:08 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-04-12 11:38 ./
+drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/lib/
--rw-r--r-- root/root 249922 2011-03-29 12:09 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/include/
--rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
--rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/lib/
+-rw-r--r-- root/root 257596 2011-04-12 11:38 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/include/
+-rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/bgzf.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
@@ -559,12 +631,35 @@ drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE
-(Reading database ... 14625 files and directories currently installed.)
+Purging /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe
+(Reading database ... 12510 files and directories currently installed.)
Removing libncurses5-dev ...
+Removing zlib1g-dev ...
Removing cdbs ...
+Removing debhelper ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing file ...
+Purging configuration files for file ...
+Removing libexpat1 ...
+Purging configuration files for libexpat1 ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing gettext-base ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing libcroco3 ...
+Purging configuration files for libcroco3 ...
+Removing libmagic1 ...
+Purging configuration files for libmagic1 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
Processing triggers for man-db ...
+Processing triggers for install-info ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110329-1210
-Build needed 00:05:01, 8968k disc space
+Finished at 20110412-1139
+Build needed 00:08:59, 9120k disc space
diff --git a/i386.log b/i386.log
index 98e8dc2..e1ce44d 100644
--- a/i386.log
+++ b/i386.log
@@ -1,68 +1,68 @@
-From buildd at biber.debian.org Tue Mar 29 05:18:46 2011
+From buildd at biber.debian.org Tue Apr 12 11:32:31 2011
Return-path: <buildd at biber.debian.org>
-Received: from kokkonen.debian.org ([82.195.75.97])
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at biber.debian.org>)
- id 1Q4RKI-0006ND-Az
- for logs at buildd.debian.org; Tue, 29 Mar 2011 05:18:46 +0000
+ id 1Q9bpf-0006Vp-DV
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 11:32:31 +0000
Received: from biber.debian.org ([2001:648:2ffc:deb:214:22ff:feb2:1268])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=biber.debian.org, EMAIL=hostmaster at biber.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at biber.debian.org>)
- id 1Q4RKE-0003t4-UZ; Tue, 29 Mar 2011 05:18:43 +0000
+ id 1Q9bpb-0004tm-2l; Tue, 12 Apr 2011 11:32:27 +0000
Received: from buildd by biber.debian.org with local (Exim 4.72)
(envelope-from <buildd at biber.debian.org>)
- id 1Q4RKC-0002d9-DS; Tue, 29 Mar 2011 05:18:40 +0000
-Message-Id: <E1Q4RKC-0002d9-DS at biber.debian.org>
+ id 1Q9bpY-0002y6-7W; Tue, 12 Apr 2011 11:32:24 +0000
+Message-Id: <E1Q9bpY-0002y6-7W at biber.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Tue, 29 Mar 2011 05:18:40 +0000
+Date: Tue, 12 Apr 2011 11:32:24 +0000
From: buildd on biber <buildd at biber.debian.org>
To: kurt at roeckx.be,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.14-1 on i386 (dist=sid)
+Subject: Log for successful build of samtools_0.1.15-1 on i386 (dist=sid)
Key-Id: 44C3EAC7
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on biber.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.14-1 (i386) 29 Mar 2011 05:16 ║
+║ samtools 0.1.15-1 (i386) 12 Apr 2011 11:30 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.14-1
-Source Version: 0.1.14-1
+Version: 0.1.15-1
+Source Version: 0.1.15-1
Architecture: i386
-Get:1 http://ftp.gr.debian.org unstable InRelease [184 kB]
-Get:2 http://ftp.gr.debian.org unstable/main Sources [5169 kB]
-Get:3 http://incoming.debian.org unstable InRelease [185 kB]
-Get:4 http://ftp.gr.debian.org unstable/contrib Sources [47.0 kB]
-Get:5 http://ftp.gr.debian.org unstable/non-free Sources [99.0 kB]
-Get:6 http://ftp.gr.debian.org unstable/main i386 Packages [7046 kB]
-Ign http://incoming.debian.org InRelease
-Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [61.6 kB]
+Get:1 http://ftp.gr.debian.org unstable InRelease [151 kB]
+Get:2 http://ftp.gr.debian.org unstable/main Sources [5265 kB]
+Get:3 http://incoming.debian.org unstable InRelease [151 kB]
+Get:4 http://ftp.gr.debian.org unstable/contrib Sources [48.2 kB]
+Get:5 http://ftp.gr.debian.org unstable/non-free Sources [97.4 kB]
+Get:6 http://ftp.gr.debian.org unstable/main i386 Packages [7149 kB]
+Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [62.6 kB]
Ign http://ftp.gr.debian.org unstable/contrib TranslationIndex
-Get:8 http://ftp.gr.debian.org unstable/main TranslationIndex [2232 B]
+Get:8 http://ftp.gr.debian.org unstable/main TranslationIndex [2264 B]
Ign http://ftp.gr.debian.org unstable/contrib Translation-en
+Ign http://incoming.debian.org InRelease
Get:9 http://incoming.debian.org Release.gpg [836 B]
-Get:10 http://incoming.debian.org unstable/main Sources [5142 kB]
-Get:11 http://incoming.debian.org unstable/contrib Sources [47.4 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
-Get:13 http://incoming.debian.org unstable/main i386 Packages [7051 kB]
-Get:14 http://incoming.debian.org unstable/contrib i386 Packages [61.6 kB]
+Get:10 http://incoming.debian.org unstable/main Sources [5265 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [48.2 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [97.4 kB]
+Get:13 http://incoming.debian.org unstable/main i386 Packages [7149 kB]
+Get:14 http://incoming.debian.org unstable/contrib i386 Packages [62.6 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [30.5 kB]
-Get:18 http://incoming.debian.org Packages [618 kB]
+Get:17 http://incoming.debian.org Sources [49.7 kB]
+Get:18 http://incoming.debian.org Packages [772 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 25.8 MB in 17s (1506 kB/s)
+Fetched 26.4 MB in 14s (1771 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +83,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 379 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (tar) [370 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (diff) [6869 B]
-Fetched 379 kB in 1s (213 kB/s)
+Need to get 383 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
+Fetched 383 kB in 1s (240 kB/s)
Download complete and in download only mode
Check arch
@@ -101,7 +101,7 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.14.5-2)
+fakeroot: already installed (1.15.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
@@ -121,14 +121,14 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.1)
+base-files: already installed (6.2)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
debianutils: already installed (3.4.4)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.15.8.10)
+dpkg: already installed (1.16.0.1)
e2fsprogs: already installed (1.41.12-2)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.6.3-3)
@@ -136,7 +136,7 @@ gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.8+20110307-1)
ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-18)
+perl-base: already installed (5.10.1-19)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.1)
@@ -146,12 +146,12 @@ bsdutils: already installed (1:2.17.2-9.1)
mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
libc6-dev: already installed (2.11.2-11)
-gcc: already installed (4:4.5.2-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.5.2-2 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.5.2-5 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.5.2-5 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8)
-dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.0.1 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.2
+Using default version 8.1.3
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -162,52 +162,64 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ libcroco3 libglib2.0-0 libmagic1 libncurses5 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db ncurses-bin po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
groff ncurses-doc less www-browser libmail-box-perl
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 20 newly installed, 0 to remove and 8 not upgraded.
-Need to get 10.7 MB of archives.
-After this operation, 29.8 MB of additional disk space will be used.
-Get:1 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 8.2.2 [200 kB]
-Get:2 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.21-5 [1125 kB]
-Get:3 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.0-1 [35.6 kB]
-Get:4 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.5.9-4 [980 kB]
-Get:5 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.04-5 [234 kB]
-Get:6 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.04-5 [49.1 kB]
-Get:7 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-3 [130 kB]
-Get:8 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.12-3 [255 kB]
-Get:9 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-2 [827 kB]
-Get:10 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
-Get:11 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.28.2-1 [1495 kB]
-Get:12 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-1 [116 kB]
-Get:13 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-3 [433 kB]
-Get:14 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-3 [1973 kB]
-Get:15 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian i386 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.gr.debian.org/debian/ unstable/main po-debconf i386 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.gr.debian.org/debian/ unstable/main debhelper i386 8.1.2 [553 kB]
-Get:18 http://ftp.gr.debian.org/debian/ unstable/main cdbs i386 0.4.92 [1268 kB]
-Get:19 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev i386 5.8+20110307-1 [466 kB]
-Get:20 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.3.4.dfsg-3 [186 kB]
+The following packages will be upgraded:
+ libncurses5 ncurses-bin
+2 upgraded, 20 newly installed, 0 to remove and 6 not upgraded.
+Need to get 11.4 MB of archives.
+After this operation, 29.9 MB of additional disk space will be used.
+Get:1 http://ftp.gr.debian.org/debian/ unstable/main ncurses-bin i386 5.9-1 [326 kB]
+Get:2 http://ftp.gr.debian.org/debian/ unstable/main libncurses5 i386 5.9-1 [361 kB]
+Get:3 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 8.2.2 [200 kB]
+Get:4 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.21-5 [1125 kB]
+Get:5 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.0-1 [35.6 kB]
+Get:6 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.6.0.1-1 [991 kB]
+Get:7 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.04-5 [234 kB]
+Get:8 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.04-5 [49.1 kB]
+Get:9 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-3 [130 kB]
+Get:10 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.12-3 [255 kB]
+Get:11 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-2 [827 kB]
+Get:12 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
+Get:13 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.28.4-1 [1498 kB]
+Get:14 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-1 [116 kB]
+Get:15 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-3 [433 kB]
+Get:16 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-3 [1973 kB]
+Get:17 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:18 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:19 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.1.3 [554 kB]
+Get:20 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
+Get:21 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev i386 5.9-1 [467 kB]
+Get:22 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.3.4.dfsg-3 [186 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.7 MB in 0s (11.3 MB/s)
+Fetched 11.4 MB in 0s (12.2 MB/s)
+(Reading database ... 10201 files and directories currently installed.)
+Preparing to replace ncurses-bin 5.8+20110307-1 (using .../ncurses-bin_5.9-1_i386.deb) ...
+Unpacking replacement ncurses-bin ...
+Setting up ncurses-bin (5.9-1) ...
+(Reading database ... 10201 files and directories currently installed.)
+Preparing to replace libncurses5 5.8+20110307-1 (using .../libncurses5_5.9-1_i386.deb) ...
+Unpacking replacement libncurses5 ...
+Setting up libncurses5 (5.9-1) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10333 files and directories currently installed.)
+(Reading database ... 10201 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_i386.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-5_i386.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_i386.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.9-4_i386.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.1-1_i386.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_i386.deb) ...
Selecting previously deselected package file.
@@ -221,7 +233,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_i386.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.2-1_i386.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_i386.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_i386.deb) ...
Selecting previously deselected package libunistring0.
@@ -229,15 +241,15 @@ Unpacking libunistring0 (from .../libunistring0_0.9.3-3_i386.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_i386.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_i386.deb) ...
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_i386.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_i386.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.3_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_i386.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_i386.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_i386.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_i386.deb) ...
Setting up bsdmainutils (8.2.2) ...
@@ -245,7 +257,7 @@ update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write)
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.5.9-4) ...
+Setting up man-db (2.6.0.1-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
@@ -253,26 +265,26 @@ Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.2-1) ...
+Setting up libglib2.0-0 (2.28.4-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
+Setting up debhelper (8.1.3) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8+20110307-1) ...
+Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
-Toolchain package versions: binutils_2.21.0.20110322-1 dpkg-dev_1.15.8.10 g++-4.5_4.5.2-7 gcc-4.5_4.5.2-7 libc6-dev_2.11.2-11 libstdc++6_4.5.2-7 libstdc++6-4.5-dev_4.5.2-7 linux-libc-dev_2.6.38-1
-Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110322-1 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.5.2-2 cpp-4.5_4.5.2-7 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-2 g++-4.5_4.5.2-7 gcc_4:4.5.2-2 gcc-4.5_4.5.2-7 gcc-4.5-base_4.5.2-7 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.5.2-7 libgdbm3_1.8.3-9 libglib2.0-0_2.28.2-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.5.2-7 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-7 libstdc++6-4.5-dev_4.5.2-7 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011d-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0.1 g++-4.5_4.5.2-8 gcc-4.5_4.5.2-8 libc6-dev_2.11.2-11 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8 linux-libc-dev_2.6.38-2
+Package versions: apt_0.8.13.2 base-files_6.2 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.5.2-5 cpp-4.5_4.5.2-8 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.1 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-5 g++-4.5_4.5.2-8 gcc_4:4.5.2-5 gcc-4.5_4.5.2-8 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0.1 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.3-2 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011e-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -283,12 +295,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.14
-dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.15-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.15
+dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
Check disc space
────────────────
@@ -303,25 +315,25 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.14-1
- dpkg-source --before-build samtools-0.1.14
+dpkg-buildpackage: source version 0.1.15-1
+ dpkg-source --before-build samtools-0.1.15
dpkg-buildpackage: host architecture i386
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 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/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 `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -330,8 +342,8 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -345,15 +357,16 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/bcftools'
+ar -cru 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 glf.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 `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -364,10 +377,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -385,25 +398,26 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/misc'
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/misc'
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/misc'
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -413,14 +427,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -444,12 +458,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtool
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-sample depth to 8000
+<mpileup> Set max per-file depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -483,7 +497,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -508,7 +522,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -523,27 +537,27 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.15-1_i386.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../samtools_0.1.14-1_i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.15-1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../samtools_0.1.15-1_i386.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-0.1.14
+ dpkg-source --after-build samtools-0.1.15
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110329-0518
+Build finished at 20110412-1132
-samtools_0.1.14-1_i386.changes:
+samtools_0.1.15-1_i386.changes:
Format: 1.8
-Date: Tue, 29 Mar 2011 13:13:54 +0900
+Date: Tue, 12 Apr 2011 19:44:41 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: i386
-Version: 0.1.14-1
+Version: 0.1.15-1
Distribution: sid
Urgency: low
Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
@@ -552,36 +566,39 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.14-1) unstable; urgency=low
+ samtools (0.1.15-1) unstable; urgency=low
.
* New upstream release.
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.2
+ (debian/control, no changes needed).
+ * debian/watch directly interrogates and downloads froms SourceForge.
Checksums-Sha1:
- 3f377fc586893e47b4e71c72a0337725f9f1122b 581312 samtools_0.1.14-1_i386.deb
- bc7b0695cd71ab87a7a1e629b72e26be4b3c1542 164874 libbam-dev_0.1.14-1_i386.deb
+ f6769201eee133381979e4bcb1f36f497d0f5e3c 587560 samtools_0.1.15-1_i386.deb
+ 30e5a53f00ba8532c3a8156f51e4c5d13375ed82 168190 libbam-dev_0.1.15-1_i386.deb
Checksums-Sha256:
- 1c3921ce6639cccac9e053cbfc3253b3388548fabf15cee3be0852d8291282d7 581312 samtools_0.1.14-1_i386.deb
- da4ebaa4d71684734323da8741f2d34ced3c5c1bef1715366be99bb89e0e5d0c 164874 libbam-dev_0.1.14-1_i386.deb
+ 8f39c955763b94089f37feec52bbd36da7a40a73d70c470ac8763aa8dec5d9e4 587560 samtools_0.1.15-1_i386.deb
+ 6316b914212af74d376eaa0f4c1e61e19e1a7f1eae34334797e027938256507f 168190 libbam-dev_0.1.15-1_i386.deb
Files:
- 7ba7f76e3366c743f20d66601e061a36 581312 science optional samtools_0.1.14-1_i386.deb
- 1c8570523c06425347a7da29409bdb1f 164874 libdevel optional libbam-dev_0.1.14-1_i386.deb
+ 716ed3a43095468adaa5898a181a14b4 587560 science optional samtools_0.1.15-1_i386.deb
+ c06abfed92ff1b516614c5eda25f719c 168190 libdevel optional libbam-dev_0.1.15-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.14-1_i386.deb
+samtools_0.1.15-1_i386.deb
──────────────────────────
new debian package, version 2.0.
- size 581312 bytes: control archive= 1787 bytes.
+ size 587560 bytes: control archive= 1786 bytes.
785 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1056
+ Installed-Size: 1072
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -594,50 +611,50 @@ samtools_0.1.14-1_i386.deb
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 2011-03-29 05:18 ./
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/lib/samtools/
--rwxr-xr-x root/root 6664 2011-03-29 05:18 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 6144 2011-03-29 05:18 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6112 2011-03-29 05:18 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10116 2011-03-29 05:18 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 17384 2011-03-29 05:18 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/bin/
--rwxr-xr-x root/root 96964 2011-03-29 05:18 ./usr/bin/bcftools
--rwxr-xr-x root/root 22584 2011-03-29 05:18 ./usr/bin/razip
--rwxr-xr-x root/root 361964 2011-03-29 05:18 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/samtools/
+-rwxr-xr-x root/root 6664 2011-04-12 11:32 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 6144 2011-04-12 11:32 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6112 2011-04-12 11:32 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10116 2011-04-12 11:32 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 17384 2011-04-12 11:32 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/bin/
+-rwxr-xr-x root/root 104676 2011-04-12 11:32 ./usr/bin/bcftools
+-rwxr-xr-x root/root 22584 2011-04-12 11:32 ./usr/bin/razip
+-rwxr-xr-x root/root 370284 2011-04-12 11:32 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 126609 2011-03-29 05:18 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-04-12 11:32 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1966 2011-03-29 05:18 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/man/man1/
--rw-r--r-- root/root 2005 2011-03-29 05:18 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 8393 2011-03-29 05:18 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-03-29 05:18 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/samtools/
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1966 2011-04-12 11:32 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/man/man1/
+-rw-r--r-- root/root 2005 2011-04-12 11:32 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 8393 2011-04-12 11:32 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-04-12 11:32 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/samtools/
-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2011-03-29 05:18 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-04-12 11:32 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
@@ -646,19 +663,19 @@ drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/samtools/
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
-libbam-dev_0.1.14-1_i386.deb
+libbam-dev_0.1.15-1_i386.deb
────────────────────────────
new debian package, version 2.0.
- size 164874 bytes: control archive= 899 bytes.
+ size 168190 bytes: control archive= 895 bytes.
673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 404
+ Installed-Size: 412
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -669,22 +686,22 @@ libbam-dev_0.1.14-1_i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/lib/
--rw-r--r-- root/root 252230 2011-03-29 05:18 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/
+-rw-r--r-- root/root 260232 2011-04-12 11:32 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/include/
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/include/
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
--rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
--rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
+-rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/bgzf.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
@@ -699,7 +716,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-ff35df57-9fa1-48d1-9b3c-7aa763415fff/build/buildd-samtools_0.1.14-1-i386-hlIVkN
+Purging /var/lib/schroot/mount/sid-i386-sbuild-04b94330-7968-42e2-8364-991a65659f4b/build/buildd-samtools_0.1.15-1-i386-_MkcrA
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -707,18 +724,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: i386
-Build-Space: 9732
+Build-Space: 9880
Build-Time: 46
Distribution: sid
-Install-Time: 36
-Job: samtools_0.1.14-1
+Install-Time: 39
+Job: samtools_0.1.15-1
Package: samtools
-Package-Time: 111
-Source-Version: 0.1.14-1
-Space: 9732
+Package-Time: 113
+Source-Version: 0.1.15-1
+Space: 9880
Status: successful
-Version: 0.1.14-1
+Version: 0.1.15-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110329-0518
-Build needed 00:01:51, 9732k disc space
+Finished at 20110412-1132
+Build needed 00:01:53, 9880k disc space
Signature with key '44C3EAC7' requested:
diff --git a/ia64.log b/ia64.log
index c4fd58d..40cf09d 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,67 +1,67 @@
-From buildd at alkman.debian.org Tue Mar 29 05:18:34 2011
-Return-path: <buildd at alkman.debian.org>
-Received: from kokkonen.debian.org ([82.195.75.97])
+From buildd at mundy.debian.org Tue Apr 12 11:34:44 2011
+Return-path: <buildd at mundy.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at alkman.debian.org>)
- id 1Q4RK5-0006Lm-O5
- for logs at buildd.debian.org; Tue, 29 Mar 2011 05:18:34 +0000
-Received: from alkman.debian.org ([192.25.206.63])
+ (Exim 4.69) (envelope-from <buildd at mundy.debian.org>)
+ id 1Q9bro-00076Q-GX
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 11:34:44 +0000
+Received: from mundy.debian.org ([192.25.206.62])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=alkman.debian.org, EMAIL=hostmaster at alkman.debian.org (verified)
+ CN=mundy.debian.org, EMAIL=hostmaster at mundy.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at alkman.debian.org>)
- id 1Q4RK1-0003r2-QZ
- for logs at buildd.debian.org; Tue, 29 Mar 2011 05:18:30 +0000
-Received: from buildd by alkman.debian.org with local (Exim 4.72)
- (envelope-from <buildd at alkman.debian.org>)
- id 1Q4RJx-0000zl-Vp; Tue, 29 Mar 2011 05:18:26 +0000
-Date: Tue, 29 Mar 2011 05:18:25 +0000
-Message-Id: <E1Q4RJx-0000zl-Vp at alkman.debian.org>
-From: buildd on alkman <buildd at alkman.debian.org>
-To: buildd-porters at alkman.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.14-1 on ia64 (dist=sid)
+ (Exim 4.69) (envelope-from <buildd at mundy.debian.org>)
+ id 1Q9brj-0004xW-OG
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 11:34:40 +0000
+Received: from buildd by mundy.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at mundy.debian.org>)
+ id 1Q9brf-00081G-Kx; Tue, 12 Apr 2011 11:34:35 +0000
+From: buildd on mundy <buildd at mundy.debian.org>
+To: buildd-porters at mundy.debian.org,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.15-1 on ia64 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
+Message-Id: <E1Q9brf-00081G-Kx at mundy.debian.org>
+Date: Tue, 12 Apr 2011 11:34:35 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alkman.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mundy.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.14-1 (ia64) 29 Mar 2011 05:14 ║
+║ samtools 0.1.15-1 (ia64) 12 Apr 2011 11:30 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.14-1
-Source Version: 0.1.14-1
+Version: 0.1.15-1
+Source Version: 0.1.15-1
Architecture: ia64
-Get:1 http://spohr.debian.org unstable InRelease [185 kB]
-Get:2 http://spohr.debian.org unstable/main Sources [5142 kB]
-Get:3 http://incoming.debian.org unstable InRelease [185 kB]
-Get:4 http://spohr.debian.org unstable/contrib Sources [47.4 kB]
-Get:5 http://spohr.debian.org unstable/non-free Sources [99.4 kB]
-Get:6 http://spohr.debian.org unstable/main ia64 Packages [6847 kB]
+Get:1 http://incoming.debian.org unstable InRelease [151 kB]
Ign http://incoming.debian.org InRelease
-Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://incoming.debian.org unstable/main Sources [5142 kB]
-Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [14 B]
+Get:2 http://incoming.debian.org Release.gpg [836 B]
+Get:3 http://spohr.debian.org unstable InRelease [151 kB]
+Get:4 http://incoming.debian.org Release [1604 B]
+Get:5 http://spohr.debian.org unstable/main Sources [5265 kB]
+Get:6 http://incoming.debian.org unstable/main Sources [5265 kB]
+Get:7 http://spohr.debian.org unstable/contrib Sources [48.2 kB]
+Get:8 http://spohr.debian.org unstable/non-free Sources [97.4 kB]
+Get:9 http://spohr.debian.org unstable/main ia64 Packages [6981 kB]
+Get:10 http://spohr.debian.org unstable/contrib ia64 Packages [52.9 kB]
Ign http://spohr.debian.org unstable/contrib TranslationIndex
-Get:10 http://spohr.debian.org unstable/main TranslationIndex [2232 B]
+Get:11 http://spohr.debian.org unstable/main TranslationIndex [2264 B]
Ign http://spohr.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [47.4 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
-Get:13 http://incoming.debian.org unstable/main ia64 Packages [6847 kB]
-Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [14 B]
+Get:12 http://incoming.debian.org unstable/contrib Sources [48.2 kB]
+Get:13 http://incoming.debian.org unstable/non-free Sources [97.4 kB]
+Get:14 http://incoming.debian.org unstable/main ia64 Packages [6981 kB]
+Get:15 http://incoming.debian.org unstable/contrib ia64 Packages [52.9 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [30.5 kB]
-Get:18 http://incoming.debian.org Packages [618 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
+Get:16 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
+Get:17 http://incoming.debian.org Sources [49.7 kB]
+Get:18 http://incoming.debian.org Packages [772 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 25.3 MB in 22s (1103 kB/s)
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Fetched 26.0 MB in 18s (1412 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +82,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 379 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (tar) [370 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (diff) [6869 B]
-Fetched 379 kB in 0s (485 kB/s)
+Need to get 383 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
+Fetched 383 kB in 0s (479 kB/s)
Download complete and in download only mode
Check arch
@@ -100,18 +100,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.14.5-2)
+fakeroot: already installed (1.15.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -120,14 +120,14 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6.1-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.1)
+base-files: already installed (6.2)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
debianutils: already installed (3.4.4)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.15.8.10)
+dpkg: already installed (1.16.0.1)
e2fsprogs: already installed (1.41.12-2)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.6.3-3)
@@ -135,7 +135,7 @@ gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.8+20110307-1)
ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-17)
+perl-base: already installed (5.10.1-19)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.1)
@@ -145,12 +145,12 @@ bsdutils: already installed (1:2.17.2-9.1)
mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
libc6.1-dev: already installed (2.11.2-13)
-gcc: already installed (4:4.4.5-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-4 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.4.5-7 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.4.5-7 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8)
-dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.0.1 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.2
+Using default version 8.1.3
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -173,40 +173,40 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 20 newly installed, 0 to remove and 23 not upgraded.
-Need to get 13.0 MB of archives.
-After this operation, 42.6 MB of additional disk space will be used.
+0 upgraded, 20 newly installed, 0 to remove and 6 not upgraded.
+Need to get 12.9 MB of archives.
+After this operation, 43.8 MB of additional disk space will be used.
Get:1 http://spohr.debian.org/debian/ unstable/main bsdmainutils ia64 8.2.2 [236 kB]
Get:2 http://spohr.debian.org/debian/ unstable/main groff-base ia64 1.21-5 [1440 kB]
Get:3 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.2.0-1 [47.2 kB]
-Get:4 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.5.9-4 [1154 kB]
+Get:4 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.6.0.1-1 [1122 kB]
Get:5 http://spohr.debian.org/debian/ unstable/main libmagic1 ia64 5.04-5 [263 kB]
Get:6 http://spohr.debian.org/debian/ unstable/main file ia64 5.04-5 [51.9 kB]
Get:7 http://spohr.debian.org/debian/ unstable/main gettext-base ia64 0.18.1.1-3 [174 kB]
Get:8 http://spohr.debian.org/debian/ unstable/main libpcre3 ia64 8.12-3 [316 kB]
Get:9 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.7.8.dfsg-2 [1181 kB]
Get:10 http://spohr.debian.org/debian/ unstable/main html2text ia64 1.3.2a-15 [134 kB]
-Get:11 http://spohr.debian.org/debian/ unstable/main libglib2.0-0 ia64 2.28.2-1 [1969 kB]
+Get:11 http://spohr.debian.org/debian/ unstable/main libglib2.0-0 ia64 2.28.4-1 [1972 kB]
Get:12 http://spohr.debian.org/debian/ unstable/main libcroco3 ia64 0.6.2-1 [155 kB]
Get:13 http://spohr.debian.org/debian/ unstable/main libunistring0 ia64 0.9.3-3 [469 kB]
Get:14 http://spohr.debian.org/debian/ unstable/main gettext ia64 0.18.1.1-3 [2453 kB]
-Get:15 http://spohr.debian.org/debian/ unstable/main intltool-debian ia64 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://spohr.debian.org/debian/ unstable/main po-debconf ia64 1.0.16+nmu1 [223 kB]
-Get:17 http://spohr.debian.org/debian/ unstable/main debhelper ia64 8.1.2 [553 kB]
-Get:18 http://spohr.debian.org/debian/ unstable/main cdbs ia64 0.4.92 [1268 kB]
+Get:15 http://spohr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://spohr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://spohr.debian.org/debian/ unstable/main debhelper all 8.1.3 [554 kB]
+Get:18 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
Get:19 http://spohr.debian.org/debian/ unstable/main libncurses5-dev ia64 5.8+20110307-1 [614 kB]
Get:20 http://spohr.debian.org/debian/ unstable/main zlib1g-dev ia64 1:1.2.3.4.dfsg-3 [224 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 13.0 MB in 0s (14.3 MB/s)
+Fetched 12.9 MB in 0s (14.3 MB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10169 files and directories currently installed.)
+(Reading database ... 10045 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_ia64.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-5_ia64.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_ia64.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.9-4_ia64.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.1-1_ia64.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_ia64.deb) ...
Selecting previously deselected package file.
@@ -220,7 +220,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_ia64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_ia64.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.2-1_ia64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_ia64.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_ia64.deb) ...
Selecting previously deselected package libunistring0.
@@ -228,13 +228,13 @@ Unpacking libunistring0 (from .../libunistring0_0.9.3-3_ia64.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_ia64.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_ia64.deb) ...
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_ia64.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_ia64.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.3_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_ia64.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_ia64.deb) ...
Selecting previously deselected package zlib1g-dev.
@@ -244,7 +244,7 @@ update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write)
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.5.9-4) ...
+Setting up man-db (2.6.0.1-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
@@ -252,14 +252,14 @@ Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.2-1) ...
+Setting up libglib2.0-0 (2.28.4-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
+Setting up debhelper (8.1.3) ...
Setting up cdbs (0.4.92) ...
Setting up libncurses5-dev (5.8+20110307-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -267,11 +267,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-mckinley ia64 (ia64)
-Toolchain package versions: binutils_2.21.0.20110302-1 dpkg-dev_1.15.8.10 g++-4.4_4.4.5-13 gcc-4.4_4.4.5-13 libc6.1-dev_2.11.2-13 libstdc++6_4.5.2-5 libstdc++6-4.4-dev_4.4.5-13 linux-libc-dev_2.6.37-2
-Package versions: apt_0.8.12 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110302-1 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-4 cpp-4.4_4.4.5-13 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-4 g++-4.4_4.4.5-13 gcc_4:4.4.5-4 gcc-4.4_4.4.5-13 gcc-4.4-base_4.4.5-13 gcc-4.5-base_4.5.2-5 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc6.1_2.11.2-13 libc6.1-dev_2.11.2-13 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:7.1-7 libgcc1_1:4.5.2-5 libgdbm3_1.8.3-9 libglib2.0-0_2.28.2-1 libgmp10_2:5.0.1+dfsg-6 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.5.2-5 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-5 libstdc++6-4.4-dev_4.4.5-13 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libunwind7_0.99-0.2 libunwind7-dev_0.99-0.2 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011c-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-bpo.5-mckinley ia64 (ia64)
+Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0.1 g++-4.4_4.4.5-15 gcc-4.4_4.4.5-15 libc6.1-dev_2.11.2-13 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 linux-libc-dev_2.6.38-2
+Package versions: apt_0.8.13.2 base-files_6.2 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-7 cpp-4.4_4.4.5-15 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.1 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-7 g++-4.4_4.4.5-15 gcc_4:4.4.5-7 gcc-4.4_4.4.5-15 gcc-4.4-base_4.4.5-15 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc6.1_2.11.2-13 libc6.1-dev_2.11.2-13 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0.1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.3-2 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libunwind7_0.99-0.2 libunwind7-dev_0.99-0.2 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011e-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -281,13 +281,14 @@ Package versions: apt_0.8.12 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binuti
Unpack source
─────────────
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.14
-dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.15-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.15
+dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
Check disc space
────────────────
@@ -296,41 +297,50 @@ Check disc space
dpkg-buildpackage
─────────────────
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.14-1
- dpkg-source --before-build samtools-0.1.14
+dpkg-buildpackage: source version 0.1.15-1
+ dpkg-source --before-build samtools-0.1.15
dpkg-buildpackage: host architecture ia64
fakeroot debian/rules clean
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/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 `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
rm -f debian/stamp-makefile-check
dh_clean
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
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -344,15 +354,16 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/bcftools'
+ar -cru 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 glf.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 `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -363,10 +374,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -384,25 +395,26 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/misc'
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/misc'
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/misc'
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -412,14 +424,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -443,14 +455,18 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtool
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-sample depth to 8000
+<mpileup> Set max per-file depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
dh_prep
@@ -482,7 +498,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -507,7 +523,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -522,65 +538,68 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_ia64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.15-1_ia64.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../samtools_0.1.14-1_ia64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.15-1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org> >../samtools_0.1.15-1_ia64.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-0.1.14
+ dpkg-source --after-build samtools-0.1.15
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110329-0518
+Build finished at 20110412-1134
-samtools_0.1.14-1_ia64.changes:
+samtools_0.1.15-1_ia64.changes:
Format: 1.8
-Date: Tue, 29 Mar 2011 13:13:54 +0900
+Date: Tue, 12 Apr 2011 19:44:41 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: ia64
-Version: 0.1.14-1
+Version: 0.1.15-1
Distribution: sid
Urgency: low
-Maintainer: ia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org>
+Maintainer: ia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org>
Changed-By: Charles Plessy <plessy at 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 (0.1.14-1) unstable; urgency=low
+ samtools (0.1.15-1) unstable; urgency=low
.
* New upstream release.
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.2
+ (debian/control, no changes needed).
+ * debian/watch directly interrogates and downloads froms SourceForge.
Checksums-Sha1:
- c5b13aa76194e732e45a2038c03fad3751ca5562 727514 samtools_0.1.14-1_ia64.deb
- 6931effef784cd0ace2a7fc5e1433d0af2cf7ed5 215156 libbam-dev_0.1.14-1_ia64.deb
+ be1bd3c93aaaadf03288167ba6bb1655ee5c62ec 734940 samtools_0.1.15-1_ia64.deb
+ 6670e1538467c88c1d41dcf459b4814d1f6a0fe9 220220 libbam-dev_0.1.15-1_ia64.deb
Checksums-Sha256:
- 09bfead42bdf5029c8b8797734dc01c75bd13bce3f00ebe1b58abfe806ccf772 727514 samtools_0.1.14-1_ia64.deb
- 58d10aaa3d1cc7a927c5d62ddaa8c4dee7242190b572112553b98d38b17a359c 215156 libbam-dev_0.1.14-1_ia64.deb
+ 64a80169be82c10e90f4b6579e294c09be3ce210d51e47062618c7afbc57eb91 734940 samtools_0.1.15-1_ia64.deb
+ f314a6ef5b167cf6b024c02a84263a238dd5831ed0f081b34cfd90ce0026e5de 220220 libbam-dev_0.1.15-1_ia64.deb
Files:
- d901a8353f01c6b0b93b48016a963dee 727514 science optional samtools_0.1.14-1_ia64.deb
- 66273a0ee8e92f9793b0728ff4c0a9c4 215156 libdevel optional libbam-dev_0.1.14-1_ia64.deb
+ a584db0e6fc201f8480ebe449f12d63d 734940 science optional samtools_0.1.15-1_ia64.deb
+ ad4f05972f350b79c73746e2d010959b 220220 libdevel optional libbam-dev_0.1.15-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.14-1_ia64.deb
+samtools_0.1.15-1_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 727514 bytes: control archive= 1781 bytes.
+ size 734940 bytes: control archive= 1785 bytes.
787 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1984
+ Installed-Size: 1748
Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -593,71 +612,71 @@ samtools_0.1.14-1_ia64.deb
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 2011-03-29 05:18 ./
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/lib/samtools/
--rwxr-xr-x root/root 30712 2011-03-29 05:18 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 13360 2011-03-29 05:18 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 13296 2011-03-29 05:18 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 22384 2011-03-29 05:18 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 14944 2011-03-29 05:18 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/bin/
--rwxr-xr-x root/root 250336 2011-03-29 05:18 ./usr/bin/bcftools
--rwxr-xr-x root/root 52520 2011-03-29 05:18 ./usr/bin/razip
--rwxr-xr-x root/root 801864 2011-03-29 05:18 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2011-03-29 05:18 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1966 2011-04-12 11:34 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2011-04-12 11:34 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2011-04-12 11:34 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/man/man1/
--rw-r--r-- root/root 2005 2011-03-29 05:18 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 430 2011-03-29 05:18 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8393 2011-03-29 05:18 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/samtools/
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-03-29 05:18 ./usr/share/doc/samtools/README.bcftools
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126609 2011-03-29 05:18 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
-
-
-libbam-dev_0.1.14-1_ia64.deb
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/man/man1/
+-rw-r--r-- root/root 8393 2011-04-12 11:34 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-04-12 11:34 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 2005 2011-04-12 11:34 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/bin/
+-rwxr-xr-x root/root 821792 2011-04-12 11:34 ./usr/bin/samtools
+-rwxr-xr-x root/root 52520 2011-04-12 11:34 ./usr/bin/razip
+-rwxr-xr-x root/root 263216 2011-04-12 11:34 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/lib/
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/lib/samtools/
+-rwxr-xr-x root/root 13296 2011-04-12 11:34 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 13360 2011-04-12 11:34 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 14944 2011-04-12 11:34 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 30712 2011-04-12 11:34 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 22384 2011-04-12 11:34 ./usr/lib/samtools/md5fa
+
+
+libbam-dev_0.1.15-1_ia64.deb
────────────────────────────
new debian package, version 2.0.
- size 215156 bytes: control archive= 896 bytes.
+ size 220220 bytes: control archive= 893 bytes.
673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 768
+ Installed-Size: 692
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -668,23 +687,23 @@ libbam-dev_0.1.14-1_ia64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/include/
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
--rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
--rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/lib/
--rw-r--r-- root/root 530970 2011-03-29 05:18 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/include/
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
+-rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/bgzf.h
+drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/lib/
+-rw-r--r-- root/root 548572 2011-04-12 11:34 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -698,7 +717,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-5dd52ac5-1458-47e7-98e4-b9ee548aeb2f/build/buildd-samtools_0.1.14-1-ia64-3DXQWn
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-7be68e6b-7380-4d4e-9038-b157c91941a9/build/buildd-samtools_0.1.15-1-ia64-SpdKwR
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -706,18 +725,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: ia64
-Build-Space: 15780
-Build-Time: 115
+Build-Space: 13888
+Build-Time: 110
Distribution: sid
-Install-Time: 59
-Job: samtools_0.1.14-1
+Install-Time: 62
+Job: samtools_0.1.15-1
Package: samtools
-Package-Time: 227
-Source-Version: 0.1.14-1
-Space: 15780
+Package-Time: 220
+Source-Version: 0.1.15-1
+Space: 13888
Status: successful
-Version: 0.1.14-1
+Version: 0.1.15-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110329-0518
-Build needed 00:03:47, 15780k disc space
+Finished at 20110412-1134
+Build needed 00:03:40, 13888k disc space
diff --git a/info b/info
index c685384..48db04e 100644
--- a/info
+++ b/info
@@ -1,14 +1,11 @@
-powerpc~1301374901~sid~successful
-kfreebsd-i386~1301374936~sid~successful
-s390~1301375007~sid~successful
-alpha~1301375148~sid~successful
-ia64~1301375914~sid~successful
-i386~1301375927~sid~successful
-kfreebsd-amd64~1301376172~sid~successful
-sparc~1301383013~sid~failed
-mipsel~1301388816~sid~successful
-hppa~1301390346~sid~successful
-hurd-i386~1301400643~sid~successful
-armel~1301467862~sid~failed
-armel~1301710029~sid~failed
-mips~1301743651~sid~successful
+i386~1302607952~sid~successful
+kfreebsd-amd64~1302607962~sid~successful
+s390~1302607983~sid~successful
+kfreebsd-i386~1302608031~sid~successful
+ia64~1302608085~sid~successful
+powerpc~1302608148~sid~successful
+sparc~1302608174~sid~failed
+hurd-i386~1302608480~sid~successful
+armel~1302610453~sid~failed
+mips~1302610493~sid~successful
+mipsel~1302632104~sid~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index 7adf97d..a5cd1c7 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,58 +1,58 @@
-From buildd at fano.debian.org Tue Mar 29 05:22:52 2011
-Return-path: <buildd at fano.debian.org>
-Received: from kokkonen.debian.org ([82.195.75.97])
+From buildd at fasch.debian.org Tue Apr 12 11:32:42 2011
+Return-path: <buildd at fasch.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at fano.debian.org>)
- id 1Q4ROF-00077a-PS
- for logs at buildd.debian.org; Tue, 29 Mar 2011 05:22:52 +0000
-Received: from fano.debian.org ([206.12.19.110])
+ (Exim 4.69) (envelope-from <buildd at fasch.debian.org>)
+ id 1Q9bpp-0006Zs-Im
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 11:32:42 +0000
+Received: from fasch.debian.org ([194.177.211.201])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=fano.debian.org, EMAIL=hostmaster at fano.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at fano.debian.org>)
- id 1Q4ROC-0003zh-0n; Tue, 29 Mar 2011 05:22:48 +0000
-Received: from buildd by fano.debian.org with local (Exim 4.72)
- (envelope-from <buildd at fano.debian.org>)
- id 1Q4RO8-00091Q-6P; Tue, 29 Mar 2011 05:22:44 +0000
-Date: Tue, 29 Mar 2011 05:22:44 +0000
-Message-Id: <E1Q4RO8-00091Q-6P at fano.debian.org>
-From: buildd on fano <buildd at fano.debian.org>
+ CN=fasch.debian.org, EMAIL=hostmaster at fasch.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at fasch.debian.org>)
+ id 1Q9bpi-0006Aq-F6; Tue, 12 Apr 2011 11:32:35 +0000
+Received: from buildd by fasch.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at fasch.debian.org>)
+ id 1Q9bph-000E5g-8K; Tue, 12 Apr 2011 11:32:33 +0000
+Date: Tue, 12 Apr 2011 11:32:33 +0000
+Message-Id: <E1Q9bph-000E5g-8K at fasch.debian.org>
+From: buildd on fasch <buildd at fasch.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,kibi at debian-ports.org
-Subject: Log for successful build of samtools_0.1.14-1 on kfreebsd-amd64
+Subject: Log for successful build of samtools_0.1.15-1 on kfreebsd-amd64
(dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fasch.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.14-1 (kfreebsd-amd64) 29 Mar 2011 05:21 ║
+║ samtools 0.1.15-1 (kfreebsd-amd64) 12 Apr 2011 11:29 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.14-1
-Source Version: 0.1.14-1
+Version: 0.1.15-1
+Source Version: 0.1.15-1
Architecture: kfreebsd-amd64
-Hit http://mirror-ubc.debian.org sid InRelease
-Hit http://mirror-ubc.debian.org sid/main Sources/DiffIndex
-Hit http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex
-Hit http://mirror-ubc.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
-Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
-Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
-Hit http://mirror-ubc.debian.org sid/main TranslationIndex
-Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
+Hit http://ftp.gr.debian.org sid InRelease
+Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:1 http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages [79.9 kB]
-Ign http://mirror-ubc.debian.org sid/contrib Translation-en
-Ign http://mirror-ubc.debian.org sid/non-free Translation-en
-Get:2 http://incoming.debian.org Release.gpg [836 B]
+Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
+Ign http://ftp.gr.debian.org sid/contrib TranslationIndex
+Hit http://ftp.gr.debian.org sid/main TranslationIndex
+Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages
+Ign http://ftp.gr.debian.org sid/contrib Translation-en
+Ign http://ftp.gr.debian.org sid/non-free Translation-en
Hit http://incoming.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
@@ -62,14 +62,14 @@ Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
Hit http://incoming.debian.org sid/main TranslationIndex
Ign http://incoming.debian.org sid/non-free TranslationIndex
-Get:3 http://incoming.debian.org Release [1604 B]
-Get:4 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages [79.9 kB]
-Get:5 http://incoming.debian.org Sources [30.9 kB]
-Get:6 http://incoming.debian.org Packages [623 kB]
+Get:2 http://incoming.debian.org Release [1604 B]
+Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages
+Get:3 http://incoming.debian.org Sources [49.7 kB]
+Get:4 http://incoming.debian.org Packages [772 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 816 kB in 7s (113 kB/s)
+Fetched 825 kB in 5s (155 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -90,11 +90,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 379 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (tar) [370 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (diff) [6869 B]
-Fetched 379 kB in 3s (123 kB/s)
+Need to get 383 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
+Fetched 383 kB in 2s (163 kB/s)
Download complete and in download only mode
Check arch
@@ -108,18 +108,24 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15-1)
+fakeroot: already installed (1.15.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libpipeline1 libpcre3 groff-base libssl0.9.8 man-db
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libpipeline1 libpcre3 groff-base libssl0.9.8 man-db
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -128,14 +134,14 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.1)
+base-files: already installed (6.3)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
debianutils: already installed (3.4.4)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.15.8.10)
+dpkg: already installed (1.16.0.1)
e2fsprogs: already installed (1.41.12-2)
findutils: already installed (4.4.2-1)
freebsd-utils: already installed (8.1-4+b1)
@@ -143,8 +149,8 @@ grep: already installed (2.6.3-3)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.8+20110307-1)
-ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-18)
+ncurses-bin: already installed (5.9-1)
+perl-base: already installed (5.10.1-19)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.1)
@@ -153,12 +159,12 @@ tar: already installed (1.25-3)
bsdutils: already installed (1:2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.5.2-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.5.2-3 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8)
-dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
+gcc: already installed (4:4.5.2-5 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.5.2-5 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.0.1 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.2
+Using default version 8.1.3
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -167,45 +173,38 @@ Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
+The following package was automatically installed and is no longer required:
+ libssl0.9.8
+Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- file gettext gettext-base groff-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db
- po-debconf
+ file gettext gettext-base html2text intltool-debian libcroco3 libglib2.0-0
+ libmagic1 libunistring0 libxml2 po-debconf
Suggested packages:
- devscripts doc-base dh-make gettext-doc groff ncurses-doc less www-browser
-debconf: delaying package configuration, since apt-utils is not installed
- libmail-box-perl
+ devscripts doc-base dh-make gettext-doc ncurses-doc libmail-box-perl
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:
- cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/10.9 MB of archives.
-After this operation, 28.9 MB of additional disk space will be used.
-Selecting previously deselected package groff-base.
-(Reading database ... 11962 files and directories currently installed.)
-Unpacking groff-base (from .../groff-base_1.21-5_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_kfreebsd-amd64.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.9-4_kfreebsd-amd64.deb) ...
+ cdbs debhelper file gettext gettext-base html2text intltool-debian libcroco3
+ libglib2.0-0 libmagic1 libncurses5-dev libunistring0 libxml2 po-debconf
+ zlib1g-dev
+debconf: delaying package configuration, since apt-utils is not installed
+0 upgraded, 15 newly installed, 0 to remove and 7 not upgraded.
+Need to get 0 B/8460 kB of archives.
+After this operation, 22.9 MB of additional disk space will be used.
Selecting previously deselected package libmagic1.
+(Reading database ... 13818 files and directories currently installed.)
Unpacking libmagic1 (from .../libmagic1_5.04-5_kfreebsd-amd64.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5_kfreebsd-amd64.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_kfreebsd-amd64.deb) ...
Selecting previously deselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_kfreebsd-amd64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-amd64.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.2-1_kfreebsd-amd64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package libunistring0.
@@ -213,47 +212,46 @@ Unpacking libunistring0 (from .../libunistring0_0.9.3-3_kfreebsd-amd64.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_kfreebsd-amd64.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_kfreebsd-amd64.deb) ...
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_kfreebsd-amd64.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_kfreebsd-amd64.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.3_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../cdbs_0.4.92_kfreebsd-amd64.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_kfreebsd-amd64.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-amd64.deb) ...
-Setting up groff-base (1.21-5) ...
-Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.5.9-4) ...
-Building database of manual pages ...
+Processing triggers for man-db ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.2-1) ...
+Setting up libglib2.0-0 (2.28.4-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
+Setting up debhelper (8.1.3) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8+20110307-1) ...
+Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+The following package was automatically installed and is no longer required:
+ libssl0.9.8
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: binutils_2.21.0.20110327-1 dpkg-dev_1.15.8.10 g++-4.5_4.5.2-7 gcc-4.5_4.5.2-7 kfreebsd-kernel-headers_0.53 libc0.1-dev_2.11.2-13 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-7
-Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-1 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.5.2-3 cpp-4.5_4.5.2-7 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-4+b1 g++_4:4.5.2-3 g++-4.5_4.5.2-7 gcc_4:4.5.2-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.5-14 gcc-4.5_4.5.2-7 gcc-4.5-base_4.5.2-7 gcc-4.6-base_4.6.0-1 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc0.1_2.11.2-13 libc0.1-dev_2.11.2-13 libcam0_8.1-5 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libedit2_2.11-20080614-2 libelfg0_0.8.13-1 libexpat1_2.0.1-7 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-1 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.2-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1 libgomp1_4.6.0-1 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.23-7 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libncursesw5_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libpng12-0_1.2.44-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-8 libsbuf0_8.1-5 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-7 libtasn1-3_2.9-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 type-handling_0.2.23 tzdata_2011d-1 ufsutils_7.3-1+b1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0.1 g++-4.5_4.5.2-8 gcc-4.5_4.5.2-8 kfreebsd-kernel-headers_0.53 libc0.1-dev_2.11.2-13 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8
+Package versions: apt_0.8.13.2 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.5.2-5 cpp-4.5_4.5.2-8 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.1 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-4+b1 g++_4:4.5.2-5 g++-4.5_4.5.2-8 gcc_4:4.5.2-5 gcc-4.4-base_4.4.5-15 gcc-4.5_4.5.2-8 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc0.1_2.11.2-13 libc0.1-dev_2.11.2-13 libcam0_8.1-5 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0.1 libedit2_2.11-20080614-2 libelfg0_0.8.13-1 libexpat1_2.0.1-7 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1+b1 libgomp1_4.6.0-2 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.25-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libpng12-0_1.2.44-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-8 libsbuf0_8.1-5 libslang2_2.2.3-3 libss2_1.41.12-2 libssl0.9.8_0.9.8o-7 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8 libtasn1-3_2.9-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8.1 man-db_2.5.9-4 mawk_1.3.3-15 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 type-handling_0.2.23 tzdata_2011e-1 ufsutils_7.3-1+b1 util-linux_2.17.2-9.1 vim_2:7.3.035+hg~8fdc12103333-1 vim-common_2:7.3.035+hg~8fdc12103333-1 vim-runtime_2:7.3.035+hg~8fdc12103333-1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -264,12 +262,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.14
-dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.15-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.15
+dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
Check disc space
────────────────
@@ -284,25 +282,25 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.14-1
- dpkg-source --before-build samtools-0.1.14
+dpkg-buildpackage: source version 0.1.15-1
+ dpkg-source --before-build samtools-0.1.15
dpkg-buildpackage: host architecture kfreebsd-amd64
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 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/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 `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -311,8 +309,8 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -326,15 +324,16 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/bcftools'
+ar -cru 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 glf.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 `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -345,10 +344,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -366,25 +365,26 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/misc'
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/misc'
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/misc'
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -394,14 +394,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -425,12 +425,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-Tntf
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-sample depth to 8000
+<mpileup> Set max per-file depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -464,7 +464,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -489,7 +489,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -504,65 +504,68 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_kfreebsd-amd64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.15-1_kfreebsd-amd64.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_0.1.14-1_kfreebsd-amd64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.15-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org> >../samtools_0.1.15-1_kfreebsd-amd64.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-0.1.14
+ dpkg-source --after-build samtools-0.1.15
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110329-0522
+Build finished at 20110412-1132
-samtools_0.1.14-1_kfreebsd-amd64.changes:
+samtools_0.1.15-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Tue, 29 Mar 2011 13:13:54 +0900
+Date: Tue, 12 Apr 2011 19:44:41 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-amd64
-Version: 0.1.14-1
+Version: 0.1.15-1
Distribution: sid
Urgency: low
-Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
+Maintainer: kfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org>
Changed-By: Charles Plessy <plessy at 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 (0.1.14-1) unstable; urgency=low
+ samtools (0.1.15-1) unstable; urgency=low
.
* New upstream release.
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.2
+ (debian/control, no changes needed).
+ * debian/watch directly interrogates and downloads froms SourceForge.
Checksums-Sha1:
- 2810422722b454637df6606051abef73fb3dfe12 595312 samtools_0.1.14-1_kfreebsd-amd64.deb
- 53922ebf32d5e742178be8656687e0e5ffc86b38 165302 libbam-dev_0.1.14-1_kfreebsd-amd64.deb
+ bdecb3f4156ed114cb5b0c9a2b8c677b5cac97a6 602150 samtools_0.1.15-1_kfreebsd-amd64.deb
+ cc2e151f4d8a5ae113f8b588e336f91ad8055a1c 168960 libbam-dev_0.1.15-1_kfreebsd-amd64.deb
Checksums-Sha256:
- d8153dd8d4518f5eb1ce5515059492ec68a36e1a7bcde9553a1ee6d4f8b4e2e9 595312 samtools_0.1.14-1_kfreebsd-amd64.deb
- 6bf8ccf2a6f3462deaa19bba8c6c701fe785d7ba696ff9683e3ff7527beb3926 165302 libbam-dev_0.1.14-1_kfreebsd-amd64.deb
+ 3f9819ebccb1d379cd218f9d12a8cfdea4477815966f6715244ddebf599e0bdd 602150 samtools_0.1.15-1_kfreebsd-amd64.deb
+ 6a54d9faa6a3398fada63982828d5cf5c7865efaf13abc66204ed34fc30af8e7 168960 libbam-dev_0.1.15-1_kfreebsd-amd64.deb
Files:
- dce1169db2836395bce68bafb8b6a2c4 595312 science optional samtools_0.1.14-1_kfreebsd-amd64.deb
- 5265f735e09d1c4b623010c30c96a1ba 165302 libdevel optional libbam-dev_0.1.14-1_kfreebsd-amd64.deb
+ 21fdc857a1eac4755bb32006758e06f2 602150 science optional samtools_0.1.15-1_kfreebsd-amd64.deb
+ fd26e727e8483ea35b476ecf053a86f3 168960 libdevel optional libbam-dev_0.1.15-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.14-1_kfreebsd-amd64.deb
+samtools_0.1.15-1_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 595312 bytes: control archive= 1788 bytes.
+ size 602150 bytes: control archive= 1793 bytes.
797 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1018
+ Installed-Size: 1042
Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -575,32 +578,32 @@ samtools_0.1.14-1_kfreebsd-amd64.deb
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 2011-03-29 05:22 ./
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-03-29 05:22 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-04-12 11:31 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-03-29 05:22 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-03-29 05:22 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8393 2011-03-29 05:22 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 2005 2011-03-29 05:22 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/samtools/
+-rw-r--r-- root/root 1966 2011-04-12 11:31 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-04-12 11:31 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8393 2011-04-12 11:31 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 2005 2011-04-12 11:31 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/samtools/
-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
@@ -613,30 +616,30 @@ drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-03-29 05:22 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/bin/
--rwxr-xr-x root/root 106312 2011-03-29 05:22 ./usr/bin/bcftools
--rwxr-xr-x root/root 24800 2011-03-29 05:22 ./usr/bin/razip
--rwxr-xr-x root/root 376080 2011-03-29 05:22 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/lib/samtools/
--rwxr-xr-x root/root 19248 2011-03-29 05:22 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8288 2011-03-29 05:22 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 8192 2011-03-29 05:22 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 11912 2011-03-29 05:22 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 8608 2011-03-29 05:22 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.14-1_kfreebsd-amd64.deb
+-rwxr-xr-x root/root 5778 2011-04-12 11:31 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/bin/
+-rwxr-xr-x root/root 114088 2011-04-12 11:31 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24800 2011-04-12 11:31 ./usr/bin/razip
+-rwxr-xr-x root/root 384272 2011-04-12 11:31 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/lib/
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19248 2011-04-12 11:31 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8288 2011-04-12 11:31 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8192 2011-04-12 11:31 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 11912 2011-04-12 11:31 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 8608 2011-04-12 11:31 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.15-1_kfreebsd-amd64.deb
──────────────────────────────────────
new debian package, version 2.0.
- size 165302 bytes: control archive= 904 bytes.
+ size 168960 bytes: control archive= 901 bytes.
683 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 458
@@ -650,21 +653,21 @@ libbam-dev_0.1.14-1_kfreebsd-amd64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/lib/
--rw-r--r-- root/root 314106 2011-03-29 05:22 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/include/
--rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
--rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/lib/
+-rw-r--r-- root/root 323908 2011-04-12 11:31 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/include/
+-rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/bgzf.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
@@ -680,22 +683,27 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1301376062-33060/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1302607781-51888/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+The following package was automatically installed and is no longer required:
+ libssl0.9.8
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
+The following packages were automatically installed and are no longer required:
+ libpipeline1 libpcre3 groff-base libssl0.9.8 man-db
+Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
- cdbs* debhelper* file* gettext* gettext-base* groff-base* html2text*
- intltool-debian* libcroco3* libglib2.0-0* libmagic1* libncurses5-dev*
- libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf*
- zlib1g-dev*
-0 upgraded, 0 newly installed, 19 to remove and 0 not upgraded.
-After this operation, 28.9 MB disk space will be freed.
-(Reading database ... 13291 files and directories currently installed.)
+ cdbs* debhelper* file* gettext* gettext-base* html2text* intltool-debian*
+ libcroco3* libglib2.0-0* libmagic1* libncurses5-dev* libunistring0* libxml2*
+ po-debconf* zlib1g-dev*
+0 upgraded, 0 newly installed, 15 to remove and 7 not upgraded.
+After this operation, 22.9 MB disk space will be freed.
+(Reading database ... 14739 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing file ...
@@ -703,10 +711,6 @@ Removing po-debconf ...
Removing intltool-debian ...
Removing gettext ...
Removing gettext-base ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
Removing html2text ...
Purging configuration files for html2text ...
Removing libcroco3 ...
@@ -716,33 +720,31 @@ Purging configuration files for libglib2.0-0 ...
Removing libmagic1 ...
Purging configuration files for libmagic1 ...
Removing libncurses5-dev ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
Removing libunistring0 ...
Purging configuration files for libunistring0 ...
Removing libxml2 ...
Purging configuration files for libxml2 ...
Removing zlib1g-dev ...
+Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-amd64
-Build-Space: 11528
-Build-Time: 41
+Build-Space: 11688
+Build-Time: 52
Distribution: sid
-Install-Time: 29
-Job: samtools_0.1.14-1
+Install-Time: 65
+Job: samtools_0.1.15-1
Package: samtools
-Package-Time: 87
-Source-Version: 0.1.14-1
-Space: 11528
+Package-Time: 139
+Source-Version: 0.1.15-1
+Space: 11688
Status: successful
-Version: 0.1.14-1
+Version: 0.1.15-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110329-0522
-Build needed 00:01:27, 11528k disc space
+Finished at 20110412-1132
+Build needed 00:02:19, 11688k disc space
+Signature with key '516A3A7B' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index 45230f7..ecc37cd 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,57 +1,57 @@
-From buildd at finzi.debian.org Tue Mar 29 05:02:16 2011
-Return-path: <buildd at finzi.debian.org>
+From buildd at field.debian.org Tue Apr 12 11:33:51 2011
+Return-path: <buildd at field.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at finzi.debian.org>)
- id 1Q4R4J-0002tN-LR
- for logs at buildd.debian.org; Tue, 29 Mar 2011 05:02:16 +0000
-Received: from finzi.debian.org ([206.12.19.111])
+ (Exim 4.69) (envelope-from <buildd at field.debian.org>)
+ id 1Q9bqx-0006sv-2f
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 11:33:51 +0000
+Received: from field.debian.org ([194.177.211.210])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=finzi.debian.org, EMAIL=hostmaster at finzi.debian.org (verified)
+ CN=field.debian.org, EMAIL=hostmaster at field.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at finzi.debian.org>)
- id 1Q4R4F-0003Ue-Ql; Tue, 29 Mar 2011 05:02:12 +0000
-Received: from buildd by finzi.debian.org with local (Exim 4.72)
- (envelope-from <buildd at finzi.debian.org>)
- id 1Q4R4B-000PSC-Ng; Tue, 29 Mar 2011 05:02:07 +0000
-Date: Tue, 29 Mar 2011 05:02:07 +0000
-Message-Id: <E1Q4R4B-000PSC-Ng at finzi.debian.org>
-From: buildd on finzi <buildd at finzi.debian.org>
+ (Exim 4.69) (envelope-from <buildd at field.debian.org>)
+ id 1Q9bqs-0004ud-Ic; Tue, 12 Apr 2011 11:33:46 +0000
+Received: from buildd by field.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at field.debian.org>)
+ id 1Q9bqp-0003sn-G3; Tue, 12 Apr 2011 11:33:43 +0000
+Date: Tue, 12 Apr 2011 11:33:43 +0000
+Message-Id: <E1Q9bqp-0003sn-G3 at field.debian.org>
+From: buildd on field <buildd at field.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,kibi at debian-ports.org
-Subject: Log for successful build of samtools_0.1.14-1 on kfreebsd-i386
+Subject: Log for successful build of samtools_0.1.15-1 on kfreebsd-i386
(dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on finzi.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on field.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.14-1 (kfreebsd-i386) 29 Mar 2011 05:00 ║
+║ samtools 0.1.15-1 (kfreebsd-i386) 12 Apr 2011 11:30 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.14-1
-Source Version: 0.1.14-1
+Version: 0.1.15-1
+Source Version: 0.1.15-1
Architecture: kfreebsd-i386
-Hit http://mirror-ubc.debian.org sid InRelease
-Hit http://mirror-ubc.debian.org sid/main Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid InRelease
+Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Hit http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex
-Hit http://mirror-ubc.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
-Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
-Hit http://mirror-ubc.debian.org sid/main TranslationIndex
-Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
-Ign http://mirror-ubc.debian.org sid/contrib Translation-en
-Ign http://mirror-ubc.debian.org sid/non-free Translation-en
-Hit http://incoming.debian.org Release.gpg
+Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
+Ign http://ftp.gr.debian.org sid/contrib TranslationIndex
+Hit http://ftp.gr.debian.org sid/main TranslationIndex
+Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Ign http://ftp.gr.debian.org sid/contrib Translation-en
+Ign http://ftp.gr.debian.org sid/non-free Translation-en
Hit http://incoming.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
@@ -61,13 +61,13 @@ Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
Hit http://incoming.debian.org sid/main TranslationIndex
Ign http://incoming.debian.org sid/non-free TranslationIndex
-Hit http://incoming.debian.org Release
-Get:1 http://incoming.debian.org Sources [30.5 kB]
-Get:2 http://incoming.debian.org Packages [608 kB]
+Get:2 http://incoming.debian.org Release [1604 B]
+Get:3 http://incoming.debian.org Sources [49.7 kB]
+Get:4 http://incoming.debian.org Packages [772 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 638 kB in 8s (73.2 kB/s)
+Fetched 825 kB in 6s (136 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -88,11 +88,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 379 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (tar) [370 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (diff) [6869 B]
-Fetched 379 kB in 2s (140 kB/s)
+Need to get 383 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
+Fetched 383 kB in 2s (180 kB/s)
Download complete and in download only mode
Check arch
@@ -106,18 +106,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15-1)
+fakeroot: already installed (1.15.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -126,14 +126,14 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.1)
+base-files: already installed (6.3)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
debianutils: already installed (3.4.4)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.15.8.10)
+dpkg: already installed (1.16.0.1)
e2fsprogs: already installed (1.41.12-2)
findutils: already installed (4.4.2-1)
freebsd-utils: already installed (8.1-4)
@@ -141,8 +141,8 @@ grep: already installed (2.6.3-3)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.8+20110307-1)
-ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-18)
+ncurses-bin: already installed (5.9-1)
+perl-base: already installed (5.10.1-19)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.1)
@@ -151,12 +151,12 @@ tar: already installed (1.25-3)
bsdutils: already installed (1:2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.5.2-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.5.2-2 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.5.2-5 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.5.2-5 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8)
-dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.0.1 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.2
+Using default version 8.1.3
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -173,23 +173,23 @@ Suggested packages:
devscripts doc-base dh-make gettext-doc groff ncurses-doc less www-browser
libmail-box-perl
Recommended packages:
- curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
- libmail-sendmail-perl
+ 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:
cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 19 newly installed, 0 to remove and 3 not upgraded.
+0 upgraded, 19 newly installed, 0 to remove and 5 not upgraded.
Need to get 0 B/10.4 MB of archives.
After this operation, 27.2 MB of additional disk space will be used.
Selecting previously deselected package groff-base.
-(Reading database ... 13556 files and directories currently installed.)
+(Reading database ... 11815 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.21-5_kfreebsd-i386.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_kfreebsd-i386.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.9-4_kfreebsd-i386.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.1-1_kfreebsd-i386.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_kfreebsd-i386.deb) ...
Selecting previously deselected package file.
@@ -203,7 +203,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_kfreebsd-i386.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-i386.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.2-1_kfreebsd-i386.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_kfreebsd-i386.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-i386.deb) ...
Selecting previously deselected package libunistring0.
@@ -215,16 +215,16 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.3_all.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_kfreebsd-i386.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_kfreebsd-i386.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-i386.deb) ...
Setting up groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.5.9-4) ...
+Setting up man-db (2.6.0.1-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
@@ -232,26 +232,26 @@ Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.2-1) ...
+Setting up libglib2.0-0 (2.28.4-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
+Setting up debhelper (8.1.3) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8+20110307-1) ...
+Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
Checking correctness of dependencies...
-Kernel: GNU/kFreeBSD 8.1-1-686 kfreebsd-i386 (i686)
-Toolchain package versions: binutils_2.21.0.20110327-1 dpkg-dev_1.15.8.10 g++-4.5_4.5.2-7 gcc-4.5_4.5.2-7 kfreebsd-kernel-headers_0.53 libc0.1-dev_2.11.2-13 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-7
-Package versions: apt_0.8.13 autotools-dev_20100122.1 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-1 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.5.2-2 cpp-4.5_4.5.2-7 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-4 g++_4:4.5.2-2 g++-4.5_4.5.2-7 gcc_4:4.5.2-2 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.5-14 gcc-4.5_4.5.2-7 gcc-4.5-base_4.5.2-7 gcc-4.6-base_4.6.0-1 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc0.1_2.11.2-13 libc0.1-dev_2.11.2-13 libcam0_8.1-5 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libedit2_2.11-20080614-2 libelfg0_0.8.13-1 libexpat1_2.0.1-7 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-1 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.2-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1 libgomp1_4.6.0-1 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.23-7 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libncursesw5_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libpng12-0_1.2.44-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-8 libsbuf0_8.1-5 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-7 libtasn1-3_2.9-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 netbase_4.45 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 type-handling_0.2.23 tzdata_2011d-1 ufsutils_7.3-1+b1 util-linux_2.17.2-9.1 vim_2:7.3.035+hg~8fdc12103333-1 vim-common_2:7.3.035+hg~8fdc12103333-1 vim-runtime_2:7.3.035+hg~8fdc12103333-1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
+Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0.1 g++-4.5_4.5.2-8 gcc-4.5_4.5.2-8 kfreebsd-kernel-headers_0.53 libc0.1-dev_2.11.2-13 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8
+Package versions: apt_0.8.13.2 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.5.2-5 cpp-4.5_4.5.2-8 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.1 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-4 g++_4:4.5.2-5 g++-4.5_4.5.2-8 gcc_4:4.5.2-5 gcc-4.4-base_4.4.5-15 gcc-4.5_4.5.2-8 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc0.1_2.11.2-13 libc0.1-dev_2.11.2-13 libcam0_8.1-5 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0.1 libedit2_2.11-20080614-2 libelfg0_0.8.13-1 libexpat1_2.0.1-7 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1+b1 libgomp1_4.6.0-2 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.25-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libpng12-0_1.2.44-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-8 libsbuf0_8.1-5 libslang2_2.2.3-3 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8 libtasn1-3_2.9-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 netbase_4.45 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 type-handling_0.2.23 tzdata_2011e-1 ufsutils_7.3-1+b1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -262,12 +262,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.14
-dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.15-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.15
+dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
Check disc space
────────────────
@@ -282,25 +282,25 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.14-1
- dpkg-source --before-build samtools-0.1.14
+dpkg-buildpackage: source version 0.1.15-1
+ dpkg-source --before-build samtools-0.1.15
dpkg-buildpackage: host architecture kfreebsd-i386
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 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/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 `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -309,8 +309,8 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -324,15 +324,16 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/bcftools'
+ar -cru 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 glf.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 `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -343,10 +344,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -364,25 +365,26 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/misc'
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/misc'
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/misc'
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -392,14 +394,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -423,12 +425,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZ
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-sample depth to 8000
+<mpileup> Set max per-file depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -462,7 +464,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -487,7 +489,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -502,65 +504,68 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_kfreebsd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.15-1_kfreebsd-i386.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../samtools_0.1.14-1_kfreebsd-i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.15-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../samtools_0.1.15-1_kfreebsd-i386.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-0.1.14
+ dpkg-source --after-build samtools-0.1.15
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110329-0501
+Build finished at 20110412-1133
-samtools_0.1.14-1_kfreebsd-i386.changes:
+samtools_0.1.15-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Tue, 29 Mar 2011 13:13:54 +0900
+Date: Tue, 12 Apr 2011 19:44:41 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-i386
-Version: 0.1.14-1
+Version: 0.1.15-1
Distribution: sid
Urgency: low
-Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org>
+Maintainer: kfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org>
Changed-By: Charles Plessy <plessy at 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 (0.1.14-1) unstable; urgency=low
+ samtools (0.1.15-1) unstable; urgency=low
.
* New upstream release.
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.2
+ (debian/control, no changes needed).
+ * debian/watch directly interrogates and downloads froms SourceForge.
Checksums-Sha1:
- db1751cbe6d180f3573a100d81181e7a3b860afb 582452 samtools_0.1.14-1_kfreebsd-i386.deb
- 390dc919f44e2888f4717b0ae2b7bce1d06ac8f3 165382 libbam-dev_0.1.14-1_kfreebsd-i386.deb
+ db4b84316a10ef99e527d0cf28e8f3e69be87a3a 588572 samtools_0.1.15-1_kfreebsd-i386.deb
+ 955ef5a1f33ac243d2d03197e80dd3ffbfa53484 168586 libbam-dev_0.1.15-1_kfreebsd-i386.deb
Checksums-Sha256:
- d2b07e3dd509a6b3f8ce644f2c876ca061b61a94c8f95b8d07a3ad60fd21a577 582452 samtools_0.1.14-1_kfreebsd-i386.deb
- 434488f487129b42b7c693218ab51eb6d84a8ac3cbba92b9ce8ef2da2ea7d66e 165382 libbam-dev_0.1.14-1_kfreebsd-i386.deb
+ 7ce964a460d5c951b11fdbd6f6768bcbd73e81d8774bd52fa98d876b93a843fd 588572 samtools_0.1.15-1_kfreebsd-i386.deb
+ 5163f38d291e1c4eeb8b4338925df64a7529eec4f642f50740e97d719f7f0276 168586 libbam-dev_0.1.15-1_kfreebsd-i386.deb
Files:
- ca3cb78bc60213a2ac7a4bba896ef19e 582452 science optional samtools_0.1.14-1_kfreebsd-i386.deb
- 0a3ac24ba10128c1550043ac0474513d 165382 libdevel optional libbam-dev_0.1.14-1_kfreebsd-i386.deb
+ 5469df2a1f7e3283d08b5a4a2de35666 588572 science optional samtools_0.1.15-1_kfreebsd-i386.deb
+ 1287f3c54405cefaea50e66aae19e9ea 168586 libdevel optional libbam-dev_0.1.15-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.14-1_kfreebsd-i386.deb
+samtools_0.1.15-1_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 582452 bytes: control archive= 1788 bytes.
- 795 bytes, 16 lines control
+ size 588572 bytes: control archive= 1787 bytes.
+ 796 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 996
+ Installed-Size: 1004
Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -573,32 +578,32 @@ samtools_0.1.14-1_kfreebsd-i386.deb
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 2011-03-29 05:01 ./
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-03-29 05:01 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-04-12 11:32 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-03-29 05:01 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-03-29 05:01 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8393 2011-03-29 05:01 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 2005 2011-03-29 05:01 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/samtools/
+-rw-r--r-- root/root 1966 2011-04-12 11:32 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-04-12 11:32 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8393 2011-04-12 11:32 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 2005 2011-04-12 11:32 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/samtools/
-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
@@ -611,30 +616,30 @@ drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-03-29 05:01 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/bin/
--rwxr-xr-x root/root 96964 2011-03-29 05:01 ./usr/bin/bcftools
--rwxr-xr-x root/root 23352 2011-03-29 05:01 ./usr/bin/razip
--rwxr-xr-x root/root 361964 2011-03-29 05:01 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/lib/samtools/
--rwxr-xr-x root/root 17424 2011-03-29 05:01 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6128 2011-03-29 05:01 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6096 2011-03-29 05:01 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10084 2011-03-29 05:01 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6616 2011-03-29 05:01 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.14-1_kfreebsd-i386.deb
+-rwxr-xr-x root/root 5778 2011-04-12 11:32 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/bin/
+-rwxr-xr-x root/root 104676 2011-04-12 11:32 ./usr/bin/bcftools
+-rwxr-xr-x root/root 23352 2011-04-12 11:32 ./usr/bin/razip
+-rwxr-xr-x root/root 371020 2011-04-12 11:32 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17424 2011-04-12 11:32 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6128 2011-04-12 11:32 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6096 2011-04-12 11:32 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10084 2011-04-12 11:32 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6616 2011-04-12 11:32 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.15-1_kfreebsd-i386.deb
─────────────────────────────────────
new debian package, version 2.0.
- size 165382 bytes: control archive= 904 bytes.
+ size 168586 bytes: control archive= 899 bytes.
682 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 394
@@ -648,21 +653,21 @@ libbam-dev_0.1.14-1_kfreebsd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/lib/
--rw-r--r-- root/root 253062 2011-03-29 05:01 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/include/
--rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
--rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/
+-rw-r--r-- root/root 261096 2011-04-12 11:32 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/include/
+-rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/bgzf.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
@@ -678,11 +683,11 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1301374820-96255/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1302607836-13199/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
@@ -691,9 +696,9 @@ The following packages will be REMOVED:
intltool-debian* libcroco3* libglib2.0-0* libmagic1* libncurses5-dev*
libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf*
zlib1g-dev*
-0 upgraded, 0 newly installed, 19 to remove and 3 not upgraded.
+0 upgraded, 0 newly installed, 19 to remove and 5 not upgraded.
After this operation, 27.2 MB disk space will be freed.
-(Reading database ... 14883 files and directories currently installed.)
+(Reading database ... 13143 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing file ...
@@ -729,18 +734,19 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-i386
-Build-Space: 9446
-Build-Time: 47
+Build-Space: 9576
+Build-Time: 53
Distribution: sid
-Install-Time: 29
-Job: samtools_0.1.14-1
+Install-Time: 77
+Job: samtools_0.1.15-1
Package: samtools
-Package-Time: 94
-Source-Version: 0.1.14-1
-Space: 9446
+Package-Time: 148
+Source-Version: 0.1.15-1
+Space: 9576
Status: successful
-Version: 0.1.14-1
+Version: 0.1.15-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110329-0501
-Build needed 00:01:34, 9446k disc space
+Finished at 20110412-1133
+Build needed 00:02:28, 9576k disc space
+Signature with key '22C61858' requested:
diff --git a/mips.log b/mips.log
index 8f1590f..bbfd28b 100644
--- a/mips.log
+++ b/mips.log
@@ -1,4 +1,4 @@
-From buildd at lucatelli.debian.org Sat Apr 02 11:27:31 2011
+From buildd at lucatelli.debian.org Tue Apr 12 12:14:47 2011
Return-path: <buildd at lucatelli.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,62 +6,63 @@ Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at lucatelli.debian.org>)
- id 1Q5yzL-0004SJ-46
- for logs at buildd.debian.org; Sat, 02 Apr 2011 11:27:31 +0000
+ id 1Q9cUY-0005t7-He
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 12:14:46 +0000
Received: from lucatelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4141])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=lucatelli.debian.org,
EMAIL=hostmaster at lucatelli.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at lucatelli.debian.org>)
- id 1Q5yzG-0001p9-4c; Sat, 02 Apr 2011 11:27:26 +0000
+ id 1Q9cUT-00060G-GL
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 12:14:42 +0000
Received: from buildd by lucatelli.debian.org with local (Exim 4.69)
- (envelope-from <buildd at lucatelli.debian.org>)
- id 1Q5yz6-00038J-NA; Sat, 02 Apr 2011 11:27:16 +0000
+ (envelope-from <buildd at lucatelli.debian.org>) id 1Q9cUK-0005Yt-9Y
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 12:14:32 +0000
From: buildd on lucatelli <buildd at lucatelli.debian.org>
-To: aba at debian.org,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.14-1 on mips (dist=sid)
+To: logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.15-1 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1Q5yz6-00038J-NA at lucatelli.debian.org>
-Date: Sat, 02 Apr 2011 11:27:16 +0000
+Message-Id: <E1Q9cUK-0005Yt-9Y at lucatelli.debian.org>
+Date: Tue, 12 Apr 2011 12:14:32 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lucatelli.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.14-1 (mips) 02 Apr 2011 10:43 ║
+║ samtools 0.1.15-1 (mips) 12 Apr 2011 11:30 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.14-1
-Source Version: 0.1.14-1
+Version: 0.1.15-1
+Source Version: 0.1.15-1
Architecture: mips
-Get:1 http://mirror-ubc.debian.org unstable InRelease [186 kB]
-Get:2 http://incoming.debian.org unstable InRelease [186 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [5192 kB]
+Get:1 http://mirror-ubc.debian.org unstable InRelease [151 kB]
+Get:2 http://incoming.debian.org unstable InRelease [151 kB]
+Get:3 http://mirror-ubc.debian.org unstable/main Sources [5265 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [5192 kB]
-Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [48.7 kB]
-Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [98.4 kB]
-Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [6876 kB]
-Get:9 http://mirror-ubc.debian.org unstable/contrib mips Packages [52.9 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5265 kB]
+Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [48.2 kB]
+Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [97.4 kB]
+Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [6928 kB]
+Get:9 http://mirror-ubc.debian.org unstable/contrib mips Packages [52.7 kB]
Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
-Get:10 http://mirror-ubc.debian.org unstable/main TranslationIndex [2232 B]
+Get:10 http://mirror-ubc.debian.org unstable/main TranslationIndex [2264 B]
Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [48.7 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [98.4 kB]
-Get:13 http://incoming.debian.org unstable/main mips Packages [6876 kB]
-Get:14 http://incoming.debian.org unstable/contrib mips Packages [52.9 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [48.2 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [97.4 kB]
+Get:13 http://incoming.debian.org unstable/main mips Packages [6928 kB]
+Get:14 http://incoming.debian.org unstable/contrib mips Packages [52.7 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [34.0 kB]
-Get:18 http://incoming.debian.org Packages [481 kB]
+Get:17 http://incoming.debian.org Sources [49.7 kB]
+Get:18 http://incoming.debian.org Packages [772 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 25.4 MB in 54s (466 kB/s)
+Fetched 25.9 MB in 59s (439 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +83,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 379 kB of source archives.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main samtools 0.1.14-1 (dsc) [1939 B]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main samtools 0.1.14-1 (tar) [370 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main samtools 0.1.14-1 (diff) [6869 B]
-Fetched 379 kB in 0s (3371 kB/s)
+Need to get 383 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
+Fetched 383 kB in 1s (337 kB/s)
Download complete and in download only mode
Check arch
@@ -100,18 +101,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15-1)
+fakeroot: already installed (1.15.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -120,14 +121,14 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.1)
+base-files: already installed (6.3)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
debianutils: already installed (3.4.4)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0)
+dpkg: already installed (1.16.0.1)
e2fsprogs: already installed (1.41.12-2)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.6.3-3)
@@ -135,7 +136,7 @@ gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.8+20110307-1)
ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-18)
+perl-base: already installed (5.10.1-19)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.1)
@@ -147,10 +148,10 @@ util-linux: already installed (2.17.2-9.1)
libc6-dev: already installed (2.11.2-11)
gcc: already installed (4:4.4.5-7 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.4.5-7 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8)
-dpkg-dev: already installed (1.16.0 >= 1.13.5 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.0.1 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.2
+Using default version 8.1.3
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -161,52 +162,64 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ libcroco3 libglib2.0-0 libmagic1 libncurses5 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db ncurses-bin po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
groff ncurses-doc less www-browser libmail-box-perl
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded.
-Need to get 10.9 MB of archives.
-After this operation, 32.6 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 8.2.2 [210 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-5 [1203 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-1 [35.7 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.5.9-4 [997 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.04-5 [239 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.04-5 [49.7 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-3 [153 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 8.12-3 [262 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-2 [837 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.28.4-1 [1505 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-1 [110 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-3 [415 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-3 [2037 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian mips 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf mips 1.0.16+nmu1 [223 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main debhelper mips 8.1.2 [553 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main cdbs mips 0.4.92 [1268 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev mips 5.8+20110307-1 [510 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
+The following packages will be upgraded:
+ libncurses5 ncurses-bin
+2 upgraded, 20 newly installed, 0 to remove and 2 not upgraded.
+Need to get 11.6 MB of archives.
+After this operation, 32.7 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main ncurses-bin mips 5.9-1 [328 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5 mips 5.9-1 [361 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 8.2.2 [210 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-5 [1203 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-1 [35.7 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.0.1-1 [996 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.04-5 [239 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.04-5 [49.7 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-3 [153 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 8.12-3 [262 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-2 [837 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.28.4-1 [1505 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-1 [110 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-3 [415 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-3 [2037 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 8.1.3 [554 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev mips 5.9-1 [509 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.9 MB in 2s (5355 kB/s)
+Fetched 11.6 MB in 2s (5350 kB/s)
+(Reading database ... 10115 files and directories currently installed.)
+Preparing to replace ncurses-bin 5.8+20110307-1 (using .../ncurses-bin_5.9-1_mips.deb) ...
+Unpacking replacement ncurses-bin ...
+Setting up ncurses-bin (5.9-1) ...
+(Reading database ... 10115 files and directories currently installed.)
+Preparing to replace libncurses5 5.8+20110307-1 (using .../libncurses5_5.9-1_mips.deb) ...
+Unpacking replacement libncurses5 ...
+Setting up libncurses5 (5.9-1) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10112 files and directories currently installed.)
+(Reading database ... 10115 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_mips.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-5_mips.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_mips.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.9-4_mips.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.1-1_mips.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_mips.deb) ...
Selecting previously deselected package file.
@@ -228,15 +241,15 @@ Unpacking libunistring0 (from .../libunistring0_0.9.3-3_mips.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_mips.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_mips.deb) ...
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_mips.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_mips.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.3_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_mips.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_mips.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_mips.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mips.deb) ...
Setting up bsdmainutils (8.2.2) ...
@@ -244,7 +257,7 @@ update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write)
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.5.9-4) ...
+Setting up man-db (2.6.0.1-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
@@ -259,19 +272,19 @@ Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
+Setting up debhelper (8.1.3) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8+20110307-1) ...
+Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
-Toolchain package versions: binutils_2.21.0.20110327-1 dpkg-dev_1.16.0 g++-4.4_4.4.5-15 gcc-4.4_4.4.5-15 libc6-dev_2.11.2-11 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 linux-libc-dev_2.6.37-2
-Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-1 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-7 cpp-4.4_4.4.5-15 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0 dpkg-dev_1.16.0 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-7 g++-4.4_4.4.5-15 gcc_4:4.4.5-7 gcc-4.4_4.4.5-15 gcc-4.4-base_4.4.5-15 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011e-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.0.20110327-3 dpkg-dev_1.16.0.1 g++-4.4_4.4.5-15 gcc-4.4_4.4.5-15 libc6-dev_2.11.2-11 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 linux-libc-dev_2.6.38-3
+Package versions: apt_0.8.13.2 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-3 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-7 cpp-4.4_4.4.5-15 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.1 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-7 g++-4.4_4.4.5-15 gcc_4:4.4.5-7 gcc-4.4_4.4.5-15 gcc-4.4-base_4.4.5-15 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0.1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.3-3 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011e-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -283,12 +296,12 @@ Unpack source
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.14
-dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.15-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.15
+dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
Check disc space
────────────────
@@ -304,8 +317,8 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.14-1
- dpkg-source --before-build samtools-0.1.14
+dpkg-buildpackage: source version 0.1.15-1
+ dpkg-source --before-build samtools-0.1.15
dpkg-buildpackage: host architecture mips
fakeroot debian/rules clean
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -316,17 +329,17 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/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 `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -339,8 +352,8 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -354,15 +367,16 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/bcftools'
+ar -cru 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 glf.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 `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -373,10 +387,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -394,25 +408,26 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/misc'
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/misc'
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/misc'
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -422,14 +437,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -453,12 +468,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtool
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-sample depth to 8000
+<mpileup> Set max per-file depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -496,7 +511,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -521,7 +536,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -536,27 +551,27 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_mips.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.15-1_mips.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org> >../samtools_0.1.14-1_mips.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.15-1_mips.deb'.
+ dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org> >../samtools_0.1.15-1_mips.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-0.1.14
+ dpkg-source --after-build samtools-0.1.15
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110402-1127
+Build finished at 20110412-1214
-samtools_0.1.14-1_mips.changes:
+samtools_0.1.15-1_mips.changes:
Format: 1.8
-Date: Tue, 29 Mar 2011 13:13:54 +0900
+Date: Tue, 12 Apr 2011 19:44:41 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mips
-Version: 0.1.14-1
+Version: 0.1.15-1
Distribution: sid
Urgency: low
Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org>
@@ -565,36 +580,39 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.14-1) unstable; urgency=low
+ samtools (0.1.15-1) unstable; urgency=low
.
* New upstream release.
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.2
+ (debian/control, no changes needed).
+ * debian/watch directly interrogates and downloads froms SourceForge.
Checksums-Sha1:
- c4a0df6c32a891ed1dadca5dc6614de6d53f722f 599612 samtools_0.1.14-1_mips.deb
- c88b5ebcdb748eaa4e135e990a5422b04ca458c8 180344 libbam-dev_0.1.14-1_mips.deb
+ 8c4fcceda767e27396a4fc8a52ca7c20fa147ba9 604934 samtools_0.1.15-1_mips.deb
+ 8c85a8e7669a5141d911c467f27c5103b04b46e1 184540 libbam-dev_0.1.15-1_mips.deb
Checksums-Sha256:
- 2e79390623f3d483cf0ad9386e452c8adc0a0738f641c50e1525b12747caf22a 599612 samtools_0.1.14-1_mips.deb
- c07b30fac7a34cda1af1de542db2bc2f37e390b26cd078c2370ffd0469af20cd 180344 libbam-dev_0.1.14-1_mips.deb
+ 7f527d67d4e178dc4b2d2b398c9aa81795915b03cf70b1d005157c7f6eb41882 604934 samtools_0.1.15-1_mips.deb
+ e0af6490110eee0a6e0dd497a66d1f7213a78540f60849fb130009e584d33323 184540 libbam-dev_0.1.15-1_mips.deb
Files:
- 005f72cf2e67eb843919a839b950bbce 599612 science optional samtools_0.1.14-1_mips.deb
- cc9a12c2ad91a0d762033fbb9e786104 180344 libdevel optional libbam-dev_0.1.14-1_mips.deb
+ e03565577e980ba81420ebdf38b615d0 604934 science optional samtools_0.1.15-1_mips.deb
+ 82c52cecb4aa8227ef12c93c5e1871ae 184540 libdevel optional libbam-dev_0.1.15-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.14-1_mips.deb
+samtools_0.1.15-1_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 599612 bytes: control archive= 1790 bytes.
+ size 604934 bytes: control archive= 1794 bytes.
785 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1208
+ Installed-Size: 1228
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -607,21 +625,21 @@ samtools_0.1.14-1_mips.deb
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 2011-04-02 11:26 ./
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/lib/
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/lib/samtools/
--rwxr-xr-x root/root 7764 2011-04-02 11:26 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 9768 2011-04-02 11:26 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 13268 2011-04-02 11:26 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7764 2011-04-02 11:26 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 19944 2011-04-02 11:26 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/bin/
--rwxr-xr-x root/root 133584 2011-04-02 11:26 ./usr/bin/bcftools
--rwxr-xr-x root/root 465228 2011-04-02 11:26 ./usr/bin/samtools
--rwxr-xr-x root/root 30712 2011-04-02 11:26 ./usr/bin/razip
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/lib/
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/lib/samtools/
+-rwxr-xr-x root/root 7764 2011-04-12 12:13 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9768 2011-04-12 12:13 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 13268 2011-04-12 12:13 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7764 2011-04-12 12:13 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 19944 2011-04-12 12:13 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/bin/
+-rwxr-xr-x root/root 142088 2011-04-12 12:13 ./usr/bin/bcftools
+-rwxr-xr-x root/root 477880 2011-04-12 12:13 ./usr/bin/samtools
+-rwxr-xr-x root/root 30712 2011-04-12 12:13 ./usr/bin/razip
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/samtools/
-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
@@ -629,49 +647,49 @@ drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/samtools/
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2011-04-02 11:26 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-04-12 12:13 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-drwxr-xr-x root/root 0 2011-04-02 11:25 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/doc/samtools/
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126609 2011-04-02 10:52 ./usr/share/doc/samtools/examples/ex1.bam.gz
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126609 2011-04-12 11:39 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1966 2011-04-02 11:26 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/man/man1/
--rw-r--r-- root/root 2005 2011-04-02 11:26 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 430 2011-04-02 11:26 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8393 2011-04-02 11:26 ./usr/share/man/man1/samtools.1.gz
-
-
-libbam-dev_0.1.14-1_mips.deb
+-rw-r--r-- root/root 1966 2011-04-12 12:13 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/man/man1/
+-rw-r--r-- root/root 2005 2011-04-12 12:13 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 430 2011-04-12 12:13 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8393 2011-04-12 12:13 ./usr/share/man/man1/samtools.1.gz
+
+
+libbam-dev_0.1.15-1_mips.deb
────────────────────────────
new debian package, version 2.0.
- size 180344 bytes: control archive= 904 bytes.
+ size 184540 bytes: control archive= 900 bytes.
673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 460
+ Installed-Size: 472
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -682,23 +700,23 @@ libbam-dev_0.1.14-1_mips.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/lib/
--rw-r--r-- root/root 309706 2011-04-02 11:26 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/include/
--rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
--rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/lib/
+-rw-r--r-- root/root 319948 2011-04-12 12:13 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/include/
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/bgzf.h
+-rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -712,7 +730,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mips-sbuild-d66e71cd-c930-45f5-a382-5f876f353c80/build/buildd-samtools_0.1.14-1-mips-NRXuaA
+Purging /var/lib/schroot/mount/sid-mips-sbuild-1b551950-178e-4287-b8db-1140f6befd10/build/buildd-samtools_0.1.15-1-mips-zd9hwI
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -720,84 +738,84 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mips
-Build-Space: 9928
-Build-Time: 2466
+Build-Space: 10108
+Build-Time: 2475
Distribution: sid
-Install-Time: 63
-Job: samtools_0.1.14-1
+Install-Time: 72
+Job: samtools_0.1.15-1
Package: samtools
-Package-Time: 2625
-Source-Version: 0.1.14-1
-Space: 9928
+Package-Time: 2647
+Source-Version: 0.1.15-1
+Space: 10108
Status: successful
-Version: 0.1.14-1
+Version: 0.1.15-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110402-1127
-Build needed 00:43:45, 9928k disc space
+Finished at 20110412-1214
+Build needed 00:44:07, 10108k disc space
+Signature with key 'F4C69470' requested:
-From buildd at rem.debian.org Tue Mar 29 08:53:36 2011
-Return-path: <buildd at rem.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at mayer.debian.org Tue Apr 12 18:15:03 2011
+Return-path: <buildd at mayer.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at rem.debian.org>)
- id 1Q4UgB-0005mD-5O
- for logs at buildd.debian.org; Tue, 29 Mar 2011 08:53:35 +0000
-Received: from rem.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d06])
+ (Exim 4.69) (envelope-from <buildd at mayer.debian.org>)
+ id 1Q9i7D-0002Va-BU
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 18:15:03 +0000
+Received: from mayer.debian.org ([140.211.166.78])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
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- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
- id 1Q4Ug5-0003w9-Cp; Tue, 29 Mar 2011 08:53:29 +0000
-Received: from buildd by rem.debian.org with local (Exim 4.72)
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- id 1Q4Ug4-0004pX-IW; Tue, 29 Mar 2011 08:53:28 +0000
-Date: Tue, 29 Mar 2011 08:53:28 +0000
-Message-Id: <E1Q4Ug4-0004pX-IW at rem.debian.org>
-From: buildd on rem <buildd at rem.debian.org>
-To: aba+buildd_rem at not.so.argh.org,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.14-1 on mipsel (dist=sid)
+ CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at mayer.debian.org>)
+ id 1Q9i78-000858-1k
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 18:14:59 +0000
+Received: from buildd by mayer.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at mayer.debian.org>)
+ id 1Q9i73-00020h-1Z; Tue, 12 Apr 2011 18:14:53 +0000
+From: buildd on mayer <buildd at mayer.debian.org>
+To: buildd-porters at mayer.debian.org,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.15-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
+Message-Id: <E1Q9i73-00020h-1Z at mayer.debian.org>
+Date: Tue, 12 Apr 2011 18:14:53 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rem.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.14-1 (mipsel) 29 Mar 2011 08:47 ║
+║ samtools 0.1.15-1 (mipsel) 12 Apr 2011 18:09 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.14-1
-Source Version: 0.1.14-1
+Version: 0.1.15-1
+Source Version: 0.1.15-1
Architecture: mipsel
-Get:1 http://mirror.ayous.org unstable InRelease [185 kB]
-Get:2 http://incoming.debian.org unstable InRelease [186 kB]
-Get:3 http://mirror.ayous.org unstable/main Sources [5142 kB]
-Get:4 http://mirror.ayous.org unstable/contrib Sources [47.4 kB]
-Get:5 http://mirror.ayous.org unstable/non-free Sources [99.4 kB]
-Get:6 http://mirror.ayous.org unstable/main mipsel Packages [6872 kB]
+Hit http://debian.oregonstate.edu sid InRelease
+Hit http://debian.oregonstate.edu sid/main Sources
+Hit http://debian.oregonstate.edu sid/contrib Sources
+Hit http://debian.oregonstate.edu sid/main mipsel Packages
+Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
+Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
+Hit http://debian.oregonstate.edu sid/main TranslationIndex
+Ign http://debian.oregonstate.edu sid/contrib Translation-en
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://incoming.debian.org Release [1604 B]
-Get:9 http://incoming.debian.org unstable/main Sources [5140 kB]
-Get:10 http://mirror.ayous.org unstable/contrib mipsel Packages [52.2 kB]
-Ign http://mirror.ayous.org unstable/contrib TranslationIndex
-Get:11 http://mirror.ayous.org unstable/main TranslationIndex [2232 B]
-Ign http://mirror.ayous.org unstable/contrib Translation-en
-Get:12 http://incoming.debian.org unstable/contrib Sources [47.4 kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
-Get:14 http://incoming.debian.org unstable/main mipsel Packages [6869 kB]
-Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [52.2 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:16 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
-Get:17 http://incoming.debian.org Sources [29.5 kB]
-Get:18 http://incoming.debian.org Packages [637 kB]
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Hit http://incoming.debian.org sid/main Sources
+Hit http://incoming.debian.org sid/contrib Sources
+Hit http://incoming.debian.org sid/main mipsel Packages
+Hit http://incoming.debian.org sid/contrib mipsel Packages
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Hit http://incoming.debian.org sid/main TranslationIndex
+Get:2 http://incoming.debian.org Release [1604 B]
+Get:3 http://incoming.debian.org Sources [44.6 kB]
+Get:4 http://incoming.debian.org Packages [720 kB]
+Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 25.5 MB in 44s (567 kB/s)
+Fetched 767 kB in 3s (206 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -815,13 +833,14 @@ 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://git.debian.org/debian-med/samtools.git
-Need to get 379 kB of source archives.
-Get:1 http://incoming.debian.org/debian/ unstable/main samtools 0.1.14-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/debian/ unstable/main samtools 0.1.14-1 (tar) [370 kB]
-Get:3 http://incoming.debian.org/debian/ unstable/main samtools 0.1.14-1 (diff) [6869 B]
-Fetched 379 kB in 1s (343 kB/s)
+Need to get 383 kB of source archives.
+Get:1 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.15-1 (dsc) [1939 B]
+Get:2 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.15-1 (tar) [374 kB]
+Get:3 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.15-1 (diff) [7005 B]
+Fetched 383 kB in 0s (5078 kB/s)
Download complete and in download only mode
Check arch
@@ -835,16 +854,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.14.5-2)
+fakeroot: already installed (1.15.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
-0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
-0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -865,10 +886,10 @@ e2fsprogs: already installed (1.41.12-2)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.6.3-3)
gzip: already installed (1.3.12-9)
-hostname: already installed (3.05)
-ncurses-base: already installed (5.7+20100313-5)
-ncurses-bin: already installed (5.7+20100313-5)
-perl-base: already installed (5.10.1-17)
+hostname: already installed (3.06)
+ncurses-base: already installed (5.8+20110307-1)
+ncurses-bin: already installed (5.8+20110307-1)
+perl-base: already installed (5.10.1-19)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.1)
@@ -878,12 +899,12 @@ bsdutils: already installed (1:2.17.2-9.1)
mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
libc6-dev: already installed (2.11.2-11)
-gcc: already installed (4:4.4.5-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-2 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.4.5-7 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.4.5-6 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8)
-dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.0 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.2
+Using default version 8.1.3
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -891,66 +912,46 @@ Checking for dependency conflicts...
Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
+Reading state information...
The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libncurses5 libpcre3 libpipeline1
- libunistring0 libxml2 man-db ncurses-bin po-debconf
+ file gettext gettext-base groff-base html2text intltool-debian libcroco3
+ libglib2.0-0 libmagic1 libncurses5 libpcre3 libpipeline1 libunistring0
+ libxml2 man-db ncurses-bin po-debconf
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff ncurses-doc less www-browser libmail-box-perl
+ devscripts doc-base dh-make gettext-doc groff ncurses-doc less www-browser
+ libmail-box-perl
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
+ cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
The following packages will be upgraded:
libncurses5 ncurses-bin
-2 upgraded, 20 newly installed, 0 to remove and 27 not upgraded.
-Need to get 11.5 MB of archives.
-After this operation, 32.7 MB of additional disk space will be used.
-Get:1 http://mirror.ayous.org/debian/ unstable/main ncurses-bin mipsel 5.8+20110307-1 [328 kB]
-Get:2 http://mirror.ayous.org/debian/ unstable/main libncurses5 mipsel 5.8+20110307-1 [358 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.2 [207 kB]
-Get:4 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-5 [1154 kB]
-Get:5 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-1 [35.1 kB]
-Get:6 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.5.9-4 [980 kB]
-Get:7 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.04-5 [238 kB]
-Get:8 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.04-5 [49.5 kB]
-Get:9 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152 kB]
-Get:10 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-3 [262 kB]
-Get:11 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-2 [833 kB]
-Get:12 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
-Get:13 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.2-1 [1496 kB]
-Get:14 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
-Get:15 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-3 [411 kB]
-Get:16 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023 kB]
-Get:17 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:19 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.1.2 [553 kB]
-Get:20 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
-Get:21 http://mirror.ayous.org/debian/ unstable/main libncurses5-dev mipsel 5.8+20110307-1 [505 kB]
-Get:22 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
+2 upgraded, 19 newly installed, 0 to remove and 12 not upgraded.
+Need to get 1193 kB/11.3 MB of archives.
+After this operation, 31.9 MB of additional disk space will be used.
+Get:1 http://debian.oregonstate.edu/debian/ sid/main ncurses-bin mipsel 5.9-1 [329 kB]
+Get:2 http://debian.oregonstate.edu/debian/ sid/main libncurses5 mipsel 5.9-1 [359 kB]
+Get:3 http://debian.oregonstate.edu/debian/ sid/main libncurses5-dev mipsel 5.9-1 [506 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.5 MB in 1s (8242 kB/s)
-(Reading database ... 10176 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.7+20100313-5 (using .../ncurses-bin_5.8+20110307-1_mipsel.deb) ...
+Fetched 1193 kB in 0s (7682 kB/s)
+(Reading database ... 10374 files and directories currently installed.)
+Preparing to replace ncurses-bin 5.8+20110307-1 (using .../ncurses-bin_5.9-1_mipsel.deb) ...
Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.8+20110307-1) ...
-(Reading database ... 10177 files and directories currently installed.)
-Preparing to replace libncurses5 5.7+20100313-5 (using .../libncurses5_5.8+20110307-1_mipsel.deb) ...
+Setting up ncurses-bin (5.9-1) ...
+(Reading database ... 10374 files and directories currently installed.)
+Preparing to replace libncurses5 5.8+20110307-1 (using .../libncurses5_5.9-1_mipsel.deb) ...
Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.8+20110307-1) ...
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 10176 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_mipsel.deb) ...
+Setting up libncurses5 (5.9-1) ...
Selecting previously deselected package groff-base.
+(Reading database ... 10374 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.21-5_mipsel.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_mipsel.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.9-4_mipsel.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.1-1_mipsel.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_mipsel.deb) ...
Selecting previously deselected package file.
@@ -964,7 +965,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_mipsel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.2-1_mipsel.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_mipsel.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mipsel.deb) ...
Selecting previously deselected package libunistring0.
@@ -976,19 +977,16 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.3_all.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_mipsel.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_mipsel.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
-Setting up bsdmainutils (8.2.2) ...
-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 groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.5.9-4) ...
+Setting up man-db (2.6.0.1-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
@@ -996,26 +994,26 @@ Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.2-1) ...
+Setting up libglib2.0-0 (2.28.4-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
+Setting up debhelper (8.1.3) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8+20110307-1) ...
+Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 27 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.20.1-16 dpkg-dev_1.15.8.10 g++-4.4_4.4.5-10 gcc-4.4_4.4.5-10 libc6-dev_2.11.2-11 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 linux-libc-dev_2.6.37-1
-Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgdbm3_1.8.3-9 libglib2.0-0_2.28.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-10 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-6 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0 g++-4.4_4.4.5-15 gcc-4.4_4.4.5-15 libc6-dev_2.11.2-11 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 linux-libc-dev_2.6.38-2
+Package versions: apt_0.8.13.2 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.4.5-7 cpp-4.4_4.4.5-15 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.63-3 dpkg_1.15.8.10 dpkg-dev_1.16.0 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-6 g++-4.4_4.4.5-15 gcc_4:4.4.5-7 gcc-4.4_4.4.5-15 gcc-4.4-base_4.4.5-15 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdevmapper1.02.1_2:1.02.63-3 libdpkg-perl_1.16.0 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.3-3 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_167-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011e-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -1025,13 +1023,14 @@ Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.14
-dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.15-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.15
+dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
Check disc space
────────────────
@@ -1040,41 +1039,50 @@ Check disc space
dpkg-buildpackage
─────────────────
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.14-1
- dpkg-source --before-build samtools-0.1.14
+dpkg-buildpackage: source version 0.1.15-1
+ dpkg-source --before-build samtools-0.1.15
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/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 `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
rm -f debian/stamp-makefile-check
dh_clean
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
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -1088,15 +1096,16 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
+ar -cru 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 glf.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 `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -1107,10 +1116,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -1128,25 +1137,26 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -1156,14 +1166,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -1187,14 +1197,18 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samto
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-sample depth to 8000
+<mpileup> Set max per-file depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
dh_prep
@@ -1226,7 +1240,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -1251,7 +1265,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -1266,65 +1280,68 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.15-1_mipsel.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org> >../samtools_0.1.14-1_mipsel.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.15-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.15-1_mipsel.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-0.1.14
+ dpkg-source --after-build samtools-0.1.15
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110329-0853
+Build finished at 20110412-1814
-samtools_0.1.14-1_mipsel.changes:
+samtools_0.1.15-1_mipsel.changes:
Format: 1.8
-Date: Tue, 29 Mar 2011 13:13:54 +0900
+Date: Tue, 12 Apr 2011 19:44:41 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.14-1
+Version: 0.1.15-1
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org>
+Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
Changed-By: Charles Plessy <plessy at 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 (0.1.14-1) unstable; urgency=low
+ samtools (0.1.15-1) unstable; urgency=low
.
* New upstream release.
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.2
+ (debian/control, no changes needed).
+ * debian/watch directly interrogates and downloads froms SourceForge.
Checksums-Sha1:
- 9e4876fbec4a8ba07353e394d60e72d6da104720 628462 samtools_0.1.14-1_mipsel.deb
- 80c9f71040529d13aa4b9f6e3012e56dc60d2688 180964 libbam-dev_0.1.14-1_mipsel.deb
+ e8a2a36bd95a0cace6b5fb0668887ea0a57ad039 630590 samtools_0.1.15-1_mipsel.deb
+ a4ef0498879bab0e622fd6ff0b2734c2ea9d2c78 185178 libbam-dev_0.1.15-1_mipsel.deb
Checksums-Sha256:
- d51b6a383c05ef3dfbd9f229300fa99faea0d5a98a86b808be5cd60da486ad2a 628462 samtools_0.1.14-1_mipsel.deb
- 3b9e78a078eb961b6f1f99c28f610ddef53093bd61788d22eb208173450fb20f 180964 libbam-dev_0.1.14-1_mipsel.deb
+ 39dba8e0ce67feb495e581be4f491fe0bb43c5e7ba10400d57f447f3f5b8e8bc 630590 samtools_0.1.15-1_mipsel.deb
+ be1db8a82299c4b8ac98d381c27aa983166bd5521bf8b16e8a5abbad848a2ee3 185178 libbam-dev_0.1.15-1_mipsel.deb
Files:
- 373e112e5c09eea2a44f8b96ae9a19a5 628462 science optional samtools_0.1.14-1_mipsel.deb
- 31c974e3d03e4840586b0ba41f8259c8 180964 libdevel optional libbam-dev_0.1.14-1_mipsel.deb
+ a99f620ad1d711deed10c0ecd08e5179 630590 science optional samtools_0.1.15-1_mipsel.deb
+ 0dfecb73c451d8002b5cf5d9201a842e 185178 libdevel optional libbam-dev_0.1.15-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.14-1_mipsel.deb
+samtools_0.1.15-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 628462 bytes: control archive= 1787 bytes.
+ size 630590 bytes: control archive= 1789 bytes.
787 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1208
+ Installed-Size: 1228
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -1337,71 +1354,71 @@ samtools_0.1.14-1_mipsel.deb
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 2011-03-29 08:52 ./
-drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/lib/samtools/
--rwxr-xr-x root/root 9768 2011-03-29 08:53 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7764 2011-03-29 08:53 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 19944 2011-03-29 08:53 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 13268 2011-03-29 08:53 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7764 2011-03-29 08:53 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-03-29 08:52 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 2005 2011-03-29 08:52 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 8393 2011-03-29 08:52 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2011-03-29 08:53 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-04-12 18:13 ./
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 18:13 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 126609 2011-03-29 08:52 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 1966 2011-03-29 08:52 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2011-04-12 18:13 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/bin/
--rwxr-xr-x root/root 465228 2011-03-29 08:53 ./usr/bin/samtools
--rwxr-xr-x root/root 133584 2011-03-29 08:53 ./usr/bin/bcftools
--rwxr-xr-x root/root 30584 2011-03-29 08:53 ./usr/bin/razip
-
-
-libbam-dev_0.1.14-1_mipsel.deb
+-rw-r--r-- root/root 1966 2011-04-12 18:14 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-04-12 18:13 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-04-12 18:13 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8393 2011-04-12 18:13 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 2005 2011-04-12 18:13 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/samtools/
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2011-04-12 18:14 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/bin/
+-rwxr-xr-x root/root 142088 2011-04-12 18:14 ./usr/bin/bcftools
+-rwxr-xr-x root/root 30584 2011-04-12 18:14 ./usr/bin/razip
+-rwxr-xr-x root/root 477880 2011-04-12 18:14 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/lib/
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19960 2011-04-12 18:14 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7764 2011-04-12 18:14 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7764 2011-04-12 18:14 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 13268 2011-04-12 18:14 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 9768 2011-04-12 18:14 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.15-1_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 180964 bytes: control archive= 906 bytes.
+ size 185178 bytes: control archive= 894 bytes.
675 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 460
+ Installed-Size: 472
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -1412,23 +1429,23 @@ libbam-dev_0.1.14-1_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-29 08:52 ./
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/include/
--rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
--rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/lib/
--rw-r--r-- root/root 309810 2011-03-29 08:53 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/lib/
+-rw-r--r-- root/root 320036 2011-04-12 18:14 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/include/
+-rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/bgzf.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1442,26 +1459,70 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-16618150-cfe1-42f6-875a-1aca472b2e4a/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-ef7274bc-3984-429a-b457-5c8f9ccc646c/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ cdbs* debhelper* file* gettext* gettext-base* groff-base* html2text*
+ intltool-debian* libcroco3* libglib2.0-0* libmagic1* libncurses5-dev*
+ libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf*
+ zlib1g-dev*
+0 upgraded, 0 newly installed, 19 to remove and 12 not upgraded.
+After this operation, 31.9 MB disk space will be freed.
+(Reading database ... 11702 files and directories currently installed.)
+Removing cdbs ...
+Removing debhelper ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libcroco3 ...
+Purging configuration files for libcroco3 ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libmagic1 ...
+Purging configuration files for libmagic1 ...
+Removing libncurses5-dev ...
+Removing libpcre3 ...
+Purging configuration files for libpcre3 ...
+Removing libpipeline1 ...
+Purging configuration files for libpipeline1 ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing zlib1g-dev ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 9952
-Build-Time: 237
+Build-Space: 10128
+Build-Time: 241
Distribution: sid
-Install-Time: 61
-Job: samtools_0.1.14-1
+Install-Time: 53
+Job: samtools_0.1.15-1
Package: samtools
-Package-Time: 374
-Source-Version: 0.1.14-1
-Space: 9952
+Package-Time: 326
+Source-Version: 0.1.15-1
+Space: 10128
Status: successful
-Version: 0.1.14-1
+Version: 0.1.15-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110329-0853
-Build needed 00:06:14, 9952k disc space
+Finished at 20110412-1814
+Build needed 00:05:26, 10128k disc space
+Signature with key '68D1B022' requested:
diff --git a/mipsel.log b/mipsel.log
index 633972e..3ed34d6 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,66 +1,65 @@
-From buildd at rem.debian.org Tue Mar 29 08:53:36 2011
-Return-path: <buildd at rem.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at mayer.debian.org Tue Apr 12 18:15:03 2011
+Return-path: <buildd at mayer.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at rem.debian.org>)
- id 1Q4UgB-0005mD-5O
- for logs at buildd.debian.org; Tue, 29 Mar 2011 08:53:35 +0000
-Received: from rem.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d06])
+ (Exim 4.69) (envelope-from <buildd at mayer.debian.org>)
+ id 1Q9i7D-0002Va-BU
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 18:15:03 +0000
+Received: from mayer.debian.org ([140.211.166.78])
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- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
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-Date: Tue, 29 Mar 2011 08:53:28 +0000
-Message-Id: <E1Q4Ug4-0004pX-IW at rem.debian.org>
-From: buildd on rem <buildd at rem.debian.org>
-To: aba+buildd_rem at not.so.argh.org,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.14-1 on mipsel (dist=sid)
+ CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
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+ id 1Q9i73-00020h-1Z; Tue, 12 Apr 2011 18:14:53 +0000
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+To: buildd-porters at mayer.debian.org,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.15-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
+Message-Id: <E1Q9i73-00020h-1Z at mayer.debian.org>
+Date: Tue, 12 Apr 2011 18:14:53 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rem.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.14-1 (mipsel) 29 Mar 2011 08:47 ║
+║ samtools 0.1.15-1 (mipsel) 12 Apr 2011 18:09 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.14-1
-Source Version: 0.1.14-1
+Version: 0.1.15-1
+Source Version: 0.1.15-1
Architecture: mipsel
-Get:1 http://mirror.ayous.org unstable InRelease [185 kB]
-Get:2 http://incoming.debian.org unstable InRelease [186 kB]
-Get:3 http://mirror.ayous.org unstable/main Sources [5142 kB]
-Get:4 http://mirror.ayous.org unstable/contrib Sources [47.4 kB]
-Get:5 http://mirror.ayous.org unstable/non-free Sources [99.4 kB]
-Get:6 http://mirror.ayous.org unstable/main mipsel Packages [6872 kB]
+Hit http://debian.oregonstate.edu sid InRelease
+Hit http://debian.oregonstate.edu sid/main Sources
+Hit http://debian.oregonstate.edu sid/contrib Sources
+Hit http://debian.oregonstate.edu sid/main mipsel Packages
+Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
+Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
+Hit http://debian.oregonstate.edu sid/main TranslationIndex
+Ign http://debian.oregonstate.edu sid/contrib Translation-en
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://incoming.debian.org Release [1604 B]
-Get:9 http://incoming.debian.org unstable/main Sources [5140 kB]
-Get:10 http://mirror.ayous.org unstable/contrib mipsel Packages [52.2 kB]
-Ign http://mirror.ayous.org unstable/contrib TranslationIndex
-Get:11 http://mirror.ayous.org unstable/main TranslationIndex [2232 B]
-Ign http://mirror.ayous.org unstable/contrib Translation-en
-Get:12 http://incoming.debian.org unstable/contrib Sources [47.4 kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
-Get:14 http://incoming.debian.org unstable/main mipsel Packages [6869 kB]
-Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [52.2 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:16 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
-Get:17 http://incoming.debian.org Sources [29.5 kB]
-Get:18 http://incoming.debian.org Packages [637 kB]
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Hit http://incoming.debian.org sid/main Sources
+Hit http://incoming.debian.org sid/contrib Sources
+Hit http://incoming.debian.org sid/main mipsel Packages
+Hit http://incoming.debian.org sid/contrib mipsel Packages
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Hit http://incoming.debian.org sid/main TranslationIndex
+Get:2 http://incoming.debian.org Release [1604 B]
+Get:3 http://incoming.debian.org Sources [44.6 kB]
+Get:4 http://incoming.debian.org Packages [720 kB]
+Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 25.5 MB in 44s (567 kB/s)
+Fetched 767 kB in 3s (206 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -78,13 +77,14 @@ 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://git.debian.org/debian-med/samtools.git
-Need to get 379 kB of source archives.
-Get:1 http://incoming.debian.org/debian/ unstable/main samtools 0.1.14-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/debian/ unstable/main samtools 0.1.14-1 (tar) [370 kB]
-Get:3 http://incoming.debian.org/debian/ unstable/main samtools 0.1.14-1 (diff) [6869 B]
-Fetched 379 kB in 1s (343 kB/s)
+Need to get 383 kB of source archives.
+Get:1 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.15-1 (dsc) [1939 B]
+Get:2 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.15-1 (tar) [374 kB]
+Get:3 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.15-1 (diff) [7005 B]
+Fetched 383 kB in 0s (5078 kB/s)
Download complete and in download only mode
Check arch
@@ -98,16 +98,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.14.5-2)
+fakeroot: already installed (1.15.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
-0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
-0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -128,10 +130,10 @@ e2fsprogs: already installed (1.41.12-2)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.6.3-3)
gzip: already installed (1.3.12-9)
-hostname: already installed (3.05)
-ncurses-base: already installed (5.7+20100313-5)
-ncurses-bin: already installed (5.7+20100313-5)
-perl-base: already installed (5.10.1-17)
+hostname: already installed (3.06)
+ncurses-base: already installed (5.8+20110307-1)
+ncurses-bin: already installed (5.8+20110307-1)
+perl-base: already installed (5.10.1-19)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.1)
@@ -141,12 +143,12 @@ bsdutils: already installed (1:2.17.2-9.1)
mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
libc6-dev: already installed (2.11.2-11)
-gcc: already installed (4:4.4.5-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-2 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.4.5-7 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.4.5-6 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8)
-dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.0 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.2
+Using default version 8.1.3
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -154,66 +156,46 @@ Checking for dependency conflicts...
Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
+Reading state information...
The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libncurses5 libpcre3 libpipeline1
- libunistring0 libxml2 man-db ncurses-bin po-debconf
+ file gettext gettext-base groff-base html2text intltool-debian libcroco3
+ libglib2.0-0 libmagic1 libncurses5 libpcre3 libpipeline1 libunistring0
+ libxml2 man-db ncurses-bin po-debconf
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff ncurses-doc less www-browser libmail-box-perl
+ devscripts doc-base dh-make gettext-doc groff ncurses-doc less www-browser
+ libmail-box-perl
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
+ cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
The following packages will be upgraded:
libncurses5 ncurses-bin
-2 upgraded, 20 newly installed, 0 to remove and 27 not upgraded.
-Need to get 11.5 MB of archives.
-After this operation, 32.7 MB of additional disk space will be used.
-Get:1 http://mirror.ayous.org/debian/ unstable/main ncurses-bin mipsel 5.8+20110307-1 [328 kB]
-Get:2 http://mirror.ayous.org/debian/ unstable/main libncurses5 mipsel 5.8+20110307-1 [358 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.2 [207 kB]
-Get:4 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-5 [1154 kB]
-Get:5 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-1 [35.1 kB]
-Get:6 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.5.9-4 [980 kB]
-Get:7 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.04-5 [238 kB]
-Get:8 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.04-5 [49.5 kB]
-Get:9 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152 kB]
-Get:10 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-3 [262 kB]
-Get:11 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-2 [833 kB]
-Get:12 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
-Get:13 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.2-1 [1496 kB]
-Get:14 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
-Get:15 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-3 [411 kB]
-Get:16 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023 kB]
-Get:17 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:19 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.1.2 [553 kB]
-Get:20 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
-Get:21 http://mirror.ayous.org/debian/ unstable/main libncurses5-dev mipsel 5.8+20110307-1 [505 kB]
-Get:22 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
+2 upgraded, 19 newly installed, 0 to remove and 12 not upgraded.
+Need to get 1193 kB/11.3 MB of archives.
+After this operation, 31.9 MB of additional disk space will be used.
+Get:1 http://debian.oregonstate.edu/debian/ sid/main ncurses-bin mipsel 5.9-1 [329 kB]
+Get:2 http://debian.oregonstate.edu/debian/ sid/main libncurses5 mipsel 5.9-1 [359 kB]
+Get:3 http://debian.oregonstate.edu/debian/ sid/main libncurses5-dev mipsel 5.9-1 [506 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.5 MB in 1s (8242 kB/s)
-(Reading database ... 10176 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.7+20100313-5 (using .../ncurses-bin_5.8+20110307-1_mipsel.deb) ...
+Fetched 1193 kB in 0s (7682 kB/s)
+(Reading database ... 10374 files and directories currently installed.)
+Preparing to replace ncurses-bin 5.8+20110307-1 (using .../ncurses-bin_5.9-1_mipsel.deb) ...
Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.8+20110307-1) ...
-(Reading database ... 10177 files and directories currently installed.)
-Preparing to replace libncurses5 5.7+20100313-5 (using .../libncurses5_5.8+20110307-1_mipsel.deb) ...
+Setting up ncurses-bin (5.9-1) ...
+(Reading database ... 10374 files and directories currently installed.)
+Preparing to replace libncurses5 5.8+20110307-1 (using .../libncurses5_5.9-1_mipsel.deb) ...
Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.8+20110307-1) ...
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 10176 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_mipsel.deb) ...
+Setting up libncurses5 (5.9-1) ...
Selecting previously deselected package groff-base.
+(Reading database ... 10374 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.21-5_mipsel.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_mipsel.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.9-4_mipsel.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.1-1_mipsel.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_mipsel.deb) ...
Selecting previously deselected package file.
@@ -227,7 +209,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_mipsel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.2-1_mipsel.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_mipsel.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mipsel.deb) ...
Selecting previously deselected package libunistring0.
@@ -239,19 +221,16 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.3_all.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_mipsel.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_mipsel.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
-Setting up bsdmainutils (8.2.2) ...
-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 groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.5.9-4) ...
+Setting up man-db (2.6.0.1-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
@@ -259,26 +238,26 @@ Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.2-1) ...
+Setting up libglib2.0-0 (2.28.4-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
+Setting up debhelper (8.1.3) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8+20110307-1) ...
+Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 27 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.20.1-16 dpkg-dev_1.15.8.10 g++-4.4_4.4.5-10 gcc-4.4_4.4.5-10 libc6-dev_2.11.2-11 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 linux-libc-dev_2.6.37-1
-Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgdbm3_1.8.3-9 libglib2.0-0_2.28.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-10 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-6 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0 g++-4.4_4.4.5-15 gcc-4.4_4.4.5-15 libc6-dev_2.11.2-11 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 linux-libc-dev_2.6.38-2
+Package versions: apt_0.8.13.2 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.4.5-7 cpp-4.4_4.4.5-15 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.63-3 dpkg_1.15.8.10 dpkg-dev_1.16.0 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-6 g++-4.4_4.4.5-15 gcc_4:4.4.5-7 gcc-4.4_4.4.5-15 gcc-4.4-base_4.4.5-15 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdevmapper1.02.1_2:1.02.63-3 libdpkg-perl_1.16.0 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.3-3 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_167-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011e-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -288,13 +267,14 @@ Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.14
-dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.15-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.15
+dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
Check disc space
────────────────
@@ -303,41 +283,50 @@ Check disc space
dpkg-buildpackage
─────────────────
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.14-1
- dpkg-source --before-build samtools-0.1.14
+dpkg-buildpackage: source version 0.1.15-1
+ dpkg-source --before-build samtools-0.1.15
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/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 `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
rm -f debian/stamp-makefile-check
dh_clean
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
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -351,15 +340,16 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
+ar -cru 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 glf.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 `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -370,10 +360,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -391,25 +381,26 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -419,14 +410,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -450,14 +441,18 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samto
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-sample depth to 8000
+<mpileup> Set max per-file depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
dh_prep
@@ -489,7 +484,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -514,7 +509,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -529,65 +524,68 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.15-1_mipsel.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org> >../samtools_0.1.14-1_mipsel.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.15-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.15-1_mipsel.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-0.1.14
+ dpkg-source --after-build samtools-0.1.15
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110329-0853
+Build finished at 20110412-1814
-samtools_0.1.14-1_mipsel.changes:
+samtools_0.1.15-1_mipsel.changes:
Format: 1.8
-Date: Tue, 29 Mar 2011 13:13:54 +0900
+Date: Tue, 12 Apr 2011 19:44:41 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.14-1
+Version: 0.1.15-1
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org>
+Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
Changed-By: Charles Plessy <plessy at 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 (0.1.14-1) unstable; urgency=low
+ samtools (0.1.15-1) unstable; urgency=low
.
* New upstream release.
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.2
+ (debian/control, no changes needed).
+ * debian/watch directly interrogates and downloads froms SourceForge.
Checksums-Sha1:
- 9e4876fbec4a8ba07353e394d60e72d6da104720 628462 samtools_0.1.14-1_mipsel.deb
- 80c9f71040529d13aa4b9f6e3012e56dc60d2688 180964 libbam-dev_0.1.14-1_mipsel.deb
+ e8a2a36bd95a0cace6b5fb0668887ea0a57ad039 630590 samtools_0.1.15-1_mipsel.deb
+ a4ef0498879bab0e622fd6ff0b2734c2ea9d2c78 185178 libbam-dev_0.1.15-1_mipsel.deb
Checksums-Sha256:
- d51b6a383c05ef3dfbd9f229300fa99faea0d5a98a86b808be5cd60da486ad2a 628462 samtools_0.1.14-1_mipsel.deb
- 3b9e78a078eb961b6f1f99c28f610ddef53093bd61788d22eb208173450fb20f 180964 libbam-dev_0.1.14-1_mipsel.deb
+ 39dba8e0ce67feb495e581be4f491fe0bb43c5e7ba10400d57f447f3f5b8e8bc 630590 samtools_0.1.15-1_mipsel.deb
+ be1db8a82299c4b8ac98d381c27aa983166bd5521bf8b16e8a5abbad848a2ee3 185178 libbam-dev_0.1.15-1_mipsel.deb
Files:
- 373e112e5c09eea2a44f8b96ae9a19a5 628462 science optional samtools_0.1.14-1_mipsel.deb
- 31c974e3d03e4840586b0ba41f8259c8 180964 libdevel optional libbam-dev_0.1.14-1_mipsel.deb
+ a99f620ad1d711deed10c0ecd08e5179 630590 science optional samtools_0.1.15-1_mipsel.deb
+ 0dfecb73c451d8002b5cf5d9201a842e 185178 libdevel optional libbam-dev_0.1.15-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.14-1_mipsel.deb
+samtools_0.1.15-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 628462 bytes: control archive= 1787 bytes.
+ size 630590 bytes: control archive= 1789 bytes.
787 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1208
+ Installed-Size: 1228
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -600,71 +598,71 @@ samtools_0.1.14-1_mipsel.deb
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 2011-03-29 08:52 ./
-drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/lib/samtools/
--rwxr-xr-x root/root 9768 2011-03-29 08:53 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7764 2011-03-29 08:53 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 19944 2011-03-29 08:53 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 13268 2011-03-29 08:53 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7764 2011-03-29 08:53 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-03-29 08:52 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 2005 2011-03-29 08:52 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 8393 2011-03-29 08:52 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2011-03-29 08:53 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-04-12 18:13 ./
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 18:13 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 126609 2011-03-29 08:52 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 1966 2011-03-29 08:52 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2011-04-12 18:13 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/bin/
--rwxr-xr-x root/root 465228 2011-03-29 08:53 ./usr/bin/samtools
--rwxr-xr-x root/root 133584 2011-03-29 08:53 ./usr/bin/bcftools
--rwxr-xr-x root/root 30584 2011-03-29 08:53 ./usr/bin/razip
-
-
-libbam-dev_0.1.14-1_mipsel.deb
+-rw-r--r-- root/root 1966 2011-04-12 18:14 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-04-12 18:13 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-04-12 18:13 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8393 2011-04-12 18:13 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 2005 2011-04-12 18:13 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/samtools/
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2011-04-12 18:14 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/bin/
+-rwxr-xr-x root/root 142088 2011-04-12 18:14 ./usr/bin/bcftools
+-rwxr-xr-x root/root 30584 2011-04-12 18:14 ./usr/bin/razip
+-rwxr-xr-x root/root 477880 2011-04-12 18:14 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/lib/
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19960 2011-04-12 18:14 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7764 2011-04-12 18:14 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7764 2011-04-12 18:14 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 13268 2011-04-12 18:14 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 9768 2011-04-12 18:14 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.15-1_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 180964 bytes: control archive= 906 bytes.
+ size 185178 bytes: control archive= 894 bytes.
675 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 460
+ Installed-Size: 472
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -675,23 +673,23 @@ libbam-dev_0.1.14-1_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-29 08:52 ./
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/include/
--rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
--rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/lib/
--rw-r--r-- root/root 309810 2011-03-29 08:53 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/lib/
+-rw-r--r-- root/root 320036 2011-04-12 18:14 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/include/
+-rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/bgzf.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -705,26 +703,70 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-16618150-cfe1-42f6-875a-1aca472b2e4a/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-ef7274bc-3984-429a-b457-5c8f9ccc646c/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ cdbs* debhelper* file* gettext* gettext-base* groff-base* html2text*
+ intltool-debian* libcroco3* libglib2.0-0* libmagic1* libncurses5-dev*
+ libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf*
+ zlib1g-dev*
+0 upgraded, 0 newly installed, 19 to remove and 12 not upgraded.
+After this operation, 31.9 MB disk space will be freed.
+(Reading database ... 11702 files and directories currently installed.)
+Removing cdbs ...
+Removing debhelper ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libcroco3 ...
+Purging configuration files for libcroco3 ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libmagic1 ...
+Purging configuration files for libmagic1 ...
+Removing libncurses5-dev ...
+Removing libpcre3 ...
+Purging configuration files for libpcre3 ...
+Removing libpipeline1 ...
+Purging configuration files for libpipeline1 ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing zlib1g-dev ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 9952
-Build-Time: 237
+Build-Space: 10128
+Build-Time: 241
Distribution: sid
-Install-Time: 61
-Job: samtools_0.1.14-1
+Install-Time: 53
+Job: samtools_0.1.15-1
Package: samtools
-Package-Time: 374
-Source-Version: 0.1.14-1
-Space: 9952
+Package-Time: 326
+Source-Version: 0.1.15-1
+Space: 10128
Status: successful
-Version: 0.1.14-1
+Version: 0.1.15-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110329-0853
-Build needed 00:06:14, 9952k disc space
+Finished at 20110412-1814
+Build needed 00:05:26, 10128k disc space
+Signature with key '68D1B022' requested:
diff --git a/powerpc.log b/powerpc.log
index 0fbfd9e..4b022d4 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,69 +1,69 @@
-From buildd at poulenc.debian.org Tue Mar 29 05:01:41 2011
-Return-path: <buildd at poulenc.debian.org>
+From buildd at porpora.debian.org Tue Apr 12 11:35:48 2011
+Return-path: <buildd at porpora.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at poulenc.debian.org>)
- id 1Q4R3l-0002mh-1V
- for logs at buildd.debian.org; Tue, 29 Mar 2011 05:01:41 +0000
-Received: from poulenc.ynic.york.ac.uk ([144.32.168.77]
- helo=poulenc.debian.org)
+ (Exim 4.69) (envelope-from <buildd at porpora.debian.org>)
+ id 1Q9bsq-0007J9-85
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 11:35:48 +0000
+Received: from porpora.ynic.york.ac.uk ([144.32.168.78]
+ helo=porpora.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=poulenc.debian.org, EMAIL=hostmaster at poulenc.debian.org (verified)
+ CN=porpora.debian.org, EMAIL=hostmaster at porpora.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at poulenc.debian.org>)
- id 1Q4R3h-0003Ua-Lv; Tue, 29 Mar 2011 05:01:37 +0000
-Received: from buildd by poulenc.debian.org with local (Exim 4.69)
- (envelope-from <buildd at poulenc.debian.org>)
- id 1Q4R3f-0003qN-CA; Tue, 29 Mar 2011 05:01:35 +0000
+ (Exim 4.69) (envelope-from <buildd at porpora.debian.org>)
+ id 1Q9bsm-00050s-08; Tue, 12 Apr 2011 11:35:44 +0000
+Received: from buildd by porpora.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at porpora.debian.org>)
+ id 1Q9bsi-0003YH-RH; Tue, 12 Apr 2011 11:35:40 +0000
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
-Date: Tue, 29 Mar 2011 05:01:35 +0000
-From: buildd on poulenc <buildd at poulenc.debian.org>
+Date: Tue, 12 Apr 2011 11:35:40 +0000
+From: buildd on porpora <buildd at porpora.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.14-1 on powerpc (dist=sid)
-Key-Id: 205E9E83
-Message-Id: <E1Q4R3f-0003qN-CA at poulenc.debian.org>
+Subject: Log for successful build of samtools_0.1.15-1 on powerpc (dist=sid)
+Key-Id: CDFA0A89
+Message-Id: <E1Q9bsi-0003YH-RH at porpora.debian.org>
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on poulenc.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on porpora.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.14-1 (powerpc) 29 Mar 2011 04:58 ║
+║ samtools 0.1.15-1 (powerpc) 12 Apr 2011 11:32 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.14-1
-Source Version: 0.1.14-1
+Version: 0.1.15-1
+Source Version: 0.1.15-1
Architecture: powerpc
-Get:1 http://ftp.uk.debian.org unstable InRelease [184 kB]
-Get:2 http://ftp.uk.debian.org unstable/main Sources [5169 kB]
-Get:3 http://incoming.debian.org unstable InRelease [185 kB]
+Get:1 http://ftp.uk.debian.org unstable InRelease [151 kB]
+Get:2 http://incoming.debian.org unstable InRelease [151 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [5265 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [5142 kB]
-Get:6 http://ftp.uk.debian.org unstable/contrib Sources [47.0 kB]
-Get:7 http://ftp.uk.debian.org unstable/non-free Sources [99.0 kB]
-Get:8 http://ftp.uk.debian.org unstable/main powerpc Packages [6965 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib powerpc Packages [51.4 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5265 kB]
+Get:6 http://ftp.uk.debian.org unstable/contrib Sources [48.2 kB]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [97.4 kB]
+Get:8 http://ftp.uk.debian.org unstable/main powerpc Packages [7058 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [48.2 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [97.4 kB]
+Get:11 http://incoming.debian.org unstable/main powerpc Packages [7058 kB]
+Get:12 http://ftp.uk.debian.org unstable/contrib powerpc Packages [52.4 kB]
Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2232 B]
+Get:13 http://ftp.uk.debian.org unstable/main TranslationIndex [2264 B]
Ign http://ftp.uk.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [47.4 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
-Get:13 http://incoming.debian.org unstable/main powerpc Packages [6970 kB]
-Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [51.4 kB]
+Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [52.4 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [30.5 kB]
-Get:18 http://incoming.debian.org Packages [608 kB]
+Get:17 http://incoming.debian.org Sources [49.7 kB]
+Get:18 http://incoming.debian.org Packages [772 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 25.7 MB in 30s (851 kB/s)
+Fetched 26.2 MB in 28s (923 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +84,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 379 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (tar) [370 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (diff) [6869 B]
-Fetched 379 kB in 1s (325 kB/s)
+Need to get 383 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
+Fetched 383 kB in 1s (350 kB/s)
Download complete and in download only mode
Check arch
@@ -102,18 +102,24 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.14.5-2)
+fakeroot: already installed (1.15.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libppl7 libppl-c2
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libppl7 libppl-c2
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -137,7 +143,7 @@ gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.8-1)
ncurses-bin: already installed (5.8-1)
-perl-base: already installed (5.10.1-17)
+perl-base: already installed (5.10.1-18)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.1)
@@ -147,12 +153,12 @@ bsdutils: already installed (1:2.17.2-9.1)
mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
libc6-dev: already installed (2.11.2-11)
-gcc: already installed (4:4.5.2-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.5.2-2 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.5.2-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.5.2-4 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8)
dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.2
+Using default version 8.1.3
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -161,54 +167,61 @@ Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
+The following packages were automatically installed and are no longer required:
+ libppl7 libppl-c2
+Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ bsdmainutils dpkg-dev file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libdpkg-perl libglib2.0-0 libmagic1 libpcre3
+ libpipeline1 libunistring0 libxml2 man-db po-debconf
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff ncurses-doc less www-browser libmail-box-perl
+ wamerican wordlist whois vacation devscripts doc-base dh-make debian-keyring
+ gettext-doc groff ncurses-doc less www-browser libmail-box-perl
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ autotools-dev libalgorithm-merge-perl curl wget lynx-cur autopoint
+ libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 20 newly installed, 0 to remove and 28 not upgraded.
-Need to get 11.0 MB of archives.
-After this operation, 31.6 MB of additional disk space will be used.
+The following packages will be upgraded:
+ dpkg-dev libdpkg-perl
+2 upgraded, 20 newly installed, 0 to remove and 15 not upgraded.
+Need to get 12.7 MB of archives.
+After this operation, 31.8 MB of additional disk space will be used.
Get:1 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.2 [209 kB]
Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-5 [1189 kB]
Get:3 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-1 [37.2 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.5.9-4 [1001 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.0.1-1 [1018 kB]
Get:5 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.04-5 [241 kB]
Get:6 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.04-5 [49.9 kB]
Get:7 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-3 [141 kB]
Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-3 [258 kB]
Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-2 [849 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.2-1 [1598 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-1 [128 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-3 [422 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-3 [2046 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.1.2 [553 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.8-1 [500 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main dpkg-dev powerpc 1.16.0.1 [871 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libdpkg-perl powerpc 1.16.0.1 [748 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.4-1 [1601 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-1 [128 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-3 [422 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-3 [2046 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian powerpc 0.35.0+20060710.1 [30.8 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main po-debconf powerpc 1.0.16+nmu1 [223 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main debhelper powerpc 8.1.3 [554 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main cdbs powerpc 0.4.92 [1268 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.8-1 [500 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.0 MB in 1s (6030 kB/s)
+Fetched 12.7 MB in 8s (1421 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10319 files and directories currently installed.)
+(Reading database ... 10241 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_powerpc.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-5_powerpc.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_powerpc.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.9-4_powerpc.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.1-1_powerpc.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_powerpc.deb) ...
Selecting previously deselected package file.
@@ -219,10 +232,14 @@ Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_powerpc.deb) ...
Selecting previously deselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_powerpc.deb) ...
+Preparing to replace dpkg-dev 1.15.8.10 (using .../dpkg-dev_1.16.0.1_powerpc.deb) ...
+Unpacking replacement dpkg-dev ...
+Preparing to replace libdpkg-perl 1.15.8.10 (using .../libdpkg-perl_1.16.0.1_powerpc.deb) ...
+Unpacking replacement libdpkg-perl ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.2-1_powerpc.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_powerpc.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_powerpc.deb) ...
Selecting previously deselected package libunistring0.
@@ -230,13 +247,13 @@ Unpacking libunistring0 (from .../libunistring0_0.9.3-3_powerpc.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_powerpc.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_powerpc.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_powerpc.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.3_powerpc.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Unpacking cdbs (from .../cdbs_0.4.92_powerpc.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.8-1_powerpc.deb) ...
Selecting previously deselected package zlib1g-dev.
@@ -246,22 +263,24 @@ update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write)
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.5.9-4) ...
+Setting up man-db (2.6.0.1-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up libdpkg-perl (1.16.0.1) ...
+Setting up dpkg-dev (1.16.0.1) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.2-1) ...
+Setting up libglib2.0-0 (2.28.4-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
+Setting up debhelper (8.1.3) ...
Setting up cdbs (0.4.92) ...
Setting up libncurses5-dev (5.8-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -269,11 +288,14 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libppl7 libppl-c2
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.26-2-powerpc64 powerpc (ppc64)
-Toolchain package versions: binutils_2.21.0.20110302-1 dpkg-dev_1.15.8.10 g++-4.5_4.5.2-5 gcc-4.5_4.5.2-5 libc6-dev_2.11.2-11 libstdc++6_4.5.2-5 libstdc++6-4.5-dev_4.5.2-5 linux-libc-dev_2.6.37-2
-Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110302-1 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.5.2-2 cpp-4.5_4.5.2-5 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-2 g++-4.5_4.5.2-5 gcc_4:4.5.2-2 gcc-4.4-base_4.4.5-13 gcc-4.5_4.5.2-5 gcc-4.5-base_4.5.2-5 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.5.2-5 libgdbm3_1.8.3-9 libglib2.0-0_2.28.2-1 libgmp10_2:5.0.1+dfsg-6 libgmp3c2_2:4.3.2+dfsg-1 libgmpxx4ldbl_2:5.0.1+dfsg-6 libgomp1_4.5.2-5 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-1 libmpfr4_3.0.0-9 libncurses5_5.8-1 libncurses5-dev_5.8-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c2_0.10.2-9 libppl-c4_0.11.2-1 libppl7_0.10.2-9 libppl9_0.11.2-1 libpwl5_0.11.2-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-5 libstdc++6-4.5-dev_4.5.2-5 libtext-charwidth-perl_0.04-6+b1 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8-1 ncurses-bin_5.8-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011c-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0.1 g++-4.5_4.5.2-8 gcc-4.5_4.5.2-8 libc6-dev_2.11.2-11 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8 linux-libc-dev_2.6.38-2
+Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.5.2-4 cpp-4.5_4.5.2-8 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-4 g++-4.5_4.5.2-8 gcc_4:4.5.2-4 gcc-4.4-base_4.4.5-15 gcc-4.5_4.5.2-8 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0.1 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-2 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.8-1 libncurses5-dev_5.8-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c2_0.10.2-9 libppl-c4_0.11.2-3 libppl7_0.10.2-9 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8 libtext-charwidth-perl_0.04-6+b1 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8-1 ncurses-bin_5.8-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011d-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -285,12 +307,12 @@ Unpack source
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.14
-dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.15-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.15
+dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
Check disc space
────────────────
@@ -306,8 +328,8 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.14-1
- dpkg-source --before-build samtools-0.1.14
+dpkg-buildpackage: source version 0.1.15-1
+ dpkg-source --before-build samtools-0.1.15
dpkg-buildpackage: host architecture powerpc
fakeroot debian/rules clean
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -318,17 +340,17 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/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 `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -341,8 +363,8 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -356,15 +378,16 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/bcftools'
+ar -cru 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 glf.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 `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -375,10 +398,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -396,25 +419,26 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/misc'
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/misc'
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/misc'
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -424,14 +448,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -455,12 +479,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samt
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-sample depth to 8000
+<mpileup> Set max per-file depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/examples'
fakeroot debian/rules binary-arch
touch debian/stamp-makefile-check
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -498,7 +522,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -523,7 +547,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -538,65 +562,68 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_powerpc.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.15-1_powerpc.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org> >../samtools_0.1.14-1_powerpc.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.15-1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org> >../samtools_0.1.15-1_powerpc.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-0.1.14
+ dpkg-source --after-build samtools-0.1.15
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110329-0501
+Build finished at 20110412-1135
-samtools_0.1.14-1_powerpc.changes:
+samtools_0.1.15-1_powerpc.changes:
Format: 1.8
-Date: Tue, 29 Mar 2011 13:13:54 +0900
+Date: Tue, 12 Apr 2011 19:44:41 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: powerpc
-Version: 0.1.14-1
+Version: 0.1.15-1
Distribution: sid
Urgency: low
-Maintainer: powerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org>
+Maintainer: powerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org>
Changed-By: Charles Plessy <plessy at 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 (0.1.14-1) unstable; urgency=low
+ samtools (0.1.15-1) unstable; urgency=low
.
* New upstream release.
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.2
+ (debian/control, no changes needed).
+ * debian/watch directly interrogates and downloads froms SourceForge.
Checksums-Sha1:
- 23f92911b4f4f57644ffd0f2e6b7249a2489217a 609078 samtools_0.1.14-1_powerpc.deb
- 155eed0613b949db7c19842579721f9745defab3 169584 libbam-dev_0.1.14-1_powerpc.deb
+ a131f3d15c4a55537e1a1b782d31412a85f03ebc 609838 samtools_0.1.15-1_powerpc.deb
+ b4c70804d95b277476351ef26cf1d6c83eceaec5 173522 libbam-dev_0.1.15-1_powerpc.deb
Checksums-Sha256:
- 038c075d8da67f36a5a3e2d0e91a9d8d2ea1d53084f1c0f786dc5b1665c40935 609078 samtools_0.1.14-1_powerpc.deb
- 3b19a3483170e5d5186f72c3e3ea8e8ea2c19a6a120451a0206aa925ab9ce468 169584 libbam-dev_0.1.14-1_powerpc.deb
+ fb1f28cd6f680e385afaa707b535ec6023013f3717f84d841af215ad859bd6c8 609838 samtools_0.1.15-1_powerpc.deb
+ d8fae678d0ca71b94adaa13baf7bf17f05efe02ee348eb41c5b49d06f0792ff5 173522 libbam-dev_0.1.15-1_powerpc.deb
Files:
- 7e04dd9c3b726829131ba2c5de342e2f 609078 science optional samtools_0.1.14-1_powerpc.deb
- 1296c5bfc7f112820687d8b006d4f477 169584 libdevel optional libbam-dev_0.1.14-1_powerpc.deb
+ a5c5027cf691b194c741fdce56a9d158 609838 science optional samtools_0.1.15-1_powerpc.deb
+ cb4fb89242d0277f45b11cf192e27c3e 173522 libdevel optional libbam-dev_0.1.15-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.14-1_powerpc.deb
+samtools_0.1.15-1_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 609078 bytes: control archive= 1788 bytes.
+ size 609838 bytes: control archive= 1785 bytes.
788 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1100
+ Installed-Size: 1120
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -609,71 +636,71 @@ samtools_0.1.14-1_powerpc.deb
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 2011-03-29 05:01 ./
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/man/man1/
--rw-r--r-- root/root 8393 2011-03-29 05:01 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 2005 2011-03-29 05:01 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 430 2011-03-29 05:01 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/samtools/
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 5778 2011-03-29 05:01 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/bin/
+-rwxr-xr-x root/root 116632 2011-04-12 11:35 ./usr/bin/bcftools
+-rwxr-xr-x root/root 402604 2011-04-12 11:35 ./usr/bin/samtools
+-rwxr-xr-x root/root 26824 2011-04-12 11:35 ./usr/bin/razip
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/samtools/
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 5778 2011-04-12 11:35 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/samtools/
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/man/man1/
+-rw-r--r-- root/root 2005 2011-04-12 11:35 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 8393 2011-04-12 11:35 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-04-12 11:35 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/doc/samtools/
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 1966 2011-03-29 05:01 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 126609 2011-03-29 05:01 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2011-04-12 11:35 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/lib/samtools/
--rwxr-xr-x root/root 7368 2011-03-29 05:01 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 11148 2011-03-29 05:01 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7992 2011-03-29 05:01 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7384 2011-03-29 05:01 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 19668 2011-03-29 05:01 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/bin/
--rwxr-xr-x root/root 392096 2011-03-29 05:01 ./usr/bin/samtools
--rwxr-xr-x root/root 26824 2011-03-29 05:01 ./usr/bin/razip
--rwxr-xr-x root/root 109892 2011-03-29 05:01 ./usr/bin/bcftools
-
-
-libbam-dev_0.1.14-1_powerpc.deb
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1966 2011-04-12 11:35 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/lib/
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19668 2011-04-12 11:35 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7992 2011-04-12 11:35 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7384 2011-04-12 11:35 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 7368 2011-04-12 11:35 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 11148 2011-04-12 11:35 ./usr/lib/samtools/md5fa
+
+
+libbam-dev_0.1.15-1_powerpc.deb
───────────────────────────────
new debian package, version 2.0.
- size 169584 bytes: control archive= 906 bytes.
+ size 173522 bytes: control archive= 896 bytes.
676 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 420
+ Installed-Size: 428
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -684,23 +711,23 @@ libbam-dev_0.1.14-1_powerpc.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/include/
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/include/
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
--rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
--rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
-drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/lib/
--rw-r--r-- root/root 269610 2011-03-29 05:01 ./usr/lib/libbam.a
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/bgzf.h
+-rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
+drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/lib/
+-rw-r--r-- root/root 278472 2011-04-12 11:35 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -714,7 +741,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-7ce15bea-2f5e-46ec-b54c-eef9e9ac79e5/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-210a4603-30fd-4fa4-a922-fee45f8bbba1/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -722,18 +749,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: powerpc
-Build-Space: 10164
-Build-Time: 78
+Build-Space: 10328
+Build-Time: 88
Distribution: sid
-Install-Time: 63
-Job: samtools_0.1.14-1
+Install-Time: 79
+Job: samtools_0.1.15-1
Package: samtools
-Package-Time: 187
-Source-Version: 0.1.14-1
-Space: 10164
+Package-Time: 214
+Source-Version: 0.1.15-1
+Space: 10328
Status: successful
-Version: 0.1.14-1
+Version: 0.1.15-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110329-0501
-Build needed 00:03:07, 10164k disc space
-Signature with key '205E9E83' requested:
+Finished at 20110412-1135
+Build needed 00:03:34, 10328k disc space
+Signature with key 'CDFA0A89' requested:
diff --git a/powerpcspe.log b/powerpcspe.log
deleted file mode 100644
index 3af7e2d..0000000
--- a/powerpcspe.log
+++ /dev/null
@@ -1,676 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><title>File `log' in samtools_0.1.12a-1_powerpcspe (Dec 3 17:51)</title><meta http-equiv="content-type" content="text/html;charset=utf-8"></head><body bgcolor="#ffffff">
-<table width="100%"><tr valign=top><td align=left><h2>File `log' in samtools_0.1.12a-1_powerpcspe (Dec 3 17:51)</h2></td><td align=right><a href="build.php?&pkg=samtools&arch=powerpcspe">samtools</a> >> <a href="build.php?&pkg=samtools&ver=0.1.12a-1&arch=powerpcspe">0.1.12a-1</a> >> <a href="build.php?&pkg=samtools&ver=0.1.12a-1&arch=powerpcspe&stamp=1291398710">Dec 3 17:51</a> >> log</td></tr></table><p><pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on baako.tec.linutronix.de
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (powerpcspe) 04 Dec 2010 18:45 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.12a-1
-Architecture: powerpcspe
-Chroot Build Dir: /var/lib/schroot/mount/spestage-0fea459c-6bbb-4543-9144-91e0da2cf54a/spestage/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ
-Start Time: 20101204-1845
-Hit http://merkur sid Release.gpg
-Hit http://merkur sid Release.gpg
-Ign http://merkur/debian/debian-ports/ sid/main Translation-en
-Hit http://merkur unreleased Release.gpg
-Ign http://merkur/debian/debian-ports/ unreleased/main Translation-en
-Hit http://merkur sid Release
-Hit http://merkur sid Release
-Hit http://merkur unreleased Release
-Hit http://merkur sid/main Sources/DiffIndex
-Hit http://ftp.de.debian.org sid Release.gpg
-Get:1 http://incoming.debian-ports.org unstable Release.gpg [835 B]
-Ign http://incoming.debian-ports.org/buildd/ unstable/main Translation-en
-Hit http://merkur sid/main powerpcspe Packages
-Hit http://merkur unreleased/main powerpcspe Packages
-Hit http://ftp.de.debian.org sid Release
-Get:2 http://incoming.debian-ports.org unstable Release [8817 B]
-Hit http://ftp.de.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian-ports.org unstable/main Sources
-Hit http://incoming.debian-ports.org unstable/main powerpcspe Packages
-Fetched 9652 B in 1s (5146 B/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://git.debian.org/debian-med/samtools.git
-Need to get 364 kB of source archives.
-Get:1 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.12a-1 (dsc) [1946 B]
-Get:2 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.12a-1 (tar) [356 kB]
-Get:3 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.12a-1 (diff) [6337 B]
-Fetched 364 kB in 1s (206 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Checking for already installed source dependencies...
-debhelper: missing
-Using default version 8.0.0
-cdbs: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for source dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0 libxml2 man-db
- po-debconf
-Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
-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:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded.
-Need to get 11.7 MB of archives.
-After this operation, 35.6 MB of additional disk space will be used.
-Get:1 http://merkur/debian/debian-ports/ sid/main bsdmainutils powerpcspe 8.0.17 [203 kB]
-Get:2 http://merkur/debian/debian-ports/ sid/main groff-base powerpcspe 1.20.1-10+b100 [1195 kB]
-Get:3 http://merkur/debian/debian-ports/ sid/main man-db powerpcspe 2.5.7-6 [1256 kB]
-Get:4 http://merkur/debian/debian-ports/ sid/main libmagic1 powerpcspe 5.04-5 [240 kB]
-Get:5 http://merkur/debian/debian-ports/ sid/main file powerpcspe 5.04-5 [49.4 kB]
-Get:6 http://merkur/debian/debian-ports/ sid/main gettext-base powerpcspe 0.18.1.1-3 [131 kB]
-Get:7 http://merkur/debian/debian-ports/ sid/main libpcre3 powerpcspe 8.02-1.1 [232 kB]
-Get:8 http://merkur/debian/debian-ports/ sid/main libxml2 powerpcspe 2.7.8.dfsg-1 [838 kB]
-Get:9 http://merkur/debian/debian-ports/ sid/main html2text powerpcspe 1.3.2a-15+b100 [104 kB]
-Get:10 http://merkur/debian/debian-ports/ sid/main libglib2.0-0 powerpcspe 2.24.2-1 [1101 kB]
-Get:11 http://merkur/debian/debian-ports/ sid/main libcroco3 powerpcspe 0.6.2-1+b100 [117 kB]
-Get:12 http://merkur/debian/debian-ports/ sid/main libunistring0 powerpcspe 0.9.3-3 [428 kB]
-Get:13 http://merkur/debian/debian-ports/ sid/main gettext powerpcspe 0.18.1.1-3 [2017 kB]
-Get:14 http://merkur/debian/debian-ports/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:15 http://merkur/debian/debian-ports/ sid/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:16 http://merkur/debian/debian-ports/ sid/main debhelper all 8.0.0 [454 kB]
-Get:17 http://merkur/debian/debian-ports/ sid/main cdbs all 0.4.89 [1240 kB]
-Get:18 http://merkur/debian/debian-ports/ sid/main libncurses5-dev powerpcspe 5.7+20100313-4 [1631 kB]
-Get:19 http://merkur/debian/debian-ports/ sid/main zlib1g-dev powerpcspe 1:1.2.3.4.dfsg-3+b110 [190 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.7 MB in 0s (16.2 MB/s)
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 10209 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_powerpcspe.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10+b100_powerpcspe.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_powerpcspe.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_powerpcspe.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5_powerpcspe.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_powerpcspe.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_powerpcspe.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_powerpcspe.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15+b100_powerpcspe.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_powerpcspe.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1+b100_powerpcspe.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_powerpcspe.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_powerpcspe.deb) ...
-Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
-Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_powerpcspe.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3+b110_powerpcspe.deb) ...
-Setting up bsdmainutils (8.0.17) ...
-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 groff-base (1.20.1-10+b100) ...
-Setting up man-db (2.5.7-6) ...
-Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.8.dfsg-1) ...
-Setting up html2text (1.3.2a-15+b100) ...
-Setting up libglib2.0-0 (2.24.2-1) ...
-Setting up libcroco3 (0.6.2-1+b100) ...
-Setting up libunistring0 (0.9.3-3) ...
-Setting up gettext (0.18.1.1-3) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.0.0) ...
-Setting up cdbs (0.4.89) ...
-Setting up libncurses5-dev (5.7+20100313-4) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3+b110) ...
-Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: Linux 2.6.36 powerpcspe (ppc)
-Toolchain package versions: libc6-dev_2.11.1-2+powerpcspe1 dpkg-dev_1.15.8.6 linux-libc-dev_2.6.32-27+powerpcspe1 gcc-4.4_4.4.4-4+powerpcspe4.5 g++-4.4_4.4.4-4+powerpcspe4.5 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.4-4+powerpcspe4.5 libstdc++6_4.4.4-4+powerpcspe4.5
-Package versions: apt_0.8.10 base-files_5.10 base-passwd_3.5.22+b110 bash_4.1-3+b111 binutils_2.20.1-15 bsdmainutils_8.0.17 bsdutils_1:2.17.2-3.3 build-essential_11.5+b100 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1+b1 cpio_2.11-5 cpp_4:4.4.4-2+powerpcspe1 cpp-4.4_4.4.4-4+powerpcspe4.5 dash_0.5.5.1-7.3 debconf_1.5.37 debconf-i18n_1.5.37 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debian-powerpcspe-archive-keyring_2009.10.13-2 debianutils_3.4.2 diff_1:3.0-1 diffutils_1:3.0-1+b110 dmsetup_2:1.02.48-4 dpkg_1.15.8.6 dpkg-dev_1.15.8.6 e2fslibs_1.41.12-2+b100 e2fsprogs_1.41.12-2+b100 fakeroot_1.14.4-2 file_5.04-5 findutils_4.4.2-1+b110 g++_4:4.4.4-2+powerpcspe1 g++-4.4_4.4.4-4+powerpcspe4.5 gcc_4:4.4.4-2+powerpcspe1 gcc-4.4_4.4.4-4+powerpcspe4.5 gcc-4.4-base_4.4.4-4+powerpcspe4.5 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4+b100 gpgv_1.4.10-4+b100 grep_2.6.3-3+b110 groff-base_1.20.1-10+b100 gzip_1.3.12-9+b110 hostname_3.05 html2text_1.3.2a-15+b100 initscripts_2.88!
- dsf-13 insserv_1.14.0-2+b100 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2+b110 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.1-2+powerpcspe1 libc-dev-bin_2.11.1-2+powerpcspe1 libc6_2.11.1-2+powerpcspe1 libc6-dev_2.11.1-2+powerpcspe1 libcomerr2_1.41.12-2+b100 libcroco3_0.6.2-1+b100 libdb4.7_4.7.25-10 libdb4.8_4.8.30-3 libdevmapper1.02.1_2:1.02.48-4 libdpkg-perl_1.15.8.6 libgcc1_1:4.4.4-4+powerpcspe4.5 libgdbm3_1.8.3-9+b110 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1+b3 libgomp1_4.4.4-4+powerpcspe4.5 liblocale-gettext-perl_1.05-6+b110 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3+b2 libmudflap0_4.4.4-4+powerpcspe4.5 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libreadline5_5.2-7+b100 libreadline6_6.1-3+b100 libselinux1_2.0.96-1 libsepol1_2.0.41-1+b110 libslang2_2.2.2-4+b100 libss2_1.41.12-2+b100 libstdc++!
- 6_4.4.4-4+powerpcspe4.5 libstdc++6-4.4-dev_4.4.4-4+powerpcspe4.5 libte
-xt-charwidth-perl_0.04-6+b110 libtext-iconv-perl_1.7-2+b110 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_164-2 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-27+powerpcspe1 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14+b100 make_3.81-8+b1 makedev_2.3.1-89 man-db_2.5.7-6 mawk_1.3.3-15+b111 mktemp_8.5-1 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sysv-rc_2.88dsf-13 sysvinit_2.88dsf-13 sysvinit-utils_2.88dsf-13 tar_1.25-2 tzdata_2010o-1 util-linux_2.17.2-3.3 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3+b110 zlib1g-dev_1:1.2.3.4.dfsg-3+b110
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
-gpgv: keyblock resource `/var/lib/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Dec 3 06:37:23 2010 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.12a
-dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.12a-1
- dpkg-source --before-build samtools-0.1.12a
-dpkg-buildpackage: host architecture powerpcspe
- /usr/bin/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 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/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 `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
-rm -f debian/stamp-makefile-check
-dh_clean
-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
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -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: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
-bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
-bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 4 has type 'size_t'
-bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 5 has type 'size_t'
-bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 6 has type 'size_t'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/bcftools'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/misc'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/bcftools'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/misc'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/misc'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
-../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 glfview ex1.glf | gzip > ex1.glfview.gz
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-sample depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/examples'
-touch debian/stamp-makefile-check
- /usr/bin/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:104: WARNING: DEB_DH_BUILDDEB_ARGS 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 ./ChangeLog
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
-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 ./ChangeLog
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev
-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: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1_powerpcspe.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1_powerpcspe.deb'.
-dpkg-genchanges -B
-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-0.1.12a
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101204-1851
-
-samtools_0.1.12a-1_powerpcspe.changes:
-Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: powerpcspe
-Version: 0.1.12a-1
-Distribution: unstable
-Urgency: low
-Maintainer: powerpcspe Build Daemon (baako) <baako at breakpoint...>
-Changed-By: Charles Plessy <plessy at debian...>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
- samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.12a-1) unstable; urgency=low
- .
- * New upstream release.
- * Use bzip2 compression for the binary packages (debian/rules).
- * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
- available in earlier versions (debian/compat, debian/control).
-Checksums-Sha1:
- 1520872c020f97f4567636194b16a0487e2c59c1 575364 samtools_0.1.12a-1_powerpcspe.deb
- 291ec6c5b5a441cb73a4fac22e0875ab2ad4c3f3 159186 libbam-dev_0.1.12a-1_powerpcspe.deb
-Checksums-Sha256:
- f43f8492b43496d5653d05f6c61d304d1d3e61179a2543838f0eee0433ba8f21 575364 samtools_0.1.12a-1_powerpcspe.deb
- 3ef5a014338bcd39f6d3a8ddcbd84a6eaba024dce1d04fe7a97c3a56897fe378 159186 libbam-dev_0.1.12a-1_powerpcspe.deb
-Files:
- f3aba6c099b24d7b68fc75bf96aed0e9 575364 science optional samtools_0.1.12a-1_powerpcspe.deb
- d2d9e4322736fa4095491f62b806876e 159186 libdevel optional libbam-dev_0.1.12a-1_powerpcspe.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.12a-1_powerpcspe.deb
-─────────────────────────────────
-
- new debian package, version 2.0.
- size 575364 bytes: control archive= 1799 bytes.
- 799 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
- Package: samtools
- Version: 0.1.12a-1
- Architecture: powerpcspe
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1044
- Depends: libc6 (>= 2.11), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
- 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 2010-12-04 18:51 ./
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/bin/
--rwxr-xr-x root/root 340232 2010-12-04 18:51 ./usr/bin/samtools
--rwxr-xr-x root/root 106488 2010-12-04 18:51 ./usr/bin/bcftools
--rwxr-xr-x root/root 24036 2010-12-04 18:51 ./usr/bin/razip
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/lib/
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/lib/samtools/
--rwxr-xr-x root/root 36448 2010-12-04 18:51 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7536 2010-12-04 18:51 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 10384 2010-12-04 18:51 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6736 2010-12-04 18:51 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 6736 2010-12-04 18:51 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/samtools/
--rwxr-xr-x root/root 2696 2010-11-17 05:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 05:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 05:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 3224 2010-11-17 05:16 ./usr/share/samtools/bcf-fix.pl
--rwxr-xr-x root/root 5989 2010-11-17 05:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 05:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2397 2010-11-17 05:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 05:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2415 2010-11-17 05:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 15255 2010-11-17 05:16 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2010-12-04 18:51 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2729 2010-11-17 05:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 12567 2010-12-02 17:41 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 14299 2010-11-17 05:16 ./usr/share/samtools/samtools.pl
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/man/man1/
--rw-r--r-- root/root 7546 2010-12-04 18:51 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2010-12-04 18:51 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/doc/samtools/
--rw-r--r-- root/root 6692 2010-12-02 22:16 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 4927 2010-12-03 06:06 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 592 2010-12-03 06:06 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 30752 2010-11-22 04:17 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 916 2010-11-17 05:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2010-12-03 06:06 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 1128 2010-12-03 06:07 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 764 2010-11-17 05:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2010-12-04 18:47 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 886 2010-11-17 05:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-11-17 05:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 3225 2010-11-17 05:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-11-17 05:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 1966 2010-12-04 18:51 ./usr/share/doc/samtools/README.bcftools
-lrwxrwxrwx root/root 0 2010-12-04 18:51 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.12a-1_powerpcspe.deb
-───────────────────────────────────
-
- new debian package, version 2.0.
- size 159186 bytes: control archive= 903 bytes.
- 680 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.12a-1
- Architecture: powerpcspe
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 388
- 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.
-
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/include/
--rw-r--r-- root/root 3188 2010-11-17 05:16 ./usr/include/faidx.h
--rw-r--r-- root/root 16522 2010-11-17 05:16 ./usr/include/khash.h
--rw-r--r-- root/root 24124 2010-11-17 05:16 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-11-17 05:16 ./usr/include/bgzf.h
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/lib/
--rw-r--r-- root/root 245202 2010-12-04 18:51 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 6692 2010-12-02 22:16 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 4927 2010-12-03 06:06 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 30752 2010-11-22 04:17 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 916 2010-11-17 05:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 1128 2010-12-03 06:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/spestage-0fea459c-6bbb-4543-9144-91e0da2cf54a/spestage/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ
-(Reading database ... 12586 files and directories currently installed.)
-Removing zlib1g-dev ...
-Removing cdbs ...
-Removing debhelper ...
-Removing po-debconf ...
-Removing libncurses5-dev ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing intltool-debian ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing gettext ...
-Removing file ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing gettext-base ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20101204-1851
-Build needed 00:06:13, 8948k disc space
-
-</pre>
-<p>
-
-<!-- Footer menu bar -->
-
-<table width="100%">
-<tr valign=top>
- <td align=left>
- <address>
-
- These scripts were derived from the buildd.debian.org, thanks to Ryan Murray.<br>
- Contact address: <<a href="mailto:admin at debian-ports.org">admin at debian-ports.org</a>>
- </address>
- </td>
- <td align=right>
- <font size=-1>(
- <a href="index.php">index</a> |
- <a href="build.php">build logs</a>
- )</font>
- </td>
-</tr>
-</table>
-<br>
-</body>
diff --git a/s390.log b/s390.log
index 986893e..0cc9798 100644
--- a/s390.log
+++ b/s390.log
@@ -1,69 +1,69 @@
-From buildd at zandonai.debian.org Tue Mar 29 05:03:26 2011
+From buildd at zandonai.debian.org Tue Apr 12 11:33:03 2011
Return-path: <buildd at zandonai.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at zandonai.debian.org>)
- id 1Q4R5S-000346-GR
- for logs at buildd.debian.org; Tue, 29 Mar 2011 05:03:26 +0000
+ id 1Q9bqB-0006gE-7j
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 11:33:03 +0000
Received: from zandonai.debian.org ([80.245.147.46])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=zandonai.debian.org,
EMAIL=hostmaster at zandonai.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at zandonai.debian.org>)
- id 1Q4R5P-0003W3-7h; Tue, 29 Mar 2011 05:03:23 +0000
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
+ id 1Q9bq4-0006BE-MW; Tue, 12 Apr 2011 11:32:56 +0000
Received: from buildd by zandonai.debian.org with local (Exim 4.69)
(envelope-from <buildd at zandonai.debian.org>)
- id 1Q4R5N-0004zZ-6m; Tue, 29 Mar 2011 05:03:21 +0000
+ id 1Q9bq4-0006MU-8O; Tue, 12 Apr 2011 11:32:56 +0000
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
-Date: Tue, 29 Mar 2011 05:03:21 +0000
+Date: Tue, 12 Apr 2011 11:32:56 +0000
From: buildd on zandonai <buildd at zandonai.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.14-1 on s390 (dist=sid)
+Subject: Log for successful build of samtools_0.1.15-1 on s390 (dist=sid)
Key-Id: 9BD94C88
-Message-Id: <E1Q4R5N-0004zZ-6m at zandonai.debian.org>
+Message-Id: <E1Q9bq4-0006MU-8O at zandonai.debian.org>
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.14-1 (s390) 29 Mar 2011 05:01 ║
+║ samtools 0.1.15-1 (s390) 12 Apr 2011 11:31 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.14-1
-Source Version: 0.1.14-1
+Version: 0.1.15-1
+Source Version: 0.1.15-1
Architecture: s390
-Get:1 http://ftp.de.debian.org unstable InRelease [184 kB]
-Get:2 http://incoming.debian.org unstable InRelease [185 kB]
-Get:3 http://ftp.de.debian.org unstable/main Sources [5169 kB]
+Get:1 http://ftp.de.debian.org unstable InRelease [151 kB]
+Get:2 http://incoming.debian.org unstable InRelease [151 kB]
+Get:3 http://ftp.de.debian.org unstable/main Sources [5265 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [5142 kB]
-Get:6 http://ftp.de.debian.org unstable/contrib Sources [47.0 kB]
-Get:7 http://ftp.de.debian.org unstable/non-free Sources [99.0 kB]
-Get:8 http://ftp.de.debian.org unstable/main s390 Packages [6883 kB]
-Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [50.4 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5265 kB]
+Get:6 http://ftp.de.debian.org unstable/contrib Sources [48.2 kB]
+Get:7 http://ftp.de.debian.org unstable/non-free Sources [97.4 kB]
+Get:8 http://ftp.de.debian.org unstable/main s390 Packages [6985 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [51.4 kB]
Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2232 B]
+Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2264 B]
Ign http://ftp.de.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [47.4 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
-Get:13 http://incoming.debian.org unstable/main s390 Packages [6888 kB]
-Get:14 http://incoming.debian.org unstable/contrib s390 Packages [50.4 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [48.2 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [97.4 kB]
+Get:13 http://incoming.debian.org unstable/main s390 Packages [6985 kB]
+Get:14 http://incoming.debian.org unstable/contrib s390 Packages [51.4 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [30.5 kB]
-Get:18 http://incoming.debian.org Packages [608 kB]
+Get:17 http://incoming.debian.org Sources [49.7 kB]
+Get:18 http://incoming.debian.org Packages [772 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 25.5 MB in 32s (786 kB/s)
+Fetched 26.0 MB in 26s (995 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +84,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 379 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (tar) [370 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (diff) [6869 B]
-Fetched 379 kB in 1s (289 kB/s)
+Need to get 383 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
+Fetched 383 kB in 1s (291 kB/s)
Download complete and in download only mode
Check arch
@@ -102,18 +102,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.14.5-2)
+fakeroot: already installed (1.15.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 19 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 19 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -147,12 +147,12 @@ bsdutils: already installed (1:2.17.2-9.1)
mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
libc6-dev: already installed (2.11.2-11)
-gcc: already installed (4:4.4.5-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-4 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.4.5-6 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.4.5-6 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8)
dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.2
+Using default version 8.1.3
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -162,53 +162,67 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ bsdmainutils dpkg-dev file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libdpkg-perl libglib2.0-0 libmagic1 libncurses5
+ libpcre3 libpipeline1 libunistring0 libxml2 man-db ncurses-bin po-debconf
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff ncurses-doc less www-browser libmail-box-perl
+ wamerican wordlist whois vacation devscripts doc-base dh-make debian-keyring
+ gettext-doc groff ncurses-doc less www-browser libmail-box-perl
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ autotools-dev libalgorithm-merge-perl curl wget lynx-cur autopoint
+ libglib2.0-data shared-mime-info libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 20 newly installed, 0 to remove and 9 not upgraded.
-Need to get 11.1 MB of archives.
-After this operation, 31.2 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.2 [208 kB]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-5 [1158 kB]
-Get:3 http://incoming.debian.org/debian/ unstable/main libglib2.0-0 s390 2.28.4-1 [1635 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.0-1 [38.7 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.5.9-4 [1015 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.04-5 [243 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main file s390 5.04-5 [50.0 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-3 [142 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.12-3 [262 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-2 [873 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
-Get:12 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-1 [128 kB]
-Get:13 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-3 [431 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-3 [2068 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main intltool-debian s390 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.de.debian.org/debian/ unstable/main po-debconf s390 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main debhelper s390 8.1.2 [553 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main cdbs s390 0.4.92 [1268 kB]
-Get:19 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.8+20110307-1 [503 kB]
-Get:20 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.3.4.dfsg-3 [193 kB]
+The following packages will be upgraded:
+ dpkg-dev libdpkg-perl libncurses5 ncurses-bin
+4 upgraded, 20 newly installed, 0 to remove and 15 not upgraded.
+Need to get 13.5 MB of archives.
+After this operation, 31.3 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main ncurses-bin s390 5.9-1 [335 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main libncurses5 s390 5.9-1 [384 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.2 [208 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-5 [1158 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.0-1 [38.7 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.0.1-1 [1017 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.04-5 [243 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main file s390 5.04-5 [50.0 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-3 [142 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.12-3 [262 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-2 [873 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main dpkg-dev s390 1.16.0.1 [871 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main libdpkg-perl s390 1.16.0.1 [748 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.28.4-1 [1635 kB]
+Get:16 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-1 [128 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-3 [431 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-3 [2068 kB]
+Get:19 http://ftp.de.debian.org/debian/ unstable/main intltool-debian s390 0.35.0+20060710.1 [30.8 kB]
+Get:20 http://ftp.de.debian.org/debian/ unstable/main po-debconf s390 1.0.16+nmu1 [223 kB]
+Get:21 http://ftp.de.debian.org/debian/ unstable/main debhelper s390 8.1.3 [554 kB]
+Get:22 http://ftp.de.debian.org/debian/ unstable/main cdbs s390 0.4.92 [1268 kB]
+Get:23 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.9-1 [504 kB]
+Get:24 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.3.4.dfsg-3 [193 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.1 MB in 3s (3234 kB/s)
+Fetched 13.5 MB in 4s (3284 kB/s)
+(Reading database ... 10051 files and directories currently installed.)
+Preparing to replace ncurses-bin 5.8+20110307-1 (using .../ncurses-bin_5.9-1_s390.deb) ...
+Unpacking replacement ncurses-bin ...
+Setting up ncurses-bin (5.9-1) ...
+(Reading database ... 10051 files and directories currently installed.)
+Preparing to replace libncurses5 5.8+20110307-1 (using .../libncurses5_5.9-1_s390.deb) ...
+Unpacking replacement libncurses5 ...
+Setting up libncurses5 (5.9-1) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10127 files and directories currently installed.)
+(Reading database ... 10051 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_s390.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-5_s390.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_s390.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.9-4_s390.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.1-1_s390.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_s390.deb) ...
Selecting previously deselected package file.
@@ -219,6 +233,10 @@ Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_s390.deb) ...
Selecting previously deselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_s390.deb) ...
+Preparing to replace dpkg-dev 1.15.8.10 (using .../dpkg-dev_1.16.0.1_s390.deb) ...
+Unpacking replacement dpkg-dev ...
+Preparing to replace libdpkg-perl 1.15.8.10 (using .../libdpkg-perl_1.16.0.1_s390.deb) ...
+Unpacking replacement libdpkg-perl ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_s390.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -234,11 +252,11 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_s390.deb)
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_s390.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_s390.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.3_s390.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.92_s390.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_s390.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_s390.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_s390.deb) ...
Setting up bsdmainutils (8.2.2) ...
@@ -246,13 +264,15 @@ update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write)
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.5.9-4) ...
+Setting up man-db (2.6.0.1-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up libdpkg-perl (1.16.0.1) ...
+Setting up dpkg-dev (1.16.0.1) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.4-1) ...
No schema files found: doing nothing.
@@ -261,19 +281,19 @@ Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
+Setting up debhelper (8.1.3) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8+20110307-1) ...
+Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-bpo.5-s390x s390 (s390x)
-Toolchain package versions: binutils_2.21.0.20110322-1 dpkg-dev_1.15.8.10 g++-4.4_4.4.5-14 gcc-4.4_4.4.5-14 libc6-dev_2.11.2-11 libstdc++6_4.5.2-6 libstdc++6-4.4-dev_4.4.5-14 linux-libc-dev_2.6.38-1
-Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110322-1 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-4 cpp-4.4_4.4.5-14 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-4 g++-4.4_4.4.5-14 gcc_4:4.4.5-4 gcc-4.4_4.4.5-14 gcc-4.4-base_4.4.5-14 gcc-4.5-base_4.5.2-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:7.1-7 libgcc1_1:4.5.2-6 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.5.2-6 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-6 libstdc++6-4.4-dev_4.4.5-14 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011d-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0.1 g++-4.4_4.4.5-15 gcc-4.4_4.4.5-15 libc6-dev_2.11.2-11 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 linux-libc-dev_2.6.38-2
+Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-6 cpp-4.4_4.4.5-15 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-6 g++-4.4_4.4.5-15 gcc_4:4.4.5-6 gcc-4.4_4.4.5-15 gcc-4.4-base_4.4.5-15 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0.1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011d-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -285,12 +305,12 @@ Unpack source
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.14
-dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.15-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.15
+dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
Check disc space
────────────────
@@ -306,8 +326,8 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.14-1
- dpkg-source --before-build samtools-0.1.14
+dpkg-buildpackage: source version 0.1.15-1
+ dpkg-source --before-build samtools-0.1.15
dpkg-buildpackage: host architecture s390
fakeroot debian/rules clean
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -318,17 +338,17 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/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 `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -341,8 +361,8 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -356,15 +376,16 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/bcftools'
+ar -cru 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 glf.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 `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -375,10 +396,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -396,25 +417,26 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/misc'
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/misc'
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/misc'
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -424,14 +446,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -455,12 +477,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtool
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-sample depth to 8000
+<mpileup> Set max per-file depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -498,7 +520,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -523,7 +545,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -538,27 +560,27 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_s390.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.15-1_s390.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_s390.deb'.
- dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.14-1_s390.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.15-1_s390.deb'.
+ dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.15-1_s390.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-0.1.14
+ dpkg-source --after-build samtools-0.1.15
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110329-0503
+Build finished at 20110412-1132
-samtools_0.1.14-1_s390.changes:
+samtools_0.1.15-1_s390.changes:
Format: 1.8
-Date: Tue, 29 Mar 2011 13:13:54 +0900
+Date: Tue, 12 Apr 2011 19:44:41 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: s390
-Version: 0.1.14-1
+Version: 0.1.15-1
Distribution: sid
Urgency: low
Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
@@ -567,36 +589,39 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.14-1) unstable; urgency=low
+ samtools (0.1.15-1) unstable; urgency=low
.
* New upstream release.
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.2
+ (debian/control, no changes needed).
+ * debian/watch directly interrogates and downloads froms SourceForge.
Checksums-Sha1:
- 7a0121edd4478eb920016cf54511717e3093b70a 599798 samtools_0.1.14-1_s390.deb
- d0e46a3d85499e7d3859187c878eae339a5149cb 170978 libbam-dev_0.1.14-1_s390.deb
+ 4569cbfe059200bc82c27c26ab2adb8a81d20a42 605506 samtools_0.1.15-1_s390.deb
+ c43a525cb31adc080f47e21846a73e1fdf444913 175010 libbam-dev_0.1.15-1_s390.deb
Checksums-Sha256:
- 2209fbe1bac794ee42c3889dd722398bf37daa9e3bc312a0901dd84555a41044 599798 samtools_0.1.14-1_s390.deb
- 542b3a1200f89417ed82a791d09f315d0c3e6e5e895ad17671c1f60a44c6b06b 170978 libbam-dev_0.1.14-1_s390.deb
+ 5bf1d2d1648531dba4e5e6843cb03f9e596822572112b635d1ffebd51b61b970 605506 samtools_0.1.15-1_s390.deb
+ 6cb6fad8ac76a1db1a9d1daabe53e8a8dadf97c0c403b3c9698db672bd39fb05 175010 libbam-dev_0.1.15-1_s390.deb
Files:
- efd3eff690deee25ef7db33b611c913d 599798 science optional samtools_0.1.14-1_s390.deb
- 16711d7315c1328e8d55379e62f7cb37 170978 libdevel optional libbam-dev_0.1.14-1_s390.deb
+ bb385611e298b1af3c85f80a9c088053 605506 science optional samtools_0.1.15-1_s390.deb
+ be0ace00cd33e2aee25ed5813333a3a9 175010 libdevel optional libbam-dev_0.1.15-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.14-1_s390.deb
+samtools_0.1.15-1_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 599798 bytes: control archive= 1779 bytes.
+ size 605506 bytes: control archive= 1782 bytes.
785 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1116
+ Installed-Size: 1136
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -609,26 +634,26 @@ samtools_0.1.14-1_s390.deb
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 2011-03-29 05:03 ./
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/bin/
--rwxr-xr-x root/root 113080 2011-03-29 05:03 ./usr/bin/bcftools
--rwxr-xr-x root/root 403648 2011-03-29 05:03 ./usr/bin/samtools
--rwxr-xr-x root/root 27380 2011-03-29 05:03 ./usr/bin/razip
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/lib/samtools/
--rwxr-xr-x root/root 11324 2011-03-29 05:03 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7188 2011-03-29 05:03 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 7188 2011-03-29 05:03 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7932 2011-03-29 05:03 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 18564 2011-03-29 05:03 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/man/man1/
--rw-r--r-- root/root 8393 2011-03-29 05:03 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-03-29 05:03 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 2005 2011-03-29 05:03 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/bin/
+-rwxr-xr-x root/root 120940 2011-04-12 11:32 ./usr/bin/bcftools
+-rwxr-xr-x root/root 415020 2011-04-12 11:32 ./usr/bin/samtools
+-rwxr-xr-x root/root 27380 2011-04-12 11:32 ./usr/bin/razip
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/samtools/
+-rwxr-xr-x root/root 11324 2011-04-12 11:32 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7188 2011-04-12 11:32 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 7188 2011-04-12 11:32 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7932 2011-04-12 11:32 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 18564 2011-04-12 11:32 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/man/man1/
+-rw-r--r-- root/root 8393 2011-04-12 11:32 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-04-12 11:32 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 2005 2011-04-12 11:32 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/samtools/
-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
@@ -638,42 +663,42 @@ drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/samtools/
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 5778 2011-03-29 05:03 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-04-12 11:32 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/doc/samtools/
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1966 2011-03-29 05:03 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1966 2011-04-12 11:32 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 126609 2011-03-29 05:03 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-04-12 11:32 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
-libbam-dev_0.1.14-1_s390.deb
+libbam-dev_0.1.15-1_s390.deb
────────────────────────────
new debian package, version 2.0.
- size 170978 bytes: control archive= 896 bytes.
+ size 175010 bytes: control archive= 893 bytes.
673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.14-1
+ Version: 0.1.15-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 416
+ Installed-Size: 424
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -684,23 +709,23 @@ libbam-dev_0.1.14-1_s390.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/include/
--rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
--rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/include/
+-rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/bgzf.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/lib/
--rw-r--r-- root/root 263338 2011-03-29 05:03 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/
+-rw-r--r-- root/root 271780 2011-04-12 11:32 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -714,7 +739,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390-sbuild-d1dabdcc-44f9-445d-84cf-4e96fe5d167b/build/buildd-samtools_0.1.14-1-s390-jqHPik
+Purging /var/lib/schroot/mount/sid-s390-sbuild-7d8a126e-7575-4dc2-96d3-db399ee093db/build/buildd-samtools_0.1.15-1-s390-z4ZdUX
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -722,18 +747,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 9836
-Build-Time: 43
+Build-Space: 10024
+Build-Time: 44
Distribution: sid
-Install-Time: 18
-Job: samtools_0.1.14-1
+Install-Time: 22
+Job: samtools_0.1.15-1
Package: samtools
-Package-Time: 102
-Source-Version: 0.1.14-1
-Space: 9836
+Package-Time: 100
+Source-Version: 0.1.15-1
+Space: 10024
Status: successful
-Version: 0.1.14-1
+Version: 0.1.15-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110329-0503
-Build needed 00:01:42, 9836k disc space
+Finished at 20110412-1132
+Build needed 00:01:40, 10024k disc space
Signature with key '9BD94C88' requested:
diff --git a/sh4.log b/sh4.log
deleted file mode 100644
index 1613501..0000000
--- a/sh4.log
+++ /dev/null
@@ -1,711 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><title>File `log' in samtools_0.1.12a-1_sh4 (Dec 3 19:28)</title><meta http-equiv="content-type" content="text/html;charset=utf-8"></head><body bgcolor="#ffffff">
-<table width="100%"><tr valign=top><td align=left><h2>File `log' in samtools_0.1.12a-1_sh4 (Dec 3 19:28)</h2></td><td align=right><a href="build.php?&pkg=samtools&arch=sh4">samtools</a> >> <a href="build.php?&pkg=samtools&ver=0.1.12a-1&arch=sh4">0.1.12a-1</a> >> <a href="build.php?&pkg=samtools&ver=0.1.12a-1&arch=sh4&stamp=1291404517">Dec 3 19:28</a> >> log</td></tr></table><p><pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on musashi
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (sh4) 03 Dec 2010 18:09 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.12a-1
-Architecture: sh4
-Chroot Build Dir: /srv/chroot/sid/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq
-Start Time: 20101203-1809
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-Hit http://ftp.debian-ports.org unstable Release.gpg
-Ign http://ftp.debian-ports.org/debian/ unstable/main Translation-en
-Hit http://incoming.debian-ports.org unstable Release.gpg
-Hit http://ftp.debian-ports.org unreleased Release.gpg
-Ign http://incoming.debian-ports.org/buildd/ unstable/main Translation-en
-Hit http://ftp.debian.org unstable Release.gpg
-Ign http://ftp.debian-ports.org/debian/ unreleased/main Translation-en
-Hit http://ftp.debian-ports.org unstable Release
-Hit http://incoming.debian-ports.org unstable Release
-Hit http://ftp.debian.org unstable Release
-Hit http://ftp.debian-ports.org unreleased Release
-Hit http://incoming.debian-ports.org unstable/main Sources
-Hit http://ftp.debian.org unstable/main Sources/DiffIndex
-Hit http://ftp.debian-ports.org unstable/main sh4 Packages
-Hit http://incoming.debian-ports.org unstable/main sh4 Packages
-Hit http://ftp.debian-ports.org unreleased/main sh4 Packages
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-
-Download source files with APT
-──────────────────────────────
-
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-Reading package lists...
-Building dependency tree...
-Reading state information...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 364 kB of source archives.
-Get:1 http://ftp.debian.org/debian/ unstable/main samtools 0.1.12a-1 (dsc) [1946 B]
-Get:2 http://ftp.debian.org/debian/ unstable/main samtools 0.1.12a-1 (tar) [356 kB]
-Get:3 http://ftp.debian.org/debian/ unstable/main samtools 0.1.12a-1 (diff) [6337 B]
-Fetched 364 kB in 5s (61.4 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Checking for already installed source dependencies...
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-debhelper: missing
-Using default version 8.0.0
-cdbs: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for source dependency conflicts...
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- file gettext gettext-base groff-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libpcre3 libunistring0 libxml2 man-db po-debconf
-Suggested packages:
- devscripts doc-base dh-make gettext-doc groff less www-browser
- libmail-box-perl
-Recommended packages:
- autotools-dev autopoint libglib2.0-data shared-mime-info xml-core
- libmail-sendmail-perl
-The following NEW packages will be installed:
- cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libunistring0 libxml2 man-db po-debconf zlib1g-dev
-debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 18 newly installed, 0 to remove and 28 not upgraded.
-Need to get 0 B/11.7 MB of archives.
-After this operation, 34.5 MB of additional disk space will be used.
-Selecting previously deselected package groff-base.
-(Reading database ... 11309 files and directories currently installed.)
-Unpacking groff-base (from .../groff-base_1.20.1-10_sh4.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_sh4.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_sh4.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../archives/file_5.04-5_sh4.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_sh4.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_sh4.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_sh4.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_sh4.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_sh4.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_sh4.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_sh4.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_sh4.deb) ...
-Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
-Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_sh4.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_sh4.deb) ...
-Processing triggers for install-info ...
-Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
-Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.8.dfsg-1) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.24.2-1) ...
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
-Setting up gettext (0.18.1.1-3) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.0.0) ...
-Setting up cdbs (0.4.89) ...
-Setting up libncurses5-dev (5.7+20100313-4) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Removing negative dependencies:
-Checking correctness of source dependencies...
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-Kernel: Linux 2.6.33.5-00003-g0ef7fb0-dirty sh4 (sh4a)
-Toolchain package versions: libc6-dev_2.11.2-7 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-26 gcc-4.4_4.4.5-8 g++-4.4_4.4.5-8 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-8 libstdc++6_4.4.5-8
-Package versions: adduser_3.112+nmu1 apt_0.8.8 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 ca-certificates_20090814+nmu2 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.4_4.4.5-8 dash_0.5.5.1-7.2 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diff_1:3.0-1 diffutils_1:3.0-1 dmsetup_2:1.02.48-4 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.5-1 g++-4.4_4.4.5-8 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-1 gcc-4.2-base_4.2.4-6 gcc-4.4_4.4.5-8 gcc-4.4-base_4.4.5-8 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gnupg-curl_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 install-info_4.13a.dfsg.1-6 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc6_2.11.2-7 libc6-dev_2.11.2-7 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcurl3-gnutls_7.21.2-1 libdb4.6_4.6.21-16 libdb4.7_4.7.25-9 libdb4.8_4.8.30-3 libdevmapper1.02.1_2:1.02.48-4 libdpkg-perl_1.15.8.5 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-8 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-8 libgpg-error0_1.6-1 libgpm2_1.20.4-3.3 libgssapi-krb5-2_1.8.3+dfsg-3 libidn11_1.18-1 libk5crypto3_1.8.3+dfsg-3 libkeyutils1_1.4-1 libkrb5-3_1.8.3+dfsg-3 libkrb5support0_1.8.3+dfsg-3 libldap-2.4-2_2.4.23-7 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-6 libsasl2-modules_2.1.23.dfsg1-6 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libssl0.9.8_0.9.8o-3 libstdc++6_4.4.5-8 libstdc++6-4.4-dev_4.4.5-8 libtasn1-3_2.7-1 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_164-2 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libvolume-id1_0.141-2 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-26 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 make_3.81-8 makedev_2.3.1-89 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 openssl_0.9.8o-2 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 po-debconf_1.0.16+nmu1 procps_1:3.2.8-9 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.24-1 tzdata_2010o-1 util-linux_2.17.2-3.3 wget_1.12-2.1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Dec 3 06:37:23 2010 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.12a
-dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.12a-1
- dpkg-source --before-build samtools-0.1.12a
-dpkg-buildpackage: host architecture sh4
- /usr/bin/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 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/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 `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
-rm -f debian/stamp-makefile-check
-dh_clean
-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
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -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: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
-bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
-bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 4 has type 'size_t'
-bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 5 has type 'size_t'
-bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 6 has type 'size_t'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/bcftools'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/misc'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/bcftools'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/misc'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/misc'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
-../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 glfview ex1.glf | gzip > ex1.glfview.gz
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-sample depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/examples'
-touch debian/stamp-makefile-check
- /usr/bin/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:104: WARNING: DEB_DH_BUILDDEB_ARGS 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 ./ChangeLog
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
-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 ./ChangeLog
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev
-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: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1_sh4.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1_sh4.deb'.
-dpkg-genchanges -B
-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-0.1.12a
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-1923
-
-samtools_0.1.12a-1_sh4.changes:
-Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: sh4
-Version: 0.1.12a-1
-Distribution: unstable
-Urgency: low
-Maintainer: Debian SH4 buildd <buildd-sh4-musashi at superh...>
-Changed-By: Charles Plessy <plessy at debian...>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
- samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.12a-1) unstable; urgency=low
- .
- * New upstream release.
- * Use bzip2 compression for the binary packages (debian/rules).
- * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
- available in earlier versions (debian/compat, debian/control).
-Checksums-Sha1:
- 2d31605bfcbc8089d19e54b874ffa04b6d46575f 589182 samtools_0.1.12a-1_sh4.deb
- b58b860721c3e454a39e7a0eff35062e65321606 174322 libbam-dev_0.1.12a-1_sh4.deb
-Checksums-Sha256:
- 120e4f0cc10646b4843b08b0bd792bafb3ddb68b937bae7b6377350817c6dbd0 589182 samtools_0.1.12a-1_sh4.deb
- 2ebada4a0bd2af10a4b3ab2badcdbf747a9fa37a7ab45cb2243f03647306b4da 174322 libbam-dev_0.1.12a-1_sh4.deb
-Files:
- 94e10ae8b21ad14bc137ba28603456ce 589182 science optional samtools_0.1.12a-1_sh4.deb
- 4e5effd8c6ffd189dac93126aacbfd89 174322 libdevel optional libbam-dev_0.1.12a-1_sh4.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.12a-1_sh4.deb
-──────────────────────────
-
- new debian package, version 2.0.
- size 589182 bytes: control archive= 1795 bytes.
- 791 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
- Package: samtools
- Version: 0.1.12a-1
- Architecture: sh4
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 988
- Depends: libc6 (>= 2.11), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
- 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 2010-12-03 19:19 ./
-drwxr-xr-x root/root 0 2010-12-03 19:20 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/bin/
--rwxr-xr-x root/root 24988 2010-12-03 19:21 ./usr/bin/razip
--rwxr-xr-x root/root 318656 2010-12-03 19:21 ./usr/bin/samtools
--rwxr-xr-x root/root 84068 2010-12-03 19:21 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2010-12-03 19:20 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 19:19 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-12-03 19:19 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7546 2010-12-03 19:19 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-12-03 19:19 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/share/doc/samtools/
--rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 126609 2010-12-03 18:29 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 1966 2010-12-03 19:20 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/share/samtools/
--rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 5778 2010-12-03 19:21 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
-drwxr-xr-x root/root 0 2010-12-03 19:20 ./usr/lib/
-drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/lib/samtools/
--rwxr-xr-x root/root 6864 2010-12-03 19:21 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 16724 2010-12-03 19:21 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6688 2010-12-03 19:21 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 9760 2010-12-03 19:21 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6624 2010-12-03 19:21 ./usr/lib/samtools/maq2sam-short
-lrwxrwxrwx root/root 0 2010-12-03 19:20 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.12a-1_sh4.deb
-────────────────────────────
-
- new debian package, version 2.0.
- size 174322 bytes: control archive= 897 bytes.
- 673 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.12a-1
- Architecture: sh4
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 384
- 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.
-
-drwxr-xr-x root/root 0 2010-12-03 19:20 ./
-drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/include/
--rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
--rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
--rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
-drwxr-xr-x root/root 0 2010-12-03 19:20 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 19:20 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/lib/
--rw-r--r-- root/root 238394 2010-12-03 19:21 ./usr/lib/libbam.a
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-Purging /srv/chroot/sid/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-W: line 16 [sid]: Deprecated key 'priority' used
-I: This option will be removed in the future; please update your configuration
-W: line 15 [sid]: Deprecated key 'location' used
-I: This option will be removed in the future; please update your configuration
-(Reading database ... 13572 files and directories currently installed.)
-Removing zlib1g-dev ...
-Removing cdbs ...
-Removing debhelper ...
-Removing po-debconf ...
-Removing libncurses5-dev ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing intltool-debian ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing gettext ...
-Removing file ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing gettext-base ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
-Processing triggers for install-info ...
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-1923
-Build needed 01:13:51, 8912k disc space
-
-</pre>
-<p>
-
-<!-- Footer menu bar -->
-
-<table width="100%">
-<tr valign=top>
- <td align=left>
- <address>
-
- These scripts were derived from the buildd.debian.org, thanks to Ryan Murray.<br>
- Contact address: <<a href="mailto:admin at debian-ports.org">admin at debian-ports.org</a>>
- </address>
- </td>
- <td align=right>
- <font size=-1>(
- <a href="index.php">index</a> |
- <a href="build.php">build logs</a>
- )</font>
- </td>
-</tr>
-</table>
-<br>
-</body>
diff --git a/sparc.log b/sparc.log
index aa43417..4b42d8b 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,4 +1,4 @@
-From buildd at schroeder.debian.org Tue Mar 29 07:16:52 2011
+From buildd at schroeder.debian.org Tue Apr 12 11:36:14 2011
Return-path: <buildd at schroeder.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,65 +6,65 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at schroeder.debian.org>)
- id 1Q4TAa-0004hN-DD
- for logs at buildd.debian.org; Tue, 29 Mar 2011 07:16:52 +0000
+ id 1Q9btF-0007O4-Un
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 11:36:14 +0000
Received: from schroeder.debian.org ([193.198.184.11])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=schroeder.debian.org,
EMAIL=hostmaster at schroeder.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
- id 1Q4TAU-0001OQ-PK
- for logs at buildd.debian.org; Tue, 29 Mar 2011 07:16:46 +0000
+ id 1Q9bt9-0006IP-CR
+ for logs at buildd.debian.org; Tue, 12 Apr 2011 11:36:07 +0000
Received: from buildd by schroeder.debian.org with local (Exim 4.69)
(envelope-from <buildd at schroeder.debian.org>)
- id 1Q4TAU-0006tp-1t; Tue, 29 Mar 2011 07:16:46 +0000
+ id 1Q9bt9-00073q-29; Tue, 12 Apr 2011 11:36:07 +0000
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
-Date: Tue, 29 Mar 2011 07:16:45 +0000
+Date: Tue, 12 Apr 2011 11:36:06 +0000
From: buildd on schroeder <buildd at schroeder.debian.org>
To: logs at buildd.debian.org,buildd-admin at schroeder.debian.org
-Subject: Log for attempted build of samtools_0.1.14-1 on sparc (dist=sid)
+Subject: Log for attempted build of samtools_0.1.15-1 on sparc (dist=sid)
Key-Id: 9BBB678A
-Message-Id: <E1Q4TAU-0006tp-1t at schroeder.debian.org>
+Message-Id: <E1Q9bt9-00073q-29 at schroeder.debian.org>
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on schroeder.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.14-1 (sparc) 29 Mar 2011 07:13 ║
+║ samtools 0.1.15-1 (sparc) 12 Apr 2011 11:32 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.14-1
-Source Version: 0.1.14-1
+Version: 0.1.15-1
+Source Version: 0.1.15-1
Architecture: sparc
-Get:1 http://ftp.carnet.hr unstable InRelease [185 kB]
-Get:2 http://incoming.debian.org unstable InRelease [185 kB]
-Get:3 http://ftp.carnet.hr unstable/main Sources [5142 kB]
-Get:4 http://ftp.carnet.hr unstable/contrib Sources [47.4 kB]
+Get:1 http://ftp.carnet.hr unstable InRelease [151 kB]
+Get:2 http://incoming.debian.org unstable InRelease [151 kB]
+Get:3 http://ftp.carnet.hr unstable/main Sources [5265 kB]
Ign http://incoming.debian.org InRelease
-Get:5 http://incoming.debian.org Release.gpg [836 B]
-Get:6 http://incoming.debian.org unstable/main Sources [5142 kB]
-Get:7 http://ftp.carnet.hr unstable/non-free Sources [99.4 kB]
-Get:8 http://ftp.carnet.hr unstable/main sparc Packages [6905 kB]
-Get:9 http://ftp.carnet.hr unstable/contrib sparc Packages [51.5 kB]
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://ftp.carnet.hr unstable/contrib Sources [48.2 kB]
+Get:6 http://incoming.debian.org unstable/main Sources [5265 kB]
+Get:7 http://ftp.carnet.hr unstable/non-free Sources [97.4 kB]
+Get:8 http://ftp.carnet.hr unstable/main sparc Packages [7009 kB]
+Get:9 http://ftp.carnet.hr unstable/contrib sparc Packages [52.5 kB]
Ign http://ftp.carnet.hr unstable/contrib TranslationIndex
-Get:10 http://ftp.carnet.hr unstable/main TranslationIndex [2232 B]
-Get:11 http://incoming.debian.org unstable/contrib Sources [47.4 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
-Get:13 http://incoming.debian.org unstable/main sparc Packages [6905 kB]
-Get:14 http://incoming.debian.org unstable/contrib sparc Packages [51.5 kB]
+Get:10 http://ftp.carnet.hr unstable/main TranslationIndex [2264 B]
+Get:11 http://incoming.debian.org unstable/contrib Sources [48.2 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [97.4 kB]
+Get:13 http://incoming.debian.org unstable/main sparc Packages [7009 kB]
+Ign http://ftp.carnet.hr unstable/contrib Translation-en
+Get:14 http://incoming.debian.org unstable/contrib sparc Packages [52.5 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Ign http://ftp.carnet.hr unstable/contrib Translation-en
-Get:17 http://incoming.debian.org Sources [30.7 kB]
-Get:18 http://incoming.debian.org Packages [630 kB]
+Get:17 http://incoming.debian.org Sources [49.7 kB]
+Get:18 http://incoming.debian.org Packages [772 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 25.5 MB in 26s (956 kB/s)
+Fetched 26.1 MB in 27s (963 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -85,11 +85,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 379 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (tar) [370 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (diff) [6869 B]
-Fetched 379 kB in 1s (309 kB/s)
+Need to get 383 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
+Fetched 383 kB in 1s (279 kB/s)
Download complete and in download only mode
Check arch
@@ -103,18 +103,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.14.5-2)
+fakeroot: already installed (1.15.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -138,7 +138,7 @@ gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.8+20110307-1)
ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-18)
+perl-base: already installed (5.10.1-19)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.1)
@@ -149,12 +149,12 @@ mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
libc6-dev: already installed (2.11.2-11)
libc6-dev-sparc64: already installed (2.11.2-11)
-gcc: already installed (4:4.4.5-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-4 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.4.5-6 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.4.5-6 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8)
dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.2
+Using default version 8.1.3
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -164,53 +164,67 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ bsdmainutils dpkg-dev file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libdpkg-perl libglib2.0-0 libmagic1 libncurses5
+ libpcre3 libpipeline1 libunistring0 libxml2 man-db ncurses-bin po-debconf
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff ncurses-doc less www-browser libmail-box-perl
+ wamerican wordlist whois vacation devscripts doc-base dh-make debian-keyring
+ gettext-doc groff ncurses-doc less www-browser libmail-box-perl
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ autotools-dev libalgorithm-merge-perl curl wget lynx-cur autopoint
+ libglib2.0-data shared-mime-info libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 20 newly installed, 0 to remove and 9 not upgraded.
-Need to get 10.9 MB of archives.
-After this operation, 30.9 MB of additional disk space will be used.
-Get:1 http://ftp.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.2 [205 kB]
-Get:2 http://incoming.debian.org/buildd-unstable/ libglib2.0-0 2.28.4-1 [1553 kB]
-Get:3 http://ftp.carnet.hr/debian/ unstable/main groff-base sparc 1.21-5 [1152 kB]
-Get:4 http://ftp.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.0-1 [35.8 kB]
-Get:5 http://ftp.carnet.hr/debian/ unstable/main man-db sparc 2.5.9-4 [1007 kB]
-Get:6 http://ftp.carnet.hr/debian/ unstable/main libmagic1 sparc 5.04-5 [239 kB]
-Get:7 http://ftp.carnet.hr/debian/ unstable/main file sparc 5.04-5 [49.5 kB]
-Get:8 http://ftp.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-3 [140 kB]
-Get:9 http://ftp.carnet.hr/debian/ unstable/main libpcre3 sparc 8.12-3 [265 kB]
-Get:10 http://ftp.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-2 [840 kB]
-Get:11 http://ftp.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:12 http://ftp.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.2-1 [119 kB]
-Get:13 http://ftp.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-3 [424 kB]
-Get:14 http://ftp.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-3 [2006 kB]
-Get:15 http://ftp.carnet.hr/debian/ unstable/main intltool-debian sparc 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.carnet.hr/debian/ unstable/main po-debconf sparc 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.carnet.hr/debian/ unstable/main debhelper sparc 8.1.2 [553 kB]
-Get:18 http://ftp.carnet.hr/debian/ unstable/main cdbs sparc 0.4.92 [1268 kB]
-Get:19 http://ftp.carnet.hr/debian/ unstable/main libncurses5-dev sparc 5.8+20110307-1 [481 kB]
-Get:20 http://ftp.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
+The following packages will be upgraded:
+ dpkg-dev libdpkg-perl libncurses5 ncurses-bin
+4 upgraded, 20 newly installed, 0 to remove and 10 not upgraded.
+Need to get 13.2 MB of archives.
+After this operation, 31.1 MB of additional disk space will be used.
+Get:1 http://ftp.carnet.hr/debian/ unstable/main ncurses-bin sparc 5.9-1 [333 kB]
+Get:2 http://ftp.carnet.hr/debian/ unstable/main libncurses5 sparc 5.9-1 [361 kB]
+Get:3 http://ftp.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.2 [205 kB]
+Get:4 http://ftp.carnet.hr/debian/ unstable/main groff-base sparc 1.21-5 [1152 kB]
+Get:5 http://ftp.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.0-1 [35.8 kB]
+Get:6 http://ftp.carnet.hr/debian/ unstable/main man-db sparc 2.6.0.1-1 [1013 kB]
+Get:7 http://ftp.carnet.hr/debian/ unstable/main libmagic1 sparc 5.04-5 [239 kB]
+Get:8 http://ftp.carnet.hr/debian/ unstable/main file sparc 5.04-5 [49.5 kB]
+Get:9 http://ftp.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-3 [140 kB]
+Get:10 http://ftp.carnet.hr/debian/ unstable/main libpcre3 sparc 8.12-3 [265 kB]
+Get:11 http://ftp.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-2 [840 kB]
+Get:12 http://ftp.carnet.hr/debian/ unstable/main dpkg-dev sparc 1.16.0.1 [871 kB]
+Get:13 http://ftp.carnet.hr/debian/ unstable/main libdpkg-perl sparc 1.16.0.1 [748 kB]
+Get:14 http://ftp.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:15 http://ftp.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.28.4-1 [1553 kB]
+Get:16 http://ftp.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.2-1 [119 kB]
+Get:17 http://ftp.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-3 [424 kB]
+Get:18 http://ftp.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-3 [2006 kB]
+Get:19 http://ftp.carnet.hr/debian/ unstable/main intltool-debian sparc 0.35.0+20060710.1 [30.8 kB]
+Get:20 http://ftp.carnet.hr/debian/ unstable/main po-debconf sparc 1.0.16+nmu1 [223 kB]
+Get:21 http://ftp.carnet.hr/debian/ unstable/main debhelper sparc 8.1.3 [554 kB]
+Get:22 http://ftp.carnet.hr/debian/ unstable/main cdbs sparc 0.4.92 [1268 kB]
+Get:23 http://ftp.carnet.hr/debian/ unstable/main libncurses5-dev sparc 5.9-1 [481 kB]
+Get:24 http://ftp.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.9 MB in 7s (1436 kB/s)
+Fetched 13.2 MB in 9s (1387 kB/s)
+(Reading database ... 10348 files and directories currently installed.)
+Preparing to replace ncurses-bin 5.8+20110307-1 (using .../ncurses-bin_5.9-1_sparc.deb) ...
+Unpacking replacement ncurses-bin ...
+Setting up ncurses-bin (5.9-1) ...
+(Reading database ... 10348 files and directories currently installed.)
+Preparing to replace libncurses5 5.8+20110307-1 (using .../libncurses5_5.9-1_sparc.deb) ...
+Unpacking replacement libncurses5 ...
+Setting up libncurses5 (5.9-1) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10488 files and directories currently installed.)
+(Reading database ... 10348 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_sparc.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-5_sparc.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_sparc.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.9-4_sparc.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.1-1_sparc.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_sparc.deb) ...
Selecting previously deselected package file.
@@ -221,6 +235,10 @@ Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_sparc.deb) ...
Selecting previously deselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_sparc.deb) ...
+Preparing to replace dpkg-dev 1.15.8.10 (using .../dpkg-dev_1.16.0.1_sparc.deb) ...
+Unpacking replacement dpkg-dev ...
+Preparing to replace libdpkg-perl 1.15.8.10 (using .../libdpkg-perl_1.16.0.1_sparc.deb) ...
+Unpacking replacement libdpkg-perl ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_sparc.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -236,11 +254,11 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_sparc.deb)
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_sparc.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_sparc.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.3_sparc.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.92_sparc.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_sparc.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_sparc.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_sparc.deb) ...
Setting up bsdmainutils (8.2.2) ...
@@ -248,13 +266,15 @@ update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write)
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.5.9-4) ...
+Setting up man-db (2.6.0.1-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up libdpkg-perl (1.16.0.1) ...
+Setting up dpkg-dev (1.16.0.1) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.4-1) ...
No schema files found: doing nothing.
@@ -263,19 +283,19 @@ Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
+Setting up debhelper (8.1.3) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8+20110307-1) ...
+Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-bpo.5-sparc64-smp sparc (sparc64)
-Toolchain package versions: binutils_2.21.0.20110322-1 dpkg-dev_1.15.8.10 g++-4.4_4.4.5-14 gcc-4.4_4.4.5-14 libc6-dev_2.11.2-11 libstdc++6_4.5.2-6 libstdc++6-4.4-dev_4.4.5-14 linux-libc-dev_2.6.38-1
-Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22+b1 bash_4.1-3 binutils_2.21.0.20110322-1 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-4 cpp-4.4_4.4.5-14 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b2 g++_4:4.4.5-4 g++-4.4_4.4.5-14 gcc_4:4.4.5-4 gcc-4.4_4.4.5-14 gcc-4.4-base_4.4.5-14 gcc-4.5-base_4.5.2-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libc6-dev-sparc64_2.11.2-11 libc6-sparc64_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-4 libdpkg-perl_1.15.8.10 libgc1c2_1:7.1-7 libgcc1_1:4.5.2-6 libgdbm3_1.8.3-9+b1 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.5.2-6 liblocale-gettext-perl_1.05-6+b1 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libss2_1.41.12-2 libstdc++6_4.5.2-6 libstdc++6-4.4-dev_4.4.5-14 libtext-charwidth-perl_0.04-6+b1 libtext-iconv-perl_1.7-2+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15+b1 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011d-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0.1 g++-4.4_4.4.5-15 gcc-4.4_4.4.5-15 libc6-dev_2.11.2-11 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 linux-libc-dev_2.6.38-2
+Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22+b1 bash_4.1-3 binutils_2.21.0.20110327-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-6 cpp-4.4_4.4.5-15 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b2 g++_4:4.4.5-6 g++-4.4_4.4.5-15 gcc_4:4.4.5-6 gcc-4.4_4.4.5-15 gcc-4.4-base_4.4.5-15 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libc6-dev-sparc64_2.11.2-11 libc6-sparc64_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-4 libdpkg-perl_1.16.0.1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9+b1 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15+b1 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011e-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -287,12 +307,12 @@ Unpack source
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.14
-dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.15-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.15
+dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
Check disc space
────────────────
@@ -308,8 +328,8 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.14-1
- dpkg-source --before-build samtools-0.1.14
+dpkg-buildpackage: source version 0.1.15-1
+ dpkg-source --before-build samtools-0.1.15
dpkg-buildpackage: host architecture sparc
fakeroot debian/rules clean
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -320,17 +340,17 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/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 `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -343,8 +363,8 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -358,15 +378,16 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/bcftools'
+ar -cru 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 glf.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 `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -377,10 +398,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -398,25 +419,26 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/misc'
-gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/misc'
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -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 -g -O2 -fPIC -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 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/misc'
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -426,27 +448,27 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
make[1]: *** [ex1.bam] Bus error
make[1]: *** Deleting file `ex1.bam'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110329-0716
+Build finished at 20110412-1136
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-1f17b091-dc18-40ea-9d8a-12962f92cec8/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-739c441c-242d-42f5-ba20-68c6841adc6d/build/buildd-samtools_0.1.15-1-sparc-UFtlab
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -454,19 +476,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 5648
+Build-Space: 5772
Build-Time: 98
Distribution: sid
Fail-Stage: build
-Install-Time: 68
-Job: samtools_0.1.14-1
+Install-Time: 80
+Job: samtools_0.1.15-1
Package: samtools
-Package-Time: 215
-Source-Version: 0.1.14-1
-Space: 5648
+Package-Time: 229
+Source-Version: 0.1.15-1
+Space: 5772
Status: attempted
-Version: 0.1.14-1
+Version: 0.1.15-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110329-0716
-Build needed 00:03:35, 5648k disc space
-Signature with key '9BBB678A' requested:
+Finished at 20110412-1136
+Build needed 00:03:49, 5772k disc space
diff --git a/sparc64.log b/sparc64.log
deleted file mode 100644
index e2415eb..0000000
--- a/sparc64.log
+++ /dev/null
@@ -1,291 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><title>File `log' in samtools_0.1.12a-1_sparc64 (Dec 3 19:46)</title><meta http-equiv="content-type" content="text/html;charset=utf-8"></head><body bgcolor="#ffffff">
-<table width="100%"><tr valign=top><td align=left><h2>File `log' in samtools_0.1.12a-1_sparc64 (Dec 3 19:46)</h2></td><td align=right><a href="build.php?&pkg=samtools&arch=sparc64">samtools</a> >> <a href="build.php?&pkg=samtools&ver=0.1.12a-1&arch=sparc64">0.1.12a-1</a> >> <a href="build.php?&pkg=samtools&ver=0.1.12a-1&arch=sparc64&stamp=1291405586">Dec 3 19:46</a> >> log</td></tr></table><p><pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on zee.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (sparc64) 03 Dec 2010 19:43 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.12a-1
-Architecture: sparc64
-Chroot Build Dir: /var/lib/schroot/mount/sid-sparc64-sbuild-f82f2939-8b43-40d2-a78b-433607da1db0/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb
-Start Time: 20101203-1943
-Hit http://debian.oregonstate.edu sid Release.gpg
-Hit http://debian.oregonstate.edu sid Release
-Hit http://debian.oregonstate.edu sid/main Sources/DiffIndex
-Hit http://ftp.debian-ports.org sid Release.gpg
-Ign http://ftp.debian-ports.org/debian/ sid/main Translation-en
-Hit http://ftp.debian-ports.org unreleased Release.gpg
-Ign http://ftp.debian-ports.org/debian/ unreleased/main Translation-en
-Hit http://incoming.debian-ports.org unstable Release.gpg
-Ign http://incoming.debian-ports.org/buildd/ unstable/main Translation-en
-Hit http://incoming.debian-ports.org unstable Release
-Hit http://ftp.debian-ports.org sid Release
-Hit http://ftp.debian-ports.org unreleased Release
-Hit http://incoming.debian-ports.org unstable/main Sources
-Hit http://ftp.debian-ports.org sid/main sparc64 Packages
-Hit http://incoming.debian-ports.org unstable/main sparc64 Packages
-Hit http://ftp.debian-ports.org unreleased/main sparc64 Packages
-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://git.debian.org/debian-med/samtools.git
-Need to get 364 kB of source archives.
-Get:1 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.12a-1 (dsc) [1946 B]
-Get:2 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.12a-1 (tar) [356 kB]
-Get:3 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.12a-1 (diff) [6337 B]
-Fetched 364 kB in 0s (3728 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Checking for already installed source dependencies...
-debhelper: already installed (8.0.0 >= 8 is satisfied)
-cdbs: missing
-libncurses5-dev: missing
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
-Checking for source dependency conflicts...
-Installing positive dependencies: cdbs libncurses5-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-Suggested packages:
- devscripts doc-base
-Recommended packages:
- autotools-dev
-The following NEW packages will be installed:
- cdbs libncurses5-dev
-debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 2 newly installed, 0 to remove and 34 not upgraded.
-Need to get 0 B/2873 kB of archives.
-After this operation, 8733 kB of additional disk space will be used.
-Selecting previously deselected package cdbs.
-(Reading database ... 31276 files and directories currently installed.)
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_sparc64.deb) ...
-Processing triggers for man-db ...
-Setting up cdbs (0.4.89) ...
-Setting up libncurses5-dev (5.7+20100313-4) ...
-Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: Linux 2.6.32-bpo.5-sparc64-smp sparc64 (sparc64)
-Toolchain package versions: libc6-dev_2.11.2-7 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-26 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-15+b1 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
-Package versions: adduser_3.112+nmu2 ant1.7_1.7.1-7 ant1.7-optional_1.7.1-7 apt_0.8.8 autoconf_2.67-2 automake_1:1.11.1-1 autotools-dev_20100122.1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15+b1 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 chrpath_0.13-2 comerr-dev_2.1-1.41.12-2 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.1 dbus_1.2.24-3 dbus-x11_1.2.24-3 debconf_1.5.36 debconf-english_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2010.06.16 debianutils_3.4.1 default-jdk_1:1.5-40 default-jre_1:1.5-40 default-jre-headless_1:1.5-40 defoma_0.11.11 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 ecj_3.5.1-1 ecj-gcj_3.5.1-1 fakeroot_1.14.4-1 fastjar_2:0.98-3 file_5.04-5 findutils_4.4.2-1 fontconfig_2.8.0-2.1 fontconfig-config_2.8.0-2.1 g++_4:4.4.5-1 g++-4.4_4.4.5-10 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-1 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gcj-4.4-base_4.4.5-9 gcj-4.4-jdk_4.4.5-9 gcj-4.4-jre_4.4.5-9 gcj-4.4-jre-headless_4.4.5-9 gcj-4.4-jre-lib_4.4.5-9 gcj-jdk_4:4.4.5-1 gcj-jre_4:4.4.5-1 gcj-jre-headless_4:4.4.5-1 gconf2_2.28.1-6 gconf2-common_2.28.1-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 ghostscript_8.71~dfsg2-6 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gsfonts_1:8.11+urwcyr1.0.7~pre44-4.2 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 java-common_0.40 krb5-multidev_1.8.3+dfsg-3 libacl1_2.2.49-4 libantlr-java_2.7.7-16 libasound2_1.0.23-2.1 libasound2-dev_1.0.23-2.1 libasyncns0_0.3-1.1 libatk1.0-0_1.30.0-1 libatk1.0-dev_1.30.0-1 libattr1_1:2.4.44-2 libaudit0_1.7.13-1+b2 libavahi-client-dev_0.6.27-3 libavahi-client3_0.6.27-3 libavahi-common-data_0.6.27-2 libavahi-common-dev_0.6.27-3 libavahi-common3_0.6.27-3 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libbz2-dev_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc6_2.11.2-7 libc6-dev_2.11.2-7 libcairo2_1.8.10-6 libcairo2-dev_1.8.10-6 libcanberra-gtk0_0.24-1 libcanberra0_0.24-1 libcap2_1:2.19-3 libcdt4_2.26.3-5+b1 libcgraph5_2.26.3-5+b1 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcups2_1.4.4-7 libcups2-dev_1.4.4-7 libcupsimage2_1.4.4-7 libdatrie1_0.2.4-1 libdb4.7_4.7.25-9~sparc64 libdb4.8_4.8.30-3 libdbus-1-3_1.2.24-3 libdbus-1-dev_1.2.24-3 libdbus-glib-1-2_0.88-2 libdjvulibre-dev_3.5.23-3 libdjvulibre-text_3.5.23-3 libdjvulibre21_3.5.23-3 libdpkg-perl_1.15.8.5 libdrm-radeon1_2.4.21-1~squeeze3 libdrm2_2.4.21-1~squeeze3 libecj-java_3.5.1-1 libecj-java-gcj_3.5.1-1 libexif-dev_0.6.19-1 libexif12_0.6.19-1 libexpat1_2.0.1-7 libexpat1-dev_2.0.1-7 libffi-dev_3.0.9-3 libffi5_3.0.9-3 libflac8_1.2.1-3 libfontconfig1_2.8.0-2.1 libfontconfig1-dev_2.8.0-2.1 libfontenc1_1:1.1.0-1 libfreetype6_2.4.2-2 libfreetype6-dev_2.4.2-2 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgcj-bc_4.4.5-1 libgcj-common_1:4.4.5-1 libgcj10_4.4.5-9 libgcj10-awt_4.4.5-9 libgcj10-dev_4.4.5-9 libgconf2-4_2.28.1-6 libgcrypt11_1.4.5-2 libgcrypt11-dev_1.4.5-2 libgd2-noxpm_2.0.36~rc1~dfsg-5 libgdbm3_1.8.3-9 libgif-dev_4.1.6-9 libgif4_4.1.6-9 libgl1-mesa-dri_7.7.1-4 libglib2.0-0_2.24.2-1 libglib2.0-dev_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls-dev_2.8.6-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-10 libgpg-error-dev_1.6-1 libgpg-error0_1.6-1 libgpm2_1.20.4-3.3 libgraph4_2.26.3-5+b1 libgraphviz-dev_2.26.3-5+b1 libgs8_8.71~dfsg2-6 libgsf-1-114_1.14.19-2 libgsf-1-common_1.14.19-2 libgssapi-krb5-2_1.8.3+dfsg-3 libgssrpc4_1.8.3+dfsg-3 libgtk2.0-0_2.20.1-2 libgtk2.0-common_2.20.1-2 libgtk2.0-dev_2.20.1-2 libgtop2-7_2.28.1-1 libgtop2-common_2.28.1-1 libgvc5_2.26.3-5+b1 libgvpr1_2.26.3-5+b1 libhunspell-1.2-0_1.2.11-1 libice-dev_2:1.0.6-2 libice6_2:1.0.6-2 libidl0_0.8.14-0.1 libilmbase-dev_1.0.1-3 libilmbase6_1.0.1-3 libjasper-dev_1.900.1-7 libjasper1_1.900.1-7 libjaxp1.3-java_1.3.05-1 libjbig2dec0_0.11-1 libjline-java_0.9.94-5 libjpeg62_6b1-1 libjpeg62-dev_6b1-1 libk5crypto3_1.8.3+dfsg-3 libkadm5clnt-mit7_1.8.3+dfsg-3 libkadm5srv-mit7_1.8.3+dfsg-3 libkdb5-4_1.8.3+dfsg-3 libkeyutils1_1.4-1 libkrb5-3_1.8.3+dfsg-3 libkrb5-dev_1.8.3+dfsg-3 libkrb5support0_1.8.3+dfsg-3 liblcms1_1.18.dfsg-1.2+b2 liblcms1-dev_1.18.dfsg-1.2+b2 libldap-2.4-2_2.4.23-7 liblocale-gettext-perl_1.05-6 liblqr-1-0_0.4.1-1 liblqr-1-0-dev_0.4.1-1 libltdl-dev_2.2.6b-2~sparc64 libltdl7_2.2.6b-2~sparc64 liblzma2_5.0.0-2 libmagic1_5.04-5 libmetacity-private0_1:2.30.1-3 libmozjs-dev_1.9.1.12-2+sparc64 libmozjs2d_1.9.1.12-2+sparc64 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libnewt0.52_0.52.11-2 libnotify1_0.5.0-2 libnspr4-0d_4.8.6-1 libnspr4-dev_4.8.6-1 libnss3-1d_3.12.8-1 libnss3-dev_3.12.8-1 libogg0_1.2.0~dfsg-1 libopenexr-dev_1.6.1-4.1 libopenexr6_1.6.1-4.1 liborbit2_1:2.14.18-0.1 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpango1.0-0_1.28.3-1 libpango1.0-common_1.28.3-1 libpango1.0-dev_1.28.3-1 libpaper1_1.1.24 libpathplan4_2.26.3-5+b1 libpcre3_8.02-1.1 libperl-dev_5.10.1-12 libperl5.10_5.10.1-12 libpixman-1-0_0.16.4-1 libpixman-1-dev_0.16.4-1 libpng12-0_1.2.44-1 libpng12-dev_1.2.44-1 libpopt0_1.16-1 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libpulse-browse0_0.9.21-3 libpulse-dev_0.9.21-3 libpulse-mainloop-glib0_0.9.21-3 libpulse0_0.9.21-3 libreadline5_5.2-7 libreadline6_6.1-3 librsvg2-2_2.26.3-1 librsvg2-dev_2.26.3-1 libsasl2-2_2.1.23.dfsg1-6 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libsm-dev_2:1.2.0-1 libsm6_2:1.2.0-1 libsndfile1_1.0.23-1 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libssl0.9.8_0.9.8o-3 libstartup-notification0_0.10-1 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtasn1-3_2.7-1 libtasn1-3-dev_2.7-1 libtdb1_1.2.7+git20101021-1 libthai-data_0.1.14-2 libthai0_0.1.14-2 libtiff4_3.9.4-5 libtiff4-dev_3.9.4-5 libtiffxx0c2_3.9.4-5 libtimedate-perl_1.2000-1 libtool_2.2.6b-2~sparc64 libudev0_164-2 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libvorbis0a_1.3.1-1 libvorbisenc2_1.3.1-1 libvorbisfile3_1.3.1-1 libwmf-dev_0.2.8.4-6.1 libwmf0.2-7_0.2.8.4-6.1 libwrap0_7.6.q-19 libx11-6_2:1.3.3-3 libx11-data_2:1.3.3-3 libx11-dev_2:1.3.3-3 libxalan2-java_2.7.1-5 libxau-dev_1:1.0.6-1 libxau6_1:1.0.6-1 libxaw7_2:1.0.8-2 libxaw7-dev_2:1.0.8-2 libxcb-atom1_0.3.6-1 libxcb-aux0_0.3.6-1 libxcb-event1_0.3.6-1 libxcb-render-util0_0.3.6-1 libxcb-render-util0-dev_0.3.6-1 libxcb-render0_1.6-1 libxcb-render0-dev_1.6-1 libxcb1_1.6-1 libxcb1-dev_1.6-1 libxcomposite-dev_1:0.4.3-1 libxcomposite1_1:0.4.3-1 libxcursor-dev_1:1.1.11-1 libxcursor1_1:1.1.11-1 libxdamage-dev_1:1.1.3-1 libxdamage1_1:1.1.3-1 libxdmcp-dev_1:1.1.0-1 libxdmcp6_1:1.1.0-1 libxdot4_2.26.3-5+b1 libxerces2-java_2.9.1-4.1 libxext-dev_2:1.1.2-1 libxext6_2:1.1.2-1 libxfixes-dev_1:4.0.5-1 libxfixes3_1:4.0.5-1 libxfont1_1:1.4.1-2 libxft-dev_2.1.14-2 libxft2_2.1.14-2 libxi-dev_2:1.3-4 libxi6_2:1.3-4 libxinerama-dev_2:1.1.1-1 libxinerama1_2:1.1.1-1 libxkbfile1_1:1.0.7-1 libxml2_2.7.8.dfsg-1 libxml2-dev_2.7.8.dfsg-1 libxml2-utils_2.7.8.dfsg-1 libxmu-dev_2:1.1.0-1 libxmu-headers_2:1.1.0-1 libxmu6_2:1.1.0-1 libxmuu1_2:1.1.0-1 libxp-dev_1:1.0.0.xsf1-2 libxp6_1:1.0.0.xsf1-2 libxpm-dev_1:3.5.9-1 libxpm4_1:3.5.9-1 libxrandr-dev_2:1.3.0-3 libxrandr2_2:1.3.0-3 libxrender-dev_1:0.9.6-1 libxrender1_1:0.9.6-1 libxt-dev_1:1.0.7-1 libxt6_1:1.0.7-1 libxtst-dev_2:1.2.0-1 libxtst6_2:1.2.0-1 linux-libc-dev_2.6.32-26 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lsb-release_3.2-26 m4_1.4.14-3 make_3.81-8 man-db_2.5.7-6 mauve_20090924-1 mawk_1.3.3-15 metacity_1:2.30.1-3 metacity-common_1:2.30.1-3 mime-support_3.51-1 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 net-tools_1.60-23 netbase_4.43 ocaml-base-nox_3.11.2-2 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-12 perl-base_5.10.1-12 perl-modules_5.10.1-16 pkg-config_0.25-1.1 po-debconf_1.0.16 procps_1:3.2.8-9 psmisc_22.13-1 python_2.6.6-3+squeeze2 python-minimal_2.6.6-3+squeeze2 python-support_1.0.11 python2.6_2.6.6-7 python2.6-minimal_2.6.6-7 readline-common_6.1-3 rhino_1.7R2-4 sed_4.2.1-7 sensible-utils_0.0.4 sgml-base_1.26+nmu1 shared-mime-info_0.71-4 sharutils_1:4.9-1 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 time_1.7-23.1 ttf-dejavu-core_2.31-1 tzdata_2010o-1 ucf_3.0025+nmu1 unzip_6.0-4 util-linux_2.17.2-3.3 wget_1.12-2.1 whiptail_0.52.11-2 x11-common_1:7.5+8 x11-xkb-utils_7.5+5 x11proto-composite-dev_1:0.4.2-1 x11proto-core-dev_7.0.19-1 x11proto-damage-dev_1:1.2.1-1 x11proto-fixes-dev_1:4.1.2-1 x11proto-input-dev_2.0.1-1 x11proto-kb-dev_1.0.5-1 x11proto-print-dev_1.0.3.xsf1-1 x11proto-randr-dev_1.3.2-1 x11proto-record-dev_1.14.1-1 x11proto-render-dev_2:0.11.1-1 x11proto-xext-dev_7.1.2-1 x11proto-xinerama-dev_1.2-2 xauth_1:1.0.5-1 xfonts-base_1:1.0.3 xfonts-encodings_1:1.0.4-1 xfonts-utils_1:7.6~1 xkb-data_1.8-2 xserver-common_2:1.7.7-9 xtrans-dev_1.2.5-1 xulrunner-1.9.1_1.9.1.12-2+sparc64 xulrunner-dev_1.9.1.12-2+sparc64 xvfb_2:1.7.7-9 xz-utils_4.999.9beta+20100810-1 zenity_2.30.0-1 zip_3.0-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Dec 3 06:37:23 2010 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.12a
-dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.12a-1
- dpkg-source --before-build samtools-0.1.12a
-dpkg-buildpackage: host architecture sparc64
- /usr/bin/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 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/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 `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
-rm -f debian/stamp-makefile-check
-dh_clean
-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
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/bcftools'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/misc'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/bcftools'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/misc'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/misc'
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-make[1]: *** [ex1.bam] Bus error
-make[1]: *** Deleting file `ex1.bam'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/examples'
-make: *** [debian/stamp-makefile-check] Error 2
-dpkg-buildpackage: error: debian/rules build gave error exit status 2
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-1946
-FAILED [dpkg-buildpackage died]
-────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc64-sbuild-f82f2939-8b43-40d2-a78b-433607da1db0/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb
-(Reading database ... 32383 files and directories currently installed.)
-Removing libncurses5-dev ...
-Removing cdbs ...
-Processing triggers for man-db ...
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-1946
-Build needed 00:02:55, 6420k disc space
-
-</pre>
-<p>
-
-<!-- Footer menu bar -->
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-<table width="100%">
-<tr valign=top>
- <td align=left>
- <address>
-
- These scripts were derived from the buildd.debian.org, thanks to Ryan Murray.<br>
- Contact address: <<a href="mailto:admin at debian-ports.org">admin at debian-ports.org</a>>
- </address>
- </td>
- <td align=right>
- <font size=-1>(
- <a href="index.php">index</a> |
- <a href="build.php">build logs</a>
- )</font>
- </td>
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-<br>
-</body>
--
Processing of sequence alignments in SAM and BAM formats.
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