[med-svn] [SCM] Processing of sequence alignments in SAM and BAM formats. branch, squeeze-backports-meta, updated. c71ae7ac5f3c25ffdd97f0cd05c621b2a36f17fd
Charles Plessy
plessy at debian.org
Mon Mar 28 01:34:00 UTC 2011
The following commit has been merged in the squeeze-backports-meta branch:
commit c71ae7ac5f3c25ffdd97f0cd05c621b2a36f17fd
Author: Charles Plessy <plessy at debian.org>
Date: Mon Mar 28 10:31:29 2011 +0900
# Collected build logs for 0.1.12a-1~bpo60+1.
diff --git a/alpha.log b/alpha.log
deleted file mode 100644
index d5b8196..0000000
--- a/alpha.log
+++ /dev/null
@@ -1,576 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/alpha received Fri Dec 3 09:30:16 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=alpha">alpha</a> >> Fri Dec 3 09:30:16 2010<pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on goedel.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (alpha) 03 Dec 2010 09:21 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.12a-1
-Architecture: alpha
-Chroot Build Dir: /var/lib/schroot/mount/sid-alpha-sbuild-8c0a09a0-0453-4a03-9ecf-2d62cbdb7eda/build/buildd-samtools_0.1.12a-1-alpha-NKtcft
-Start Time: 20101203-0921
-Get:1 http://ftp.de.debian.org sid Release.gpg [835 B]
-Ign http://ftp.de.debian.org/debian/ sid/contrib Translation-en
-Ign http://ftp.de.debian.org/debian/ sid/main Translation-en
-Get:2 http://ftp.de.debian.org sid Release [104 kB]
-Get:3 http://incoming.debian.org sid Release.gpg [835 B]
-Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
-Ign http://incoming.debian.org/debian/ sid/main Translation-en
-Get:4 http://ftp.de.debian.org sid/main alpha Packages/DiffIndex [2038 B]
-Get:5 http://incoming.debian.org Release.gpg [835 B]
-Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:6 http://incoming.debian.org sid Release [104 kB]
-Hit http://ftp.de.debian.org sid/contrib alpha Packages/DiffIndex
-Get:7 http://ftp.de.debian.org sid/main alpha 2010-12-01-1412.04.pdiff [499 B]
-Get:8 http://incoming.debian.org Release [1604 B]
-Get:9 http://ftp.de.debian.org sid/main alpha 2010-12-01-1412.04.pdiff [499 B]
-Get:10 http://ftp.de.debian.org sid/main alpha 2010-12-01-1412.04.pdiff [499 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 alpha Packages/DiffIndex [2038 B]
-Hit http://incoming.debian.org sid/contrib alpha Packages/DiffIndex
-Get:13 http://incoming.debian.org Sources [8014 B]
-Get:14 http://incoming.debian.org Packages [169 kB]
-Get:15 http://incoming.debian.org sid/main 2010-12-03-0208.36.pdiff [3044 B]
-Get:16 http://incoming.debian.org sid/main alpha 2010-12-03-0208.36.pdiff [10.1 kB]
-Get:17 http://incoming.debian.org sid/main 2010-12-03-0208.36.pdiff [3044 B]
-Get:18 http://incoming.debian.org sid/main alpha 2010-12-03-0208.36.pdiff [10.1 kB]
-Get:19 http://incoming.debian.org sid/main 2010-12-03-0208.36.pdiff [3044 B]
-Get:20 http://ftp.de.debian.org sid/main alpha 2010-12-01-2014.11.pdiff [1392 B]
-Get:21 http://ftp.de.debian.org sid/main alpha 2010-12-01-2014.11.pdiff [1392 B]
-Get:22 http://incoming.debian.org sid/main alpha 2010-12-03-0208.36.pdiff [10.1 kB]
-Get:23 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:24 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:25 http://ftp.de.debian.org sid/main alpha 2010-12-01-2014.11.pdiff [1392 B]
-Get:26 http://incoming.debian.org sid/main alpha 2010-12-03-0810.19.pdiff [798 B]
-Get:27 http://incoming.debian.org sid/main alpha 2010-12-03-0810.19.pdiff [798 B]
-Get:28 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:29 http://ftp.de.debian.org sid/main alpha 2010-12-02-0209.58.pdiff [1681 B]
-Get:30 http://ftp.de.debian.org sid/main alpha 2010-12-02-0209.58.pdiff [1681 B]
-Get:31 http://incoming.debian.org sid/main alpha 2010-12-03-0810.19.pdiff [798 B]
-Get:32 http://ftp.de.debian.org sid/main alpha 2010-12-02-0209.58.pdiff [1681 B]
-Get:33 http://ftp.de.debian.org sid/main alpha 2010-12-02-0815.49.pdiff [225 B]
-Get:34 http://ftp.de.debian.org sid/main alpha 2010-12-02-0815.49.pdiff [225 B]
-Get:35 http://ftp.de.debian.org sid/main alpha 2010-12-02-0815.49.pdiff [225 B]
-Get:36 http://ftp.de.debian.org sid/main alpha 2010-12-02-1418.14.pdiff [26.1 kB]
-Get:37 http://ftp.de.debian.org sid/main alpha 2010-12-02-1418.14.pdiff [26.1 kB]
-Get:38 http://ftp.de.debian.org sid/main alpha 2010-12-02-1418.14.pdiff [26.1 kB]
-Get:39 http://ftp.de.debian.org sid/main alpha 2010-12-02-2015.37.pdiff [35.1 kB]
-Get:40 http://ftp.de.debian.org sid/main alpha 2010-12-02-2015.37.pdiff [35.1 kB]
-Get:41 http://ftp.de.debian.org sid/main alpha 2010-12-02-2015.37.pdiff [35.1 kB]
-Get:42 http://ftp.de.debian.org sid/main alpha 2010-12-03-0208.36.pdiff [10.1 kB]
-Get:43 http://ftp.de.debian.org sid/main alpha 2010-12-03-0208.36.pdiff [10.1 kB]
-Get:44 http://ftp.de.debian.org sid/main alpha 2010-12-03-0208.36.pdiff [10.1 kB]
-Get:45 http://ftp.de.debian.org sid/main alpha 2010-12-03-0810.19.pdiff [798 B]
-Get:46 http://ftp.de.debian.org sid/main alpha 2010-12-03-0810.19.pdiff [798 B]
-Get:47 http://ftp.de.debian.org sid/main alpha 2010-12-03-0810.19.pdiff [798 B]
-Fetched 485 kB in 42s (11.5 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 364 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
-Fetched 364 kB in 1s (334 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: missing
-Checking for source dependency conflicts...
-Installing positive dependencies: cdbs libncurses5-dev zlib1g-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 zlib1g-dev
-debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 3 newly installed, 0 to remove and 46 not upgraded.
-Need to get 0 B/3121 kB of archives.
-After this operation, 9556 kB of additional disk space will be used.
-Selecting previously deselected package cdbs.
-(Reading database ... 13765 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_alpha.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_alpha.deb) ...
-Processing triggers for man-db ...
-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...
-Kernel: Linux 2.6.26-2-alpha-generic alpha (alpha)
-Toolchain package versions: libc6.1-dev_2.11.2-7 dpkg-dev_1.15.8.4 linux-libc-dev_2.6.32-27 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
-Package versions: apt_0.8.8 asciidoc_8.5.2-1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 binutils-dev_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.3_4.3.5-3 cpp-4.4_4.4.5-10 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2009.01.31 debianutils_3.4 diffutils_1:3.0-1 docbook-xml_4.5-7 docbook-xsl_1.75.2+dfsg-5 dpkg_1.15.8.4 dpkg-dev_1.15.8.4 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++_4:4.4.4-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-1 gcc-4.3_4.3.5-3 gcc-4.3-base_4.3.5-3 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-2 gettext-base_0.18.1.1-2 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_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-11 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc6.1_2.11.2-7 libc6.1-dev_2.11.2-7 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-3 libdpkg-perl_1.15.8.4 libelf-dev_0.148-1 libelf1_0.148-1 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-10 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 libpam-modules_1.1.1-3 libpam-runtime_1.1.1-3 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libssl0.9.8_0.9.8o-3 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_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 libxml2-utils_2.7.7.dfsg-4 libxslt1.1_1.1.26-6 linux-libc-dev_2.6.32-27 login_1:4.1.4.2-1 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-4 mawk_1.3.3-15 mime-support_3.48-1 module-init-tools_3.12-1 mount_2.17.2-3.1 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2-1 patch_2.6-2 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 po-debconf_1.0.16 python_2.6.6-3+squeeze2 python-minimal_2.6.6-3+squeeze2 python2.6_2.6.6-7 python2.6-minimal_2.6.6-7 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sgml-base_1.26+nmu1 sgml-data_2.0.4 sudo_1.7.2p7-1 sysv-rc_2.88dsf-11 sysvinit_2.88dsf-11 sysvinit-utils_2.88dsf-11 tar_1.23-2.1 tzdata_2010o-1 util-linux_2.17.2-3.1 xml-core_0.13 xmlto_0.0.23-2 xsltproc_1.1.26-6 xz-utils_4.999.9beta+20100713-1 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 alpha
- /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-alpha-NKtcft/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/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-alpha-NKtcft/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/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-alpha-NKtcft/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/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-alpha-NKtcft/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
-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
-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-alpha-NKtcft/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/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-alpha-NKtcft/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/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-alpha-NKtcft/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/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-alpha-NKtcft/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/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-alpha-NKtcft/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/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-alpha-NKtcft/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/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-alpha-NKtcft/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-alpha-NKtcft/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-alpha-NKtcft/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
-[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'
-[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
-[mpileup] 1 samples in 1 input files
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-<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-alpha-NKtcft/samtools-0.1.12a/examples'
- /usr/bin/fakeroot debian/rules binary-arch
-touch debian/stamp-makefile-check
-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-alpha-NKtcft/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-alpha-NKtcft/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-alpha-NKtcft/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_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_0.1.12a-1_alpha.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 20101203-0930
-
-samtools_0.1.12a-1_alpha.changes:
-Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: alpha
-Version: 0.1.12a-1
-Distribution: unstable
-Urgency: low
-Maintainer: Debian Build Daemon <buildd_alpha-goedel at buildd...>
-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:
- e386da50ad8f4b31c12c471a3ee2e92af0868f6e 596686 samtools_0.1.12a-1_alpha.deb
- ca438ab8033960703fc2010cf168bd0df1e89bb5 187896 libbam-dev_0.1.12a-1_alpha.deb
-Checksums-Sha256:
- 9694d7c3e75170dc00a9743e3ff2a74586c122ab77940d4552d855d03c312297 596686 samtools_0.1.12a-1_alpha.deb
- d75f2196ea5c327e83095b580dc38f8572e307b757dbd80f85cd1bae91f1d259 187896 libbam-dev_0.1.12a-1_alpha.deb
-Files:
- ccd175cc94346c4fca39c74db4373826 596686 science optional samtools_0.1.12a-1_alpha.deb
- 844a3e6973cc5cb3b9a1a2ba51319355 187896 libdevel optional libbam-dev_0.1.12a-1_alpha.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.12a-1_alpha.deb
-────────────────────────────
-
- new debian package, version 2.0.
- size 596686 bytes: control archive= 1796 bytes.
- 795 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
- Package: samtools
- Version: 0.1.12a-1
- Architecture: alpha
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1132
- Depends: libc6.1 (>= 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 09:29 ./
-drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:29 ./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 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 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2010-12-03 09:29 ./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 2010-12-03 09:24 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2010-12-03 09:29 ./usr/share/doc/samtools/README.bcftools
--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
-drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-12-03 09:29 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7546 2010-12-03 09:29 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-12-03 09:29 ./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 12567 2010-12-02 16:41 ./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 15255 2010-11-17 04:16 ./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 2010-12-03 09:29 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/bin/
--rwxr-xr-x root/root 111048 2010-12-03 09:29 ./usr/bin/bcftools
--rwxr-xr-x root/root 31568 2010-12-03 09:29 ./usr/bin/razip
--rwxr-xr-x root/root 410632 2010-12-03 09:29 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/lib/
-drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/lib/samtools/
--rwxr-xr-x root/root 22296 2010-12-03 09:29 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 9728 2010-12-03 09:29 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 9728 2010-12-03 09:29 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 15320 2010-12-03 09:29 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 11136 2010-12-03 09:29 ./usr/lib/samtools/md5sum-lite
-lrwxrwxrwx root/root 0 2010-12-03 09:29 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.12a-1_alpha.deb
-──────────────────────────────
-
- new debian package, version 2.0.
- size 187896 bytes: control archive= 895 bytes.
- 675 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.12a-1
- Architecture: alpha
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 616
- 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 09:29 ./
-drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:29 ./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 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
--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 09:29 ./usr/lib/
--rw-r--r-- root/root 475670 2010-12-03 09:29 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/include/
--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
--rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-alpha-sbuild-8c0a09a0-0453-4a03-9ecf-2d62cbdb7eda/build/buildd-samtools_0.1.12a-1-alpha-NKtcft
-(Reading database ... 14898 files and directories currently installed.)
-Removing libncurses5-dev ...
-Removing cdbs ...
-Removing zlib1g-dev ...
-Processing triggers for man-db ...
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0930
-Build needed 00:08:29, 11404k disc space
-
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/armel.log b/armel.log
index 7fd5195..14c43a7 100644
--- a/armel.log
+++ b/armel.log
@@ -1,41 +1,95 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/armel received Fri Dec 3 09:28:30 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=armel">armel</a> >> Fri Dec 3 09:28:30 2010<pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on arnold.debian.org
+From buildd at alwyn.debian.org Tue Mar 15 05:55:58 2011
+Return-path: <buildd at alwyn.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 alwyn.debian.org>)
+ id 1PzNEc-0003oa-HC
+ for logs at buildd.debian.org; Tue, 15 Mar 2011 05:55:58 +0000
+Received: from alwyn.islands.arm.com ([217.140.96.59] helo=alwyn.debian.org)
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=alwyn.debian.org, EMAIL=hostmaster at alwyn.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at alwyn.debian.org>)
+ id 1PzNEa-0002DU-G4
+ for logs at buildd.debian.org; Tue, 15 Mar 2011 05:55:56 +0000
+Received: from buildd by alwyn.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at alwyn.debian.org>)
+ id 1PzNEX-000144-VM; Tue, 15 Mar 2011 05:55:54 +0000
+From: buildd on alwyn <buildd at alwyn.debian.org>
+To: buildd-porters at alwyn.debian.org,logs at buildd.debian.org
+Subject: Log for attempted build of samtools_0.1.12a-1~bpo60+1 on armel
+ (dist=squeeze-backports)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1PzNEX-000144-VM at alwyn.debian.org>
+Date: Tue, 15 Mar 2011 05:55:53 +0000
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.5 (14 Nov 2010) on alwyn.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (armel) 03 Dec 2010 09:22 ║
+║ samtools 0.1.12a-1~bpo60+1 (armel) 15 Mar 2011 05:48 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.12a-1~bpo60+1
Architecture: armel
-Chroot Build Dir: /var/lib/schroot/mount/sid-armel-sbuild-933fddaf-1beb-4ac8-bf61-db1837fff3ba/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0
-Start Time: 20101203-0922
-Get:1 http://ftp.uk.debian.org unstable Release.gpg [835B]
-Ign http://ftp.uk.debian.org/debian/ unstable/contrib Translation-en
-Ign http://ftp.uk.debian.org/debian/ unstable/main Translation-en
-Get:2 http://ftp.uk.debian.org unstable Release [104kB]
-Get:3 http://incoming.debian.org unstable Release.gpg [835B]
-Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
-Ign http://incoming.debian.org/debian/ unstable/main Translation-en
-Get:4 http://ftp.uk.debian.org unstable/main Sources [4071kB]
-Get:5 http://incoming.debian.org Release.gpg [835B]
-Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:6 http://incoming.debian.org unstable Release [104kB]
-Get:7 http://incoming.debian.org Release [1604B]
-Get:8 http://incoming.debian.org unstable/main Sources [4071kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib Sources [38.7kB]
-Get:10 http://ftp.uk.debian.org unstable/non-free Sources [83.8kB]
-Get:11 http://ftp.uk.debian.org unstable/main armel Packages [6754kB]
-Get:12 http://incoming.debian.org unstable/contrib Sources [38.7kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [83.8kB]
-Get:14 http://incoming.debian.org unstable/main armel Packages [6754kB]
-Get:15 http://ftp.uk.debian.org unstable/contrib armel Packages [49.6kB]
-Get:16 http://incoming.debian.org unstable/contrib armel Packages [49.6kB]
-Get:17 http://incoming.debian.org Sources [8014B]
-Get:18 http://incoming.debian.org Packages [169kB]
-Fetched 22.4MB in 50s (440kB/s)
+Chroot Build Dir: /var/lib/schroot/mount/squeeze-backports-armel-sbuild-15211ee0-9d28-4fa1-9fd8-ce4f7f552cd9/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf
+Start Time: 20110315-0548
+Get:1 http://ftp.uk.debian.org squeeze Release.gpg [1671 B]
+Ign http://ftp.uk.debian.org/debian/ squeeze/contrib Translation-en
+Ign http://ftp.uk.debian.org/debian/ squeeze/main Translation-en
+Get:2 http://ftp.uk.debian.org squeeze-proposed-updates Release.gpg [835 B]
+Ign http://ftp.uk.debian.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://ftp.uk.debian.org/debian/ squeeze-proposed-updates/main Translation-en
+Get:3 http://ftp.uk.debian.org squeeze Release [69.3 kB]
+Get:4 http://ftp.uk.debian.org squeeze-proposed-updates Release [59.6 kB]
+Get:5 http://ftp.uk.debian.org squeeze/main Sources [3720 kB]
+Get:6 http://ftp.debian.org squeeze Release.gpg [1671 B]
+Ign http://ftp.debian.org/debian/ squeeze/contrib Translation-en
+Ign http://ftp.debian.org/debian/ squeeze/main Translation-en
+Get:7 http://ftp.debian.org squeeze-proposed-updates Release.gpg [835 B]
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/main Translation-en
+Get:8 http://ftp.debian.org squeeze Release [69.3 kB]
+Get:9 http://ftp.debian.org squeeze-proposed-updates Release [59.6 kB]
+Get:10 http://ftp.debian.org squeeze/main Sources [3720 kB]
+Get:11 http://backports-master.debian.org squeeze-backports Release.gpg [835 B]
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/contrib Translation-en
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/main Translation-en
+Get:12 http://backports-master.debian.org Release.gpg [835 B]
+Ign http://backports-master.debian.org/buildd/squeeze-backports/ Translation-en
+Get:13 http://backports-master.debian.org squeeze-backports Release [61.2 kB]
+Get:14 http://backports-master.debian.org Release [1644 B]
+Get:15 http://ftp.uk.debian.org squeeze/contrib Sources [33.9 kB]
+Get:16 http://ftp.uk.debian.org squeeze/non-free Sources [61.7 kB]
+Get:17 http://ftp.debian.org squeeze/contrib Sources [33.9 kB]
+Get:18 http://ftp.debian.org squeeze/non-free Sources [61.7 kB]
+Get:19 http://backports-master.debian.org squeeze-backports/main Sources [9340 B]
+Get:20 http://ftp.uk.debian.org squeeze/main armel Packages [6421 kB]
+Get:21 http://ftp.debian.org squeeze/main armel Packages [6421 kB]
+Get:22 http://backports-master.debian.org squeeze-backports/contrib Sources [14 B]
+Get:23 http://backports-master.debian.org squeeze-backports/non-free Sources [14 B]
+Get:24 http://backports-master.debian.org squeeze-backports/main armel Packages [18.1 kB]
+Get:25 http://backports-master.debian.org squeeze-backports/contrib armel Packages [14 B]
+Get:26 http://backports-master.debian.org Sources [605 B]
+Get:27 http://backports-master.debian.org Packages [11.8 kB]
+Get:28 http://ftp.uk.debian.org squeeze/contrib armel Packages [45.1 kB]
+Get:29 http://ftp.uk.debian.org squeeze-proposed-updates/main Sources [37.7 kB]
+Get:30 http://ftp.uk.debian.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:31 http://ftp.uk.debian.org squeeze-proposed-updates/non-free Sources [926 B]
+Get:32 http://ftp.uk.debian.org squeeze-proposed-updates/main armel Packages [105 kB]
+Get:33 http://ftp.uk.debian.org squeeze-proposed-updates/contrib armel Packages [14 B]
+Get:34 http://ftp.debian.org squeeze/contrib armel Packages [45.1 kB]
+Get:35 http://ftp.debian.org squeeze-proposed-updates/main Sources [37.7 kB]
+Get:36 http://ftp.debian.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:37 http://ftp.debian.org squeeze-proposed-updates/non-free Sources [926 B]
+Get:38 http://ftp.debian.org squeeze-proposed-updates/main armel Packages [105 kB]
+Get:39 http://ftp.debian.org squeeze-proposed-updates/contrib armel Packages [14 B]
+Fetched 21.2 MB in 45s (464 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -54,152 +108,209 @@ 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:
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 364kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337B]
-Fetched 364kB in 1s (279kB/s)
+Need to get 363 kB of source archives.
+Get:1 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (dsc) [1338 B]
+Get:2 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (tar) [356 kB]
+Get:3 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (diff) [6406 B]
+Fetched 363 kB in 1s (215 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
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install build dependencies (aptitude-based 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 libncurses5 libpcre3 libunistring0 libxml2
- man-db ncurses-bin po-debconf
+ libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5 libsigc++-2.0-0c2a
+ libsqlite3-0 libxapian22
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ tasksel debtags libcwidget-dev xapian-tools
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libgpm2 xml-core libmail-sendmail-perl
+ aptitude-doc-en aptitude-doc apt-xapian-index libparse-debianchangelog-perl
+ libgpm2
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
-The following packages will be upgraded:
- libncurses5 ncurses-bin
-2 upgraded, 19 newly installed, 0 to remove and 61 not upgraded.
-Need to get 12.0MB of archives.
-After this operation, 34.3MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main ncurses-bin armel 5.7+20100313-4 [319kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main libncurses5 armel 5.7+20100313-4 [344kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.0.17 [204kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.20.1-10 [1038kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.5.7-6 [1222kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.04-5 [237kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.04-5 [49.4kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-3 [129kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.02-1.1 [234kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-1 [817kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.24.2-1 [1050kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.2-1 [113kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-3 [410kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-3 [1981kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.0.0 [454kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.89 [1240kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 5.7+20100313-4 [1603kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.3.4.dfsg-3 [190kB]
+ aptitude libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5
+ libsigc++-2.0-0c2a libsqlite3-0 libxapian22
+0 upgraded, 8 newly installed, 0 to remove and 6 not upgraded.
+Need to get 6016 kB of archives.
+After this operation, 16.6 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ squeeze/main libboost-iostreams1.42.0 armel 1.42.0-4 [57.3 kB]
+Get:2 http://ftp.uk.debian.org/debian/ squeeze/main libncursesw5 armel 5.7+20100313-5 [368 kB]
+Get:3 http://ftp.uk.debian.org/debian/ squeeze/main libsigc++-2.0-0c2a armel 2.2.4.2-1 [37.9 kB]
+Get:4 http://ftp.uk.debian.org/debian/ squeeze/main libcwidget3 armel 0.5.16-3 [278 kB]
+Get:5 http://ftp.uk.debian.org/debian/ squeeze/main libxapian22 armel 1.2.3-2 [1062 kB]
+Get:6 http://ftp.uk.debian.org/debian/ squeeze/main libept1 armel 1.0.4 [132 kB]
+Get:7 http://ftp.uk.debian.org/debian/ squeeze/main libsqlite3-0 armel 3.7.3-1 [378 kB]
+Get:8 http://ftp.uk.debian.org/debian/ squeeze/main aptitude armel 0.6.3-3.2 [3703 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 12.0MB in 9s (1325kB/s)
-(Reading database ... 9961 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.7+20100313-2 (using .../ncurses-bin_5.7+20100313-4_armel.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.7+20100313-4) ...
-(Reading database ... 9961 files and directories currently installed.)
-Preparing to replace libncurses5 5.7+20100313-2 (using .../libncurses5_5.7+20100313-4_armel.deb) ...
-Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.7+20100313-4) ...
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 9961 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_armel.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_armel.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_armel.deb) ...
+Fetched 6016 kB in 2s (2905 kB/s)
+Selecting previously deselected package libboost-iostreams1.42.0.
+(Reading database ... 10019 files and directories currently installed.)
+Unpacking libboost-iostreams1.42.0 (from .../libboost-iostreams1.42.0_1.42.0-4_armel.deb) ...
+Selecting previously deselected package libncursesw5.
+Unpacking libncursesw5 (from .../libncursesw5_5.7+20100313-5_armel.deb) ...
+Selecting previously deselected package libsigc++-2.0-0c2a.
+Unpacking libsigc++-2.0-0c2a (from .../libsigc++-2.0-0c2a_2.2.4.2-1_armel.deb) ...
+Selecting previously deselected package libcwidget3.
+Unpacking libcwidget3 (from .../libcwidget3_0.5.16-3_armel.deb) ...
+Selecting previously deselected package libxapian22.
+Unpacking libxapian22 (from .../libxapian22_1.2.3-2_armel.deb) ...
+Selecting previously deselected package libept1.
+Unpacking libept1 (from .../libept1_1.0.4_armel.deb) ...
+Selecting previously deselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.3-1_armel.deb) ...
+Selecting previously deselected package aptitude.
+Unpacking aptitude (from .../aptitude_0.6.3-3.2_armel.deb) ...
+Setting up libboost-iostreams1.42.0 (1.42.0-4) ...
+Setting up libncursesw5 (5.7+20100313-5) ...
+Setting up libsigc++-2.0-0c2a (2.2.4.2-1) ...
+Setting up libcwidget3 (0.5.16-3) ...
+Setting up libxapian22 (1.2.3-2) ...
+Setting up libept1 (1.0.4) ...
+Setting up libsqlite3-0 (3.7.3-1) ...
+Setting up aptitude (0.6.3-3.2) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode.
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/buildd-samtools-armel-GSUoxO/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously deselected package sbuild-build-depends-samtools-dummy.
+(Reading database ... 10227 files and directories currently installed.)
+Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
+dpkg: dependency problems prevent configuration of sbuild-build-depends-samtools-dummy:
+ sbuild-build-depends-samtools-dummy depends on debhelper (>= 8); however:
+ Package debhelper is not installed.
+ sbuild-build-depends-samtools-dummy depends on cdbs; however:
+ Package cdbs is not installed.
+ sbuild-build-depends-samtools-dummy depends on libncurses5-dev; however:
+ Package libncurses5-dev is not installed.
+ sbuild-build-depends-samtools-dummy depends on zlib1g-dev; however:
+ Package zlib1g-dev is not installed.
+dpkg: error processing sbuild-build-depends-samtools-dummy (--install):
+ dependency problems - leaving unconfigured
+Errors were encountered while processing:
+ sbuild-build-depends-samtools-dummy
+aptitude -y --without-recommends -o APT::Install-Recommends=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-samtools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Tier=55000 -o Aptitude::ProblemResolver::Remove-Essential-Tier=maximum install sbuild-build-depends-samtools-dummy
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
+The following NEW packages will be installed:
+ bsdmainutils{a} cdbs{a} debhelper{a} file{a} gettext{a} gettext-base{a}
+ groff-base{a} html2text{a} intltool-debian{a} libcroco3{a}
+ libglib2.0-0{a} libmagic1{a} libncurses5-dev{a} libpcre3{a}
+ libunistring0{a} libxml2{a} man-db{a} po-debconf{a} zlib1g-dev{a}
+The following partially installed packages will be configured:
+ sbuild-build-depends-samtools-dummy
+0 packages upgraded, 19 newly installed, 0 to remove and 6 not upgraded.
+Need to get 11.3 MB of archives. After unpacking 34.3 MB will be used.
+Writing extended state information...
+Get:1 http://ftp.uk.debian.org/debian/ squeeze/main libmagic1 armel 5.04-5 [237 kB]
+Get:2 http://ftp.uk.debian.org/debian/ squeeze/main file armel 5.04-5 [49.4 kB]
+Get:3 http://ftp.uk.debian.org/debian/ squeeze/main html2text armel 1.3.2a-15 [97.0 kB]
+Get:4 http://ftp.uk.debian.org/debian/ squeeze/main libpcre3 armel 8.02-1.1 [234 kB]
+Get:5 http://ftp.uk.debian.org/debian/ squeeze/main libglib2.0-0 armel 2.24.2-1 [1050 kB]
+Get:6 http://ftp.uk.debian.org/debian/ squeeze/main libxml2 armel 2.7.8.dfsg-2 [816 kB]
+Get:7 http://ftp.uk.debian.org/debian/ squeeze/main libcroco3 armel 0.6.2-1 [113 kB]
+Get:8 http://ftp.uk.debian.org/debian/ squeeze/main libunistring0 armel 0.9.3-3 [410 kB]
+Get:9 http://ftp.uk.debian.org/debian/ squeeze/main gettext-base armel 0.18.1.1-3 [129 kB]
+Get:10 http://ftp.uk.debian.org/debian/ squeeze/main gettext armel 0.18.1.1-3 [1981 kB]
+Get:11 http://ftp.uk.debian.org/debian/ squeeze/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:12 http://ftp.uk.debian.org/debian/ squeeze/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:13 http://ftp.uk.debian.org/debian/ squeeze/main groff-base armel 1.20.1-10 [1038 kB]
+Get:14 http://ftp.uk.debian.org/debian/ squeeze/main bsdmainutils armel 8.0.13 [202 kB]
+Get:15 http://ftp.uk.debian.org/debian/ squeeze/main man-db armel 2.5.7-8 [1226 kB]
+Get:16 http://ftp.uk.debian.org/debian/ squeeze/main debhelper all 8.0.0 [454 kB]
+Get:17 http://ftp.uk.debian.org/debian/ squeeze/main cdbs all 0.4.89 [1240 kB]
+Get:18 http://ftp.uk.debian.org/debian/ squeeze/main libncurses5-dev armel 5.7+20100313-5 [1607 kB]
+Get:19 http://ftp.uk.debian.org/debian/ squeeze/main zlib1g-dev armel 1:1.2.3.4.dfsg-3 [190 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 11.3 MB in 4s (2533 kB/s)
Selecting previously deselected package libmagic1.
+(Reading database ... 10227 files and directories currently installed.)
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 libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_armel.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_armel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.02-1.1_armel.deb) ...
Selecting previously deselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_armel.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_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-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_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_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously deselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.20.1-10_armel.deb) ...
+Selecting previously deselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_armel.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.5.7-8_armel.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_armel.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_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 (8.0.17) ...
-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) ...
-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 libpcre3 (8.02-1.1) ...
Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
+Setting up gettext-base (0.18.1.1-3) ...
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 groff-base (1.20.1-10) ...
+Setting up bsdmainutils (8.0.13) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
+Setting up man-db (2.5.7-8) ...
+debconf: unable to initialize frontend: Dialog
+debconf: (TERM is not set, so the dialog frontend is not usable.)
+debconf: falling back to frontend: Readline
+debconf: unable to initialize frontend: Readline
+debconf: (This frontend requires a controlling tty.)
+debconf: falling back to frontend: Teletype
+Building database of manual pages ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
-Setting up libncurses5-dev (5.7+20100313-4) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Removing negative dependencies:
-Checking correctness of source dependencies...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
Kernel: Linux 2.6.32 armel (armv5tel)
-Toolchain package versions: libc6-dev_2.11.2-5 dpkg-dev_1.15.8.4 linux-libc-dev_2.6.32-21 gcc-4.4_4.4.4-13 g++-4.4_4.4.4-13 binutils_2.20.1-14 libstdc++6-4.4-dev_4.4.4-13 libstdc++6_4.4.4-13
-Package versions: apt_0.8.1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-14 bsdmainutils_8.0.17 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-5 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-13 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 diffutils_1:3.0-1 dpkg_1.15.8.4 dpkg-dev_1.15.8.4 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++_4:4.4.4-2 g++-4.4_4.4.4-13 gcc_4:4.4.4-2 gcc-4.4_4.4.4-13 gcc-4.4-base_4.4.4-13 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_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-3 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.1 libbz2-1.0_1.0.5-5 libc-bin_2.11.2-5 libc-dev-bin_2.11.2-5 libc6_2.11.2-5 libc6-dev_2.11.2-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.4 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-13 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-13 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-4 libpam-runtime_1.1.1-4 libpam0g_1.1.1-4 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libss2_1.41.12-2 libstdc++6_4.4.4-13 libstdc++6-4.4-dev_4.4.4-13 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 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.1 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-21 login_1:4.1.4.2-1+b2 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2-1+b2 patch_2.6-2 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.2p7-1 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-2.1 tzdata_2010l-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6-dev_2.11.2-10 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-8 g++-4.4_4.4.5-8 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-8 libstdc++6_4.4.5-8
+Package versions: apt_0.8.10.3 aptitude_0.6.3-3.2 base-files_6.0 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.0.13 bsdutils_1:2.17.2-9 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-8 dash_0.5.5.1-7.4 debconf_1.5.36.1 debconf-i18n_1.5.36.1 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 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_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-8 gcc_4:4.4.5-1 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 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-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 libboost-iostreams1.42.0_1.42.0-4 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 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcwidget3_0.5.16-3 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.10 libept1_1.0.4 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-8 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-8 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 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 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libsigc++-2.0-0c2a_2.2.4.2-1 libslang2_2.2.2-4 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libstdc++6_4.4.5-8 libstdc++6-4.4-dev_4.4.5-8 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_2:0.1.12-16 libuuid1_2.17.2-9 libxapian22_1.2.3-2 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-30 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-23.2squeeze1 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 mount_2.17.2-9 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6-2 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 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2.squeeze.1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.23-3 tzdata_2010o-1 util-linux_2.17.2-9 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -210,13 +321,13 @@ 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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Thu Feb 17 08:40:32 2011 UTC using DSA key ID BAFEC7F2
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1~bpo60+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
+dpkg-source: info: unpacking samtools_0.1.12a-1~bpo60+1.debian.tar.gz
Check disc space
────────────────
@@ -231,46 +342,46 @@ 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-buildpackage: source version 0.1.12a-1~bpo60+1
dpkg-source --before-build samtools-0.1.12a
dpkg-buildpackage: host architecture armel
/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-armel-F8yvZ0/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
+/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~bpo60+1-armel-af5axf/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/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-armel-F8yvZ0/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/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-armel-F8yvZ0/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/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-armel-F8yvZ0/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/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 "."
+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-armel-F8yvZ0/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
+/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~bpo60+1-armel-af5axf/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/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'
+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
@@ -285,8 +396,8 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-armel-F8yvZ0/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/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
@@ -297,10 +408,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-armel-F8yvZ0/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/samtools-0.1.12a/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/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
@@ -317,24 +428,24 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-armel-F8yvZ0/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/misc'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/samtools-0.1.12a'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/samtools-0.1.12a/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/samtools-0.1.12a/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/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-armel-F8yvZ0/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/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-armel-F8yvZ0/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/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
@@ -344,31 +455,30 @@ 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-armel-F8yvZ0/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/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-armel-F8yvZ0/samtools-0.1.12a'
+make[1]: Nothing to be done for `lib'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/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-armel-F8yvZ0/samtools-0.1.12a/examples'
+/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~bpo60+1-armel-af5axf/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.
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_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/examples'
+make[1]: *** Deleting file `ex1.bam'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf/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 20101203-0928
+Build finished at 20110315-0555
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armel-sbuild-933fddaf-1beb-4ac8-bf61-db1837fff3ba/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0
+Purging /var/lib/schroot/mount/squeeze-backports-armel-sbuild-15211ee0-9d28-4fa1-9fd8-ce4f7f552cd9/build/buildd-samtools_0.1.12a-1~bpo60+1-armel-af5axf
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0928
-Build needed 00:06:06, 4988k disc space
+Finished at 20110315-0555
+Build needed 00:06:59, 4984k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
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 94f526d..0000000
--- a/hppa.log
+++ /dev/null
@@ -1,531 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/hppa received Fri Dec 3 09:25:30 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=hppa">hppa</a> >> Fri Dec 3 09:25:30 2010<pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on penalosa.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (hppa) 03 Dec 2010 09:21 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.12a-1
-Architecture: hppa
-Chroot Build Dir: /var/lib/schroot/mount/sid-hppa-sbuild-6f59b41d-9d09-44f5-adc7-d30a4b15c4ec/build/buildd-samtools_0.1.12a-1-hppa-luOI2H
-Start Time: 20101203-0921
-Get:1 http://spohr.debian.org sid Release.gpg [835 B]
-Ign http://spohr.debian.org/debian/ sid/contrib Translation-en
-Ign http://spohr.debian.org/debian/ sid/main Translation-en
-Get:2 http://spohr.debian.org sid Release [104 kB]
-Get:3 http://incoming.debian.org sid Release.gpg [835 B]
-Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
-Ign http://incoming.debian.org/debian/ sid/main Translation-en
-Get:4 http://incoming.debian.org Release.gpg [835 B]
-Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:5 http://incoming.debian.org sid Release [104 kB]
-Get:6 http://spohr.debian.org sid/main Sources/DiffIndex [2038 B]
-Get:7 http://incoming.debian.org Release [1604 B]
-Hit http://spohr.debian.org sid/contrib Sources/DiffIndex
-Get:8 http://spohr.debian.org sid/main hppa Packages/DiffIndex [2038 B]
-Hit http://spohr.debian.org sid/contrib hppa Packages/DiffIndex
-Get:9 http://spohr.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:10 http://spohr.debian.org sid/main hppa 2010-12-03-0810.19.pdiff [798 B]
-Get:11 http://spohr.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:12 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
-Get:13 http://spohr.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:14 http://spohr.debian.org sid/main hppa 2010-12-03-0810.19.pdiff [798 B]
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Get:15 http://incoming.debian.org sid/main hppa Packages/DiffIndex [2038 B]
-Hit http://incoming.debian.org sid/contrib hppa Packages/DiffIndex
-Get:16 http://incoming.debian.org Sources [8014 B]
-Get:17 http://incoming.debian.org Packages [169 kB]
-Get:18 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:19 http://spohr.debian.org sid/main hppa 2010-12-03-0810.19.pdiff [798 B]
-Get:20 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:21 http://incoming.debian.org sid/main hppa 2010-12-03-0810.19.pdiff [798 B]
-Get:22 http://incoming.debian.org sid/main hppa 2010-12-03-0810.19.pdiff [798 B]
-Get:23 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:24 http://incoming.debian.org sid/main hppa 2010-12-03-0810.19.pdiff [798 B]
-Fetched 399 kB in 16s (23.8 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 364 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
-Fetched 364 kB in 1s (356 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: already installed (0.4.89)
-libncurses5-dev: already installed (5.7+20100313-4)
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
-Checking for source dependency conflicts...
-Installing positive dependencies:
-Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: Linux 2.6.32-5-parisc64 hppa (parisc64)
-Toolchain package versions: libc6-dev_2.11.2-7 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-27 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
-Package versions: apt_0.8.8 autoconf_2.67-2 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bison_1:2.4.1.dfsg-3 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 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 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 diffstat_1.53-1 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+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-10 gcc_4:4.4.5-1 gcc-4.2-base_4.2.4-6 gcc-4.3-base_4.3.5-4 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_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 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 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 libextutils-parsexs-perl_2.220600-1 libffi-dev_3.0.9-3 libffi5_3.0.9-3 libgc1c2_1:6.8-1.2 libgcc4_4.4.5-10 libgdbm-dev_1.8.3-9 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-10 libice-dev_2:1.0.7-1 libice6_2:1.0.7-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmodule-build-perl_0.360700-1 libmpfr1ldbl_2.4.2-3 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 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libreadline5_5.2-7 libreadline5-dev_5.2-7 libreadline6_6.1-3 libruby1.8_1.8.7.302-2 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4+b1 libsm-dev_2:1.2.0-1 libsm6_2:1.2.0-1 libss2_1.41.12-2 libssl-dev_0.9.8o-3 libssl0.9.8_0.9.8o-3 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 libudev0_164-2 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libx11-6_2:1.3.3-4 libx11-data_2:1.3.3-4 libx11-dev_2:1.3.3-4 libxau-dev_1:1.0.6-1 libxau6_1:1.0.6-1 libxcb1_1.6-1 libxcb1-dev_1.6-1 libxdmcp-dev_1:1.1.0-1 libxdmcp6_1:1.1.0-1 libxml2_2.7.8.dfsg-1 libxt-dev_1:1.0.7-1 libxt6_1:1.0.7-1 libyaml-0-2_0.1.3-1 libyaml-dev_0.1.3-1 libyaml-perl_0.71-1 linux-libc-dev_2.6.32-27 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14 m4_1.4.14-3 make_3.81-8 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 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 quilt_0.48-7 readline-common_6.1-3 ruby1.8_1.8.7.302-2 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tcl8.4_8.4.19-4 tcl8.4-dev_8.4.19-4 tk8.4_8.4.19-4 tk8.4-dev_8.4.19-4 tzdata_2010m-1 util-linux_2.17.2-3.3 x11-common_1:7.5+8 x11proto-core-dev_7.0.19-1 x11proto-input-dev_2.0.1-1 x11proto-kb-dev_1.0.5-1 xtrans-dev_1.2.6-1 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
-─────────────
-
-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 hppa
- /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-hppa-luOI2H/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/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-hppa-luOI2H/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/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-hppa-luOI2H/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/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-hppa-luOI2H/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/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-hppa-luOI2H/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/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-hppa-luOI2H/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/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-hppa-luOI2H/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/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-hppa-luOI2H/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/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-hppa-luOI2H/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/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-hppa-luOI2H/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/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-hppa-luOI2H/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-hppa-luOI2H/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-hppa-luOI2H/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-hppa-luOI2H/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-hppa-luOI2H/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-hppa-luOI2H/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-hppa-luOI2H/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_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_0.1.12a-1_hppa.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 20101203-0925
-
-samtools_0.1.12a-1_hppa.changes:
-Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: hppa
-Version: 0.1.12a-1
-Distribution: unstable
-Urgency: low
-Maintainer: hppa Build Daemon (penalosa) <buildd_hppa-penalosa at buildd...>
-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:
- 38a0581663a751865211c666d624f338d134be58 563494 samtools_0.1.12a-1_hppa.deb
- aedbae40c00f4a206d289e25de9d512220153045 166206 libbam-dev_0.1.12a-1_hppa.deb
-Checksums-Sha256:
- 37423289380391653718ec54186e2da7732f45d156f73fb63920c34ec1dc2c59 563494 samtools_0.1.12a-1_hppa.deb
- 5c3ec027e567c144274ef99667fa00e40b66dc5d4afa1a4a2dc98de2c418cce4 166206 libbam-dev_0.1.12a-1_hppa.deb
-Files:
- bf86cb9d32756635a4a69f3af457aca2 563494 science optional samtools_0.1.12a-1_hppa.deb
- e89a9ebbcc3c3116d0ef46cbd839a6ba 166206 libdevel optional libbam-dev_0.1.12a-1_hppa.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.12a-1_hppa.deb
-───────────────────────────
-
- new debian package, version 2.0.
- size 563494 bytes: control archive= 1792 bytes.
- 793 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
- Package: samtools
- Version: 0.1.12a-1
- Architecture: hppa
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1024
- 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 09:24 ./
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/bin/
--rwxr-xr-x root/root 93004 2010-12-03 09:24 ./usr/bin/bcftools
--rwxr-xr-x root/root 341032 2010-12-03 09:24 ./usr/bin/samtools
--rwxr-xr-x root/root 26556 2010-12-03 09:24 ./usr/bin/razip
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/lib/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/lib/samtools/
--rwxr-xr-x root/root 11744 2010-12-03 09:24 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7880 2010-12-03 09:24 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 18492 2010-12-03 09:24 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8744 2010-12-03 09:24 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7880 2010-12-03 09:24 ./usr/lib/samtools/maq2sam-short
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1966 2010-12-03 09:24 ./usr/share/doc/samtools/README.bcftools
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./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 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 126609 2010-12-03 09:24 ./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 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 30752 2010-11-22 03:17 ./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 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-12-03 09:24 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7546 2010-12-03 09:24 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/samtools/
--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
--rwxr-xr-x root/root 5778 2010-12-03 09:24 ./usr/share/samtools/varfilter.py
--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 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.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 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
-lrwxrwxrwx root/root 0 2010-12-03 09:24 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.12a-1_hppa.deb
-─────────────────────────────
-
- new debian package, version 2.0.
- size 166206 bytes: control archive= 899 bytes.
- 674 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.12a-1
- Architecture: hppa
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 416
- 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 09:24 ./
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./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 09:24 ./usr/lib/
--rw-r--r-- root/root 270726 2010-12-03 09:24 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
--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
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-hppa-sbuild-6f59b41d-9d09-44f5-adc7-d30a4b15c4ec/build/buildd-samtools_0.1.12a-1-hppa-luOI2H
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0925
-Build needed 00:03:25, 9004k disc space
-
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/hurd-i386.log b/hurd-i386.log
deleted file mode 100644
index 050b682..0000000
--- a/hurd-i386.log
+++ /dev/null
@@ -1,627 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/hurd-i386 received Fri Dec 3 09:52:18 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=hurd-i386">hurd-i386</a> >> Fri Dec 3 09:52:18 2010<pre>
-sbuild (Debian sbuild) 0.59.1 (31 Jan 2010) on bach.debian.net
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (hurd-i386) 03 déc. 2010 09:24 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.12a-1
-Architecture: hurd-i386
-Chroot Build Dir: /home/buildd/build/chroot-unstable/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq
-Start Time: 20101203-0924
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-
-Update APT
-──────────
-
-Ign file: ./ Release.gpg
-Ign file:/build/local-debs/ ./ Translation-en
-Ign file: ./ Release
-Ign file: ./ Packages
-Get:1 http://ftp.debian-ports.org unreleased Release.gpg [835 B]
-Ign http://ftp.debian-ports.org/debian/ unreleased/main Translation-en
-Get:2 http://ftp.debian-ports.org unreleased Release [17.4 kB]
-Get:3 http://incoming.debian.org Release.gpg [835 B]
-Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:4 http://ftp.uk.debian.org sid Release.gpg [835 B]
-Ign http://ftp.uk.debian.org/debian/ sid/contrib Translation-en
-Ign http://ftp.uk.debian.org/debian/ sid/main Translation-en
-Ign http://ftp.uk.debian.org/debian/ sid/non-free Translation-en
-Get:5 http://incoming.debian.org Release [1604 B]
-Get:6 http://ftp.uk.debian.org sid Release [104 kB]
-Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
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-Hit http://ftp.uk.debian.org sid/contrib hurd-i386 Packages/DiffIndex
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-Get:19 http://ftp.uk.debian.org sid/non-free hurd-i386 2010-12-01-1412.04.pdiff [257 B]
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-Get:45 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-0209.58.pdiff [6767 B]
-Get:46 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-0209.58.pdiff [6767 B]
-Get:47 http://ftp.uk.debian.org sid/main 2010-12-02-0209.58.pdiff [5265 B]
-Get:48 http://ftp.uk.debian.org sid/non-free 2010-12-02-2015.37.pdiff [394 B]
-Get:49 http://ftp.uk.debian.org sid/main 2010-12-02-0815.49.pdiff [2245 B]
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-Get:51 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-0209.58.pdiff [6767 B]
-Get:52 http://ftp.uk.debian.org sid/main 2010-12-02-0815.49.pdiff [2245 B]
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-Get:54 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-0815.49.pdiff [225 B]
-Get:55 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-0815.49.pdiff [225 B]
-Get:56 http://ftp.uk.debian.org sid/main 2010-12-02-1418.14.pdiff [2470 B]
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-Get:58 http://ftp.uk.debian.org sid/main 2010-12-02-1418.14.pdiff [2470 B]
-Get:59 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-1418.14.pdiff [7365 B]
-Get:60 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-1418.14.pdiff [7365 B]
-Get:61 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-1418.14.pdiff [7365 B]
-Get:62 http://ftp.uk.debian.org sid/main 2010-12-02-2015.37.pdiff [2371 B]
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-Get:65 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-2015.37.pdiff [1050 B]
-Get:66 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-2015.37.pdiff [1050 B]
-Get:67 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-2015.37.pdiff [1050 B]
-Get:68 http://ftp.uk.debian.org sid/main 2010-12-03-0208.36.pdiff [3044 B]
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-Get:72 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-03-0208.36.pdiff [1801 B]
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-Get:74 http://ftp.uk.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:75 http://ftp.uk.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:76 http://ftp.uk.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:77 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-03-0810.19.pdiff [797 B]
-Get:78 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-03-0810.19.pdiff [797 B]
-Get:79 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-03-0810.19.pdiff [797 B]
-Fetched 395 kB in 16min 11s (407 B/s)
-Reading package lists...
-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://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
-Fetched 364 kB in 1s (191 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: missing
-Checking for source dependency conflicts...
-Installing positive dependencies: 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:
- libpopt0 libwrap0 adduser libsysfs2 libusb-0.1-4p
-Use 'apt-get autoremove' to remove them.
-Suggested packages:
- devscripts doc-base
-Recommended packages:
- autotools-dev
-The following NEW packages will be installed:
- cdbs libncurses5-dev zlib1g-dev
-0 upgraded, 3 newly installed, 0 to remove and 34 not upgraded.
-Need to get 0 B/2996 kB of archives.
-After this operation, 8770 kB of additional disk space will be used.
-WARNING: The following packages cannot be authenticated!
- cdbs libncurses5-dev zlib1g-dev
-Authentication warning overridden.
-Selecting previously deselected package cdbs.
-(Reading database ... 11907 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_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 ...
-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...
-Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: libc0.3-dev_2.11.2-7 dpkg-dev_1.15.8.5 hurd-dev_20100926-1 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
-Package versions: adduser_3.112+nmu1 apt_0.8.8 apt-utils_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_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-10 dash_0.5.5.1-7 debconf_1.5.35 debconf-english_1.5.35 debfoster_2.6-2 debhelper_8.0.0 debian-archive-keyring_2010.08.28 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_1.15.8.5 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_4:4.4.5-1 gcc-4.2-base_4.2.4-6+b1 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 gnumach_2:1.3.99.dfsg.git20100732-1 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_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 hurd_20100926-1 hurd-dev_20100926-1 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 libattr1_1:2.4.44-2 libblkid1_2.16.2-0 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc0.3_2.11.2-7 libc0.3-dev_2.11.2-7 libc0.3-xen_2.11.2-7 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libexpat1_2.0.1-7 libfontconfig1_2.8.0-2.1 libfreetype6_2.4.2-2.1 libgcc1_1:4.4.5-10 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_2.8.5-2 libgomp1_4.4.5-10 libgpg-error0_1.6-1 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_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libparted0debian1_2.3-3+hurd.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libpopt0_1.16-1 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-5.1 libsasl2-modules_2.1.23.dfsg1-5.1 libslang2_2.1.4-3 libss2_1.41.12-2 libssl0.9.8_0.9.8o-3 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libsysfs2_2.1.0+repack-1 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 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-1 lsb-base_3.2-25 make_3.81-8 man-db_2.5.7-4 mawk_1.3.3-15 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 netbase_4.42 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 procps_1:3.2.7-11 psmisc_22.3-1 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-bitstream-vera_1.10-8 ttf-dejavu-core_2.31-1 ttf-freefont_20090104-7 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
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ 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-source --before-build samtools-0.1.12a
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.12a-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 -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/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-hurd-i386-baH8wq/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/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-hurd-i386-baH8wq/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/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-hurd-i386-baH8wq/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/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
-/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-test -x debian/rules
-mkdir -p "."
-/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-hurd-i386-baH8wq/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/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
-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. 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-hurd-i386-baH8wq/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/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-hurd-i386-baH8wq/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/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-hurd-i386-baH8wq/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/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-hurd-i386-baH8wq/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/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-hurd-i386-baH8wq/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/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-hurd-i386-baH8wq/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-hurd-i386-baH8wq/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-hurd-i386-baH8wq/samtools-0.1.12a/examples'
-../samtools faidx ex1.fa
-[sam_header_read2] 2 sequences loaded.
-../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
-../samtools index ex1.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"a";print}}' | ../samtools view -bS - > ex1a.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-(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...
-[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'
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-[mpileup] 1 samples in 1 input files
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-<mpileup> Set max per-sample depth to 8000
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-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-hurd-i386-baH8wq/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-hurd-i386-baH8wq/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/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-hurd-i386-baH8wq/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_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_0.1.12a-1_hurd-i386.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 20101203-0951
-
-samtools_0.1.12a-1_hurd-i386.changes:
-Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: hurd-i386
-Version: 0.1.12a-1
-Distribution: unstable
-Urgency: low
-Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-bach at buildd...>
-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:
- fc6e365d7c892b4387863d76ea111b7472b3c561 547110 samtools_0.1.12a-1_hurd-i386.deb
- 44e8ea42aae8953667c17f5ae653bab19787b73f 157814 libbam-dev_0.1.12a-1_hurd-i386.deb
-Checksums-Sha256:
- a8ed8afefbcae83803779faab971bc7c5bc61f39b7bf0ce3c43b418a61d172fa 547110 samtools_0.1.12a-1_hurd-i386.deb
- ba7fdaf7613cb931823565aae39623efcc209dd80631393f62ecc333d9cf0efc 157814 libbam-dev_0.1.12a-1_hurd-i386.deb
-Files:
- 6627d972decf32161f0019456b9e585a 547110 science optional samtools_0.1.12a-1_hurd-i386.deb
- 35fb52d023b0d946c4bdf2b5418b1b75 157814 libdevel optional libbam-dev_0.1.12a-1_hurd-i386.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.12a-1_hurd-i386.deb
-────────────────────────────────
-
- new debian package, version 2.0.
- size 547110 bytes: control archive= 1801 bytes.
- 799 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
- Package: samtools
- Version: 0.1.12a-1
- Architecture: hurd-i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 976
- Depends: libc0.3 (>= 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 09:48 ./
-drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:48 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:49 ./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 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 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2010-12-03 09:49 ./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 2010-12-03 09:47 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2010-12-03 09:49 ./usr/share/doc/samtools/README.bcftools
--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
-drwxr-xr-x root/root 0 2010-12-03 09:48 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-12-03 09:48 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7546 2010-12-03 09:48 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-12-03 09:50 ./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 12567 2010-12-02 16:41 ./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 15255 2010-11-17 04:16 ./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 2010-12-03 09:50 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/bin/
--rwxr-xr-x root/root 80068 2010-12-03 09:49 ./usr/bin/bcftools
--rwxr-xr-x root/root 23788 2010-12-03 09:49 ./usr/bin/razip
--rwxr-xr-x root/root 313996 2010-12-03 09:49 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/lib/
-drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/lib/samtools/
--rwxr-xr-x root/root 17488 2010-12-03 09:49 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6336 2010-12-03 09:49 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6320 2010-12-03 09:49 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10084 2010-12-03 09:49 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6920 2010-12-03 09:49 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.12a-1_hurd-i386.deb
-──────────────────────────────────
-
- new debian package, version 2.0.
- size 157814 bytes: control archive= 904 bytes.
- 679 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.12a-1
- Architecture: hurd-i386
- 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 2010-12-03 09:49 ./
-drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:50 ./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 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
--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 09:50 ./usr/lib/
--rw-r--r-- root/root 243684 2010-12-03 09:50 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/include/
--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
--rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-Purging /home/buildd/build/chroot-unstable/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq
-(Reading database ... 13045 files and directories currently installed.)
-Removing libncurses5-dev ...
-Removing cdbs ...
-Removing zlib1g-dev ...
-Processing triggers for man-db ...
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0951
-Build needed 00:27:27, 8428k disc space
-
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/i386.log b/i386.log
index ddecfd3..595da6e 100644
--- a/i386.log
+++ b/i386.log
@@ -1,41 +1,94 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/i386 received Fri Dec 3 09:22:26 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=i386">i386</a> >> Fri Dec 3 09:22:26 2010<pre>
+From buildd at biber.debian.org Fri Feb 18 16:30:50 2011
+Return-path: <buildd at biber.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
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+ 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 1PqTEH-0006BJ-ST
+ for logs at buildd.debian.org; Fri, 18 Feb 2011 16:30:50 +0000
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+ 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)
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+ id 1PqTEF-00017O-4f; Fri, 18 Feb 2011 16:30:47 +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_0.1.12a-1~bpo60+1 on i386
+ (dist=squeeze-backports)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1PqTEF-00017O-4f at biber.debian.org>
+Date: Fri, 18 Feb 2011 16:30:47 +0000
+Delivered-To: logs at buildd.debian.org
+
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on biber.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (i386) 03 Dec 2010 09:20 ║
+║ samtools 0.1.12a-1~bpo60+1 (i386) 18 Feb 2011 16:27 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.12a-1~bpo60+1
Architecture: i386
-Chroot Build Dir: /var/lib/schroot/mount/sid-i386-sbuild-844f11ba-9f87-46e7-97e1-8ee812a9f6ca/build/buildd-samtools_0.1.12a-1-i386-61mbY2
-Start Time: 20101203-0920
-Get:1 http://ftp.gr.debian.org unstable Release.gpg [835 B]
-Ign http://ftp.gr.debian.org/debian/ unstable/contrib Translation-en
-Ign http://ftp.gr.debian.org/debian/ unstable/main Translation-en
-Get:2 http://ftp.gr.debian.org unstable Release [104 kB]
-Get:3 http://ftp.gr.debian.org unstable/main Sources [4071 kB]
-Get:4 http://incoming.debian.org unstable Release.gpg [835 B]
-Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
-Ign http://incoming.debian.org/debian/ unstable/main Translation-en
-Get:5 http://ftp.gr.debian.org unstable/contrib Sources [38.7 kB]
-Get:6 http://ftp.gr.debian.org unstable/non-free Sources [83.8 kB]
-Get:7 http://ftp.gr.debian.org unstable/main i386 Packages [6931 kB]
-Get:8 http://incoming.debian.org Release.gpg [835 B]
-Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:9 http://incoming.debian.org unstable Release [104 kB]
-Get:10 http://ftp.gr.debian.org unstable/contrib i386 Packages [61.2 kB]
-Get:11 http://incoming.debian.org Release [1604 B]
-Get:12 http://incoming.debian.org unstable/main Sources [4071 kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [38.7 kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [83.8 kB]
-Get:15 http://incoming.debian.org unstable/main i386 Packages [6931 kB]
-Get:16 http://incoming.debian.org unstable/contrib i386 Packages [61.2 kB]
-Get:17 http://incoming.debian.org Sources [8014 B]
-Get:18 http://incoming.debian.org Packages [169 kB]
-Fetched 22.8 MB in 17s (1287 kB/s)
+Chroot Build Dir: /var/lib/schroot/mount/squeeze-backports-i386-sbuild-72ac29b1-2514-4a84-bd64-2f217b4a4f55/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT
+Start Time: 20110218-1627
+Hit http://ftp.gr.debian.org squeeze Release.gpg
+Ign http://ftp.gr.debian.org/debian/ squeeze/contrib Translation-en
+Ign http://ftp.gr.debian.org/debian/ squeeze/main Translation-en
+Get:1 http://ftp.gr.debian.org squeeze-proposed-updates Release.gpg [835 B]
+Ign http://ftp.gr.debian.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://ftp.gr.debian.org/debian/ squeeze-proposed-updates/main Translation-en
+Hit http://ftp.gr.debian.org squeeze Release
+Get:2 http://ftp.gr.debian.org squeeze-proposed-updates Release [58.4 kB]
+Hit http://ftp.gr.debian.org squeeze/main Sources
+Hit http://ftp.gr.debian.org squeeze/contrib Sources
+Get:3 http://ftp.gr.debian.org squeeze/non-free Sources [61.7 kB]
+Hit http://ftp.gr.debian.org squeeze/main i386 Packages
+Hit http://ftp.gr.debian.org squeeze/contrib i386 Packages
+Get:4 http://ftp.gr.debian.org squeeze-proposed-updates/main Sources [12.5 kB]
+Get:5 http://ftp.gr.debian.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:6 http://ftp.gr.debian.org squeeze-proposed-updates/non-free Sources [14 B]
+Get:7 http://ftp.gr.debian.org squeeze-proposed-updates/main i386 Packages [44.8 kB]
+Get:8 http://ftp.gr.debian.org squeeze-proposed-updates/contrib i386 Packages [14 B]
+Get:9 http://ftp.debian.org squeeze Release.gpg [1671 B]
+Ign http://ftp.debian.org/debian/ squeeze/contrib Translation-en
+Ign http://ftp.debian.org/debian/ squeeze/main Translation-en
+Get:10 http://ftp.debian.org squeeze-proposed-updates Release.gpg [835 B]
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/main Translation-en
+Get:11 http://ftp.debian.org squeeze Release [69.3 kB]
+Get:12 http://backports-master.debian.org squeeze-backports Release.gpg [835 B]
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/contrib Translation-en
+Get:13 http://ftp.debian.org squeeze-proposed-updates Release [58.4 kB]
+Get:14 http://ftp.debian.org squeeze/main Sources [3720 kB]
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/main Translation-en
+Get:15 http://backports-master.debian.org Release.gpg [835 B]
+Ign http://backports-master.debian.org/buildd/squeeze-backports/ Translation-en
+Get:16 http://backports-master.debian.org squeeze-backports Release [61.2 kB]
+Get:17 http://backports-master.debian.org Release [1644 B]
+Get:18 http://backports-master.debian.org squeeze-backports/main Sources [4232 B]
+Get:19 http://ftp.debian.org squeeze/contrib Sources [33.9 kB]
+Get:20 http://ftp.debian.org squeeze/non-free Sources [61.7 kB]
+Get:21 http://ftp.debian.org squeeze/main i386 Packages [6565 kB]
+Get:22 http://backports-master.debian.org squeeze-backports/contrib Sources [14 B]
+Get:23 http://backports-master.debian.org squeeze-backports/non-free Sources [14 B]
+Get:24 http://backports-master.debian.org squeeze-backports/main i386 Packages [12.5 kB]
+Get:25 http://backports-master.debian.org squeeze-backports/contrib i386 Packages [14 B]
+Get:26 http://backports-master.debian.org Sources [1846 B]
+Get:27 http://backports-master.debian.org Packages [3793 B]
+Get:28 http://ftp.debian.org squeeze/contrib i386 Packages [54.1 kB]
+Get:29 http://ftp.debian.org squeeze-proposed-updates/main Sources [12.5 kB]
+Get:30 http://ftp.debian.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:31 http://ftp.debian.org squeeze-proposed-updates/non-free Sources [14 B]
+Get:32 http://ftp.debian.org squeeze-proposed-updates/main i386 Packages [44.8 kB]
+Get:33 http://ftp.debian.org squeeze-proposed-updates/contrib i386 Packages [14 B]
+Fetched 10.9 MB in 9s (1097 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -54,140 +107,209 @@ 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:
+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://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
-Fetched 364 kB in 1s (253 kB/s)
+Need to get 363 kB of source archives.
+Get:1 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (dsc) [1338 B]
+Get:2 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (tar) [356 kB]
+Get:3 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (diff) [6406 B]
+Fetched 363 kB in 2s (148 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
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install build dependencies (aptitude-based 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
+ libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5 libsigc++-2.0-0c2a
+ libsqlite3-0 libxapian22
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ tasksel debtags libcwidget-dev xapian-tools
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ aptitude-doc-en aptitude-doc apt-xapian-index libparse-debianchangelog-perl
+ libgpm2
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 40 not upgraded.
-Need to get 11.4 MB of archives.
-After this operation, 34.5 MB of additional disk space will be used.
-Get:1 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 8.0.17 [199 kB]
-Get:2 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.20.1-10 [1128 kB]
-Get:3 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.5.7-6 [1240 kB]
-Get:4 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.04-5 [234 kB]
-Get:5 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.04-5 [49.1 kB]
-Get:6 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-3 [130 kB]
-Get:7 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.02-1.1 [231 kB]
-Get:8 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-1 [827 kB]
-Get:9 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
-Get:10 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.24.2-1 [1029 kB]
-Get:11 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-1 [116 kB]
-Get:12 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-3 [433 kB]
-Get:13 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-3 [1973 kB]
-Get:14 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:15 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:16 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.0.0 [454 kB]
-Get:17 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.89 [1240 kB]
-Get:18 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev i386 5.7+20100313-4 [1601 kB]
-Get:19 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.3.4.dfsg-3 [186 kB]
+ aptitude libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5
+ libsigc++-2.0-0c2a libsqlite3-0 libxapian22
+0 upgraded, 8 newly installed, 0 to remove and 2 not upgraded.
+Need to get 7055 kB of archives.
+After this operation, 19.2 MB of additional disk space will be used.
+Get:1 http://ftp.gr.debian.org/debian/ squeeze/main libboost-iostreams1.42.0 i386 1.42.0-4 [59.2 kB]
+Get:2 http://ftp.gr.debian.org/debian/ squeeze/main libncursesw5 i386 5.7+20100313-5 [374 kB]
+Get:3 http://ftp.gr.debian.org/debian/ squeeze/main libsigc++-2.0-0c2a i386 2.2.4.2-1 [39.9 kB]
+Get:4 http://ftp.gr.debian.org/debian/ squeeze/main libcwidget3 i386 0.5.16-3 [302 kB]
+Get:5 http://ftp.gr.debian.org/debian/ squeeze/main libxapian22 i386 1.2.3-2 [1933 kB]
+Get:6 http://ftp.gr.debian.org/debian/ squeeze/main libept1 i386 1.0.4 [148 kB]
+Get:7 http://ftp.gr.debian.org/debian/ squeeze/main libsqlite3-0 i386 3.7.3-1 [386 kB]
+Get:8 http://ftp.gr.debian.org/debian/ squeeze/main aptitude i386 0.6.3-3.2 [3813 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.4 MB in 1s (7238 kB/s)
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 10160 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_i386.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_i386.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_i386.deb) ...
+Fetched 7055 kB in 0s (9939 kB/s)
+Selecting previously deselected package libboost-iostreams1.42.0.
+(Reading database ... 10175 files and directories currently installed.)
+Unpacking libboost-iostreams1.42.0 (from .../libboost-iostreams1.42.0_1.42.0-4_i386.deb) ...
+Selecting previously deselected package libncursesw5.
+Unpacking libncursesw5 (from .../libncursesw5_5.7+20100313-5_i386.deb) ...
+Selecting previously deselected package libsigc++-2.0-0c2a.
+Unpacking libsigc++-2.0-0c2a (from .../libsigc++-2.0-0c2a_2.2.4.2-1_i386.deb) ...
+Selecting previously deselected package libcwidget3.
+Unpacking libcwidget3 (from .../libcwidget3_0.5.16-3_i386.deb) ...
+Selecting previously deselected package libxapian22.
+Unpacking libxapian22 (from .../libxapian22_1.2.3-2_i386.deb) ...
+Selecting previously deselected package libept1.
+Unpacking libept1 (from .../libept1_1.0.4_i386.deb) ...
+Selecting previously deselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.3-1_i386.deb) ...
+Selecting previously deselected package aptitude.
+Unpacking aptitude (from .../aptitude_0.6.3-3.2_i386.deb) ...
+Setting up libboost-iostreams1.42.0 (1.42.0-4) ...
+Setting up libncursesw5 (5.7+20100313-5) ...
+Setting up libsigc++-2.0-0c2a (2.2.4.2-1) ...
+Setting up libcwidget3 (0.5.16-3) ...
+Setting up libxapian22 (1.2.3-2) ...
+Setting up libept1 (1.0.4) ...
+Setting up libsqlite3-0 (3.7.3-1) ...
+Setting up aptitude (0.6.3-3.2) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode.
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/buildd-samtools-i386-L1TuvZ/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously deselected package sbuild-build-depends-samtools-dummy.
+(Reading database ... 10386 files and directories currently installed.)
+Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
+dpkg: dependency problems prevent configuration of sbuild-build-depends-samtools-dummy:
+ sbuild-build-depends-samtools-dummy depends on debhelper (>= 8); however:
+ Package debhelper is not installed.
+ sbuild-build-depends-samtools-dummy depends on cdbs; however:
+ Package cdbs is not installed.
+ sbuild-build-depends-samtools-dummy depends on libncurses5-dev; however:
+ Package libncurses5-dev is not installed.
+ sbuild-build-depends-samtools-dummy depends on zlib1g-dev; however:
+ Package zlib1g-dev is not installed.
+dpkg: error processing sbuild-build-depends-samtools-dummy (--install):
+ dependency problems - leaving unconfigured
+Errors were encountered while processing:
+ sbuild-build-depends-samtools-dummy
+aptitude -y --without-recommends -o APT::Install-Recommends=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-samtools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Tier=55000 -o Aptitude::ProblemResolver::Remove-Essential-Tier=maximum install sbuild-build-depends-samtools-dummy
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
+The following NEW packages will be installed:
+ bsdmainutils{a} cdbs{a} debhelper{a} file{a} gettext{a} gettext-base{a}
+ groff-base{a} html2text{a} intltool-debian{a} libcroco3{a}
+ libglib2.0-0{a} libmagic1{a} libncurses5-dev{a} libpcre3{a}
+ libunistring0{a} libxml2{a} man-db{a} po-debconf{a} zlib1g-dev{a}
+The following partially installed packages will be configured:
+ sbuild-build-depends-samtools-dummy
+0 packages upgraded, 19 newly installed, 0 to remove and 2 not upgraded.
+Need to get 11.4 MB of archives. After unpacking 34.5 MB will be used.
+Writing extended state information...
+Get:1 http://ftp.gr.debian.org/debian/ squeeze/main libmagic1 i386 5.04-5 [234 kB]
+Get:2 http://ftp.gr.debian.org/debian/ squeeze/main file i386 5.04-5 [49.1 kB]
+Get:3 http://ftp.gr.debian.org/debian/ squeeze/main html2text i386 1.3.2a-15 [101 kB]
+Get:4 http://ftp.gr.debian.org/debian/ squeeze/main libpcre3 i386 8.02-1.1 [231 kB]
+Get:5 http://ftp.gr.debian.org/debian/ squeeze/main libglib2.0-0 i386 2.24.2-1 [1029 kB]
+Get:6 http://ftp.gr.debian.org/debian/ squeeze/main libxml2 i386 2.7.8.dfsg-2 [827 kB]
+Get:7 http://ftp.gr.debian.org/debian/ squeeze/main libcroco3 i386 0.6.2-1 [116 kB]
+Get:8 http://ftp.gr.debian.org/debian/ squeeze/main libunistring0 i386 0.9.3-3 [433 kB]
+Get:9 http://ftp.gr.debian.org/debian/ squeeze/main gettext-base i386 0.18.1.1-3 [130 kB]
+Get:10 http://ftp.gr.debian.org/debian/ squeeze/main gettext i386 0.18.1.1-3 [1973 kB]
+Get:11 http://ftp.gr.debian.org/debian/ squeeze/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:12 http://ftp.gr.debian.org/debian/ squeeze/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:13 http://ftp.gr.debian.org/debian/ squeeze/main groff-base i386 1.20.1-10 [1128 kB]
+Get:14 http://ftp.gr.debian.org/debian/ squeeze/main bsdmainutils i386 8.0.13 [198 kB]
+Get:15 http://ftp.gr.debian.org/debian/ squeeze/main man-db i386 2.5.7-8 [1240 kB]
+Get:16 http://ftp.gr.debian.org/debian/ squeeze/main debhelper all 8.0.0 [454 kB]
+Get:17 http://ftp.gr.debian.org/debian/ squeeze/main cdbs all 0.4.89 [1240 kB]
+Get:18 http://ftp.gr.debian.org/debian/ squeeze/main libncurses5-dev i386 5.7+20100313-5 [1597 kB]
+Get:19 http://ftp.gr.debian.org/debian/ squeeze/main zlib1g-dev i386 1:1.2.3.4.dfsg-3 [186 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 11.4 MB in 1s (10.6 MB/s)
Selecting previously deselected package libmagic1.
+(Reading database ... 10386 files and directories currently installed.)
Unpacking libmagic1 (from .../libmagic1_5.04-5_i386.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../archives/file_5.04-5_i386.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_i386.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_i386.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_i386.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.02-1.1_i386.deb) ...
Selecting previously deselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_i386.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_i386.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_i386.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-3_i386.deb) ...
+Selecting previously deselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_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_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously deselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.20.1-10_i386.deb) ...
+Selecting previously deselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_i386.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.5.7-8_i386.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_i386.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_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 (8.0.17) ...
-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) ...
-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 libpcre3 (8.02-1.1) ...
Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
+Setting up gettext-base (0.18.1.1-3) ...
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 groff-base (1.20.1-10) ...
+Setting up bsdmainutils (8.0.13) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
+Setting up man-db (2.5.7-8) ...
+debconf: unable to initialize frontend: Dialog
+debconf: (TERM is not set, so the dialog frontend is not usable.)
+debconf: falling back to frontend: Readline
+debconf: unable to initialize frontend: Readline
+debconf: (This frontend requires a controlling tty.)
+debconf: falling back to frontend: Teletype
+Building database of manual pages ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
-Setting up libncurses5-dev (5.7+20100313-4) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Removing negative dependencies:
-Checking correctness of source dependencies...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
Kernel: Linux 2.6.26-2-amd64 i386 (x86_64)
-Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-26 gcc-4.4_4.4.5-6 g++-4.4_4.4.5-6 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-6 libstdc++6_4.4.5-6
-Package versions: apt_0.8.8 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.17 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-6 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 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 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-6 gcc_4:4.4.5-1 gcc-4.4_4.4.5-6 gcc-4.4-base_4.4.5-6 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_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 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_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-6 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_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 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-6 libstdc++6-4.4-dev_4.4.5-6 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_2:0.1.12-16 libuuid1_2.17.2-3.3 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 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 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010m-1 util-linux_2.17.2-3.3 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: libc6-dev_2.11.2-10 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-8 g++-4.4_4.4.5-8 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-8 libstdc++6_4.4.5-8
+Package versions: apt_0.8.10.3 aptitude_0.6.3-3.2 base-files_6.0 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.0.13 bsdutils_1:2.17.2-9 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-8 dash_0.5.5.1-7.4 debconf_1.5.36.1 debconf-i18n_1.5.36.1 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 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_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-8 gcc_4:4.4.5-1 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 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-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 libboost-iostreams1.42.0_1.42.0-4 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 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcwidget3_0.5.16-3 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.10 libept1_1.0.4 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-8 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-8 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 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 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libsigc++-2.0-0c2a_2.2.4.2-1 libslang2_2.2.2-4 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libstdc++6_4.4.5-8 libstdc++6-4.4-dev_4.4.5-8 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_2:0.1.12-16 libuuid1_2.17.2-9 libxapian22_1.2.3-2 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-30 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-23.2squeeze1 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 mount_2.17.2-9 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6-2 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 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2.squeeze.1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.23-3 tzdata_2010o-1 util-linux_2.17.2-9 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -198,13 +320,13 @@ 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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Thu Feb 17 08:40:32 2011 UTC using DSA key ID BAFEC7F2
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1~bpo60+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
+dpkg-source: info: unpacking samtools_0.1.12a-1~bpo60+1.debian.tar.gz
Check disc space
────────────────
@@ -219,46 +341,46 @@ 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-buildpackage: source version 0.1.12a-1~bpo60+1
dpkg-source --before-build samtools-0.1.12a
dpkg-buildpackage: host architecture 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 -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
+/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~bpo60+1-i386-1SPWgT/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/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-i386-61mbY2/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/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-i386-61mbY2/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/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-i386-61mbY2/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/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 "."
+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-i386-61mbY2/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
+/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~bpo60+1-i386-1SPWgT/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/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'
+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
@@ -273,8 +395,8 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-i386-61mbY2/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/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
@@ -285,10 +407,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-i386-61mbY2/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/samtools-0.1.12a/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/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
@@ -305,24 +427,24 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-i386-61mbY2/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/misc'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/samtools-0.1.12a'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/samtools-0.1.12a/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/samtools-0.1.12a/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/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-i386-61mbY2/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/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-i386-61mbY2/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/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
@@ -332,50 +454,50 @@ 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-i386-61mbY2/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/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-i386-61mbY2/samtools-0.1.12a'
+make[1]: Nothing to be done for `lib'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/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-i386-61mbY2/samtools-0.1.12a/examples'
+/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~bpo60+1-i386-1SPWgT/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 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
+../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
+../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
+(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'
+[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
+[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
+<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'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/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 "."
+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
@@ -401,8 +523,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/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
@@ -426,7 +548,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -441,69 +563,66 @@ 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_i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1~bpo60+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_0.1.12a-1_i386.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1~bpo60+1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../samtools_0.1.12a-1~bpo60+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-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0922
+Build finished at 20110218-1630
-samtools_0.1.12a-1_i386.changes:
+samtools_0.1.12a-1~bpo60+1_i386.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Thu, 17 Feb 2011 13:13:09 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: i386
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.12a-1~bpo60+1
+Distribution: squeeze-backports
Urgency: low
-Maintainer: i386 Build Daemon <buildd_i386-biber at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: i386 Build Daemon <buildd_i386-biber 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 (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.12a-1~bpo60+1) squeeze-backports; 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).
+ * Backported for Squeeze (no changes needed).
Checksums-Sha1:
- 8bbc22fe2849d2f019694e26cdec4c5897b6403f 546556 samtools_0.1.12a-1_i386.deb
- 3100d9b3b95c7d5cf63da6695e5184ab2fb0022a 157736 libbam-dev_0.1.12a-1_i386.deb
+ 6876a23cd9464e88eeb7c59bf1ddbf7f65a63169 546696 samtools_0.1.12a-1~bpo60+1_i386.deb
+ af2f5688707680db91ce8f849822770b3528b737 157784 libbam-dev_0.1.12a-1~bpo60+1_i386.deb
Checksums-Sha256:
- d71ed16a874a920a546e1e9f59ac0654b81ec25aec236b666e66608efb8b0c1f 546556 samtools_0.1.12a-1_i386.deb
- 941cd899a521e70c7c16d194c3ef695ba41aaebfe8f430ac54d9ab5afd6fa34e 157736 libbam-dev_0.1.12a-1_i386.deb
+ c400771f941c1433f922f552bc6ee7442732668444416f626c0a4f0506f09f61 546696 samtools_0.1.12a-1~bpo60+1_i386.deb
+ a14f0ed289fd2d5059193026ef54dc746623165811a06bb0f0a39daebace566e 157784 libbam-dev_0.1.12a-1~bpo60+1_i386.deb
Files:
- 62d7a4320ab6b1e376f9457fe30067fd 546556 science optional samtools_0.1.12a-1_i386.deb
- e3ea536c41192f0320873286684eda1d 157736 libdevel optional libbam-dev_0.1.12a-1_i386.deb
+ e0240f55af334bea6fc9511719d002f5 546696 science optional samtools_0.1.12a-1~bpo60+1_i386.deb
+ 04093a53a29365fd37ffc021896b6ecf 157784 libdevel optional libbam-dev_0.1.12a-1~bpo60+1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_i386.deb
-───────────────────────────
+samtools_0.1.12a-1~bpo60+1_i386.deb
+───────────────────────────────────
new debian package, version 2.0.
- size 546556 bytes: control archive= 1793 bytes.
- 791 bytes, 16 lines control
+ size 546696 bytes: control archive= 1804 bytes.
+ 799 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.12a-1~bpo60+1
Architecture: i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 976
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -515,49 +634,49 @@ samtools_0.1.12a-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 2010-12-03 09:22 ./
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/lib/
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/lib/samtools/
--rwxr-xr-x root/root 6680 2010-12-03 09:22 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 6176 2010-12-03 09:22 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6160 2010-12-03 09:22 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 9908 2010-12-03 09:22 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 17224 2010-12-03 09:22 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/bin/
--rwxr-xr-x root/root 80068 2010-12-03 09:22 ./usr/bin/bcftools
--rwxr-xr-x root/root 23692 2010-12-03 09:22 ./usr/bin/razip
--rwxr-xr-x root/root 313964 2010-12-03 09:22 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./usr/
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./usr/lib/
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./usr/lib/samtools/
+-rwxr-xr-x root/root 6680 2011-02-18 16:30 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 6176 2011-02-18 16:30 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6160 2011-02-18 16:30 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9908 2011-02-18 16:30 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 17224 2011-02-18 16:30 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./usr/bin/
+-rwxr-xr-x root/root 80068 2011-02-18 16:30 ./usr/bin/bcftools
+-rwxr-xr-x root/root 23692 2011-02-18 16:30 ./usr/bin/razip
+-rwxr-xr-x root/root 313964 2011-02-18 16:30 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./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 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.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 09:22 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-02-15 05:37 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./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 2010-12-03 09:22 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-02-18 16:30 ./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 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1966 2010-12-03 09:22 ./usr/share/doc/samtools/README.bcftools
--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 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/man/man1/
--rw-r--r-- root/root 7546 2010-12-03 09:22 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2010-12-03 09:22 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/samtools/
+-rw-r--r-- root/root 1966 2011-02-18 16:30 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 4927 2011-02-15 05:37 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1031 2011-02-15 05:37 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./usr/share/man/man1/
+-rw-r--r-- root/root 7546 2011-02-18 16:30 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-02-18 16:30 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./usr/share/samtools/
-rwxr-xr-x root/root 12567 2010-12-02 16:41 ./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 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2010-12-03 09:22 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-02-18 16:30 ./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
@@ -565,21 +684,21 @@ drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/samtools/
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
-lrwxrwxrwx root/root 0 2010-12-03 09:22 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+lrwxrwxrwx root/root 0 2011-02-18 16:30 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.12a-1_i386.deb
-─────────────────────────────
+libbam-dev_0.1.12a-1~bpo60+1_i386.deb
+─────────────────────────────────────
new debian package, version 2.0.
- size 157736 bytes: control archive= 897 bytes.
- 674 bytes, 15 lines control
+ size 157784 bytes: control archive= 904 bytes.
+ 682 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.12a-1~bpo60+1
Architecture: i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 388
Section: libdevel
Priority: optional
@@ -591,19 +710,19 @@ libbam-dev_0.1.12a-1_i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/lib/
--rw-r--r-- root/root 243680 2010-12-03 09:22 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./usr/
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./usr/lib/
+-rw-r--r-- root/root 243680 2011-02-18 16:30 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./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 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
-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
--rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/include/
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 4927 2011-02-15 05:37 ./usr/share/doc/libbam-dev/copyright
+drwxr-xr-x root/root 0 2011-02-18 16:30 ./usr/include/
-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
@@ -616,10 +735,9 @@ drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-i386-sbuild-844f11ba-9f87-46e7-97e1-8ee812a9f6ca/build/buildd-samtools_0.1.12a-1-i386-61mbY2
+Purging /var/lib/schroot/mount/squeeze-backports-i386-sbuild-72ac29b1-2514-4a84-bd64-2f217b4a4f55/build/buildd-samtools_0.1.12a-1~bpo60+1-i386-1SPWgT
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0922
-Build needed 00:01:48, 8432k disc space
+Finished at 20110218-1630
+Build needed 00:02:59, 8432k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/ia64.log b/ia64.log
index 228f1d3..c87b6eb 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,51 +1,95 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/ia64 received Fri Dec 3 09:24:25 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=ia64">ia64</a> >> Fri Dec 3 09:24:25 2010<pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on caballero.debian.org
+From buildd at mundy.debian.org Mon Mar 14 23:39:08 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 mundy.debian.org>)
+ id 1PzHLw-0003hC-0W
+ for logs at buildd.debian.org; Mon, 14 Mar 2011 23:39:08 +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=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 mundy.debian.org>)
+ id 1PzHLt-0002XO-L1
+ for logs at buildd.debian.org; Mon, 14 Mar 2011 23:39:06 +0000
+Received: from buildd by mundy.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at mundy.debian.org>)
+ id 1PzHLo-0007H4-KZ; Mon, 14 Mar 2011 23:39:00 +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_0.1.12a-1~bpo60+1 on ia64
+ (dist=squeeze-backports)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1PzHLo-0007H4-KZ at mundy.debian.org>
+Date: Mon, 14 Mar 2011 23:39:00 +0000
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.5 (14 Nov 2010) on mundy.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (ia64) 03 Dec 2010 09:22 ║
+║ samtools 0.1.12a-1~bpo60+1 (ia64) 14 Mar 2011 23:35 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.12a-1~bpo60+1
Architecture: ia64
-Chroot Build Dir: /var/lib/schroot/mount/sid-ia64-sbuild-ec894d00-3834-4b0f-8e8c-e53553a07378/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc
-Start Time: 20101203-0922
-Get:1 http://mirror.positive-internet.com sid Release.gpg [835 B]
-Ign http://mirror.positive-internet.com/debian/ sid/contrib Translation-en
-Ign http://mirror.positive-internet.com/debian/ sid/main Translation-en
-Get:2 http://mirror.positive-internet.com sid Release [104 kB]
-Get:3 http://mirror.positive-internet.com sid/main Sources/DiffIndex [2038 B]
-Get:4 http://incoming.debian.org sid Release.gpg [835 B]
-Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
-Ign http://incoming.debian.org/debian/ sid/main Translation-en
-Get:5 http://incoming.debian.org Release.gpg [835 B]
-Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Hit http://mirror.positive-internet.com sid/contrib Sources/DiffIndex
-Get:6 http://mirror.positive-internet.com sid/main ia64 Packages/DiffIndex [2038 B]
-Hit http://mirror.positive-internet.com sid/contrib ia64 Packages/DiffIndex
-Get:7 http://mirror.positive-internet.com sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:8 http://incoming.debian.org sid Release [104 kB]
-Get:9 http://incoming.debian.org Release [1604 B]
-Get:10 http://mirror.positive-internet.com sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:11 http://mirror.positive-internet.com sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:12 http://mirror.positive-internet.com sid/main ia64 2010-12-03-0810.19.pdiff [798 B]
-Get:13 http://mirror.positive-internet.com sid/main ia64 2010-12-03-0810.19.pdiff [798 B]
-Get:14 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Get:15 http://incoming.debian.org sid/main ia64 Packages/DiffIndex [2038 B]
-Hit http://incoming.debian.org sid/contrib ia64 Packages/DiffIndex
-Get:16 http://incoming.debian.org Sources [8014 B]
-Get:17 http://incoming.debian.org Packages [169 kB]
-Get:18 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:19 http://mirror.positive-internet.com sid/main ia64 2010-12-03-0810.19.pdiff [798 B]
-Get:20 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:21 http://incoming.debian.org sid/main ia64 2010-12-03-0810.19.pdiff [798 B]
-Get:22 http://incoming.debian.org sid/main ia64 2010-12-03-0810.19.pdiff [798 B]
-Get:23 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:24 http://incoming.debian.org sid/main ia64 2010-12-03-0810.19.pdiff [798 B]
-Fetched 399 kB in 11s (36.2 kB/s)
+Chroot Build Dir: /var/lib/schroot/mount/squeeze-backports-ia64-sbuild-64a0aa24-b2e0-414c-b874-7d59927d70a8/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5
+Start Time: 20110314-2335
+Hit http://spohr.debian.org squeeze Release.gpg
+Ign http://spohr.debian.org/debian/ squeeze/contrib Translation-en
+Ign http://spohr.debian.org/debian/ squeeze/main Translation-en
+Get:1 http://spohr.debian.org squeeze-proposed-updates Release.gpg [835 B]
+Ign http://spohr.debian.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://spohr.debian.org/debian/ squeeze-proposed-updates/main Translation-en
+Hit http://spohr.debian.org squeeze Release
+Get:2 http://spohr.debian.org squeeze-proposed-updates Release [59.0 kB]
+Get:3 http://backports-master.debian.org squeeze-backports Release.gpg [835 B]
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/contrib Translation-en
+Hit http://spohr.debian.org squeeze/main Sources
+Hit http://spohr.debian.org squeeze/contrib Sources
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/main Translation-en
+Get:4 http://backports-master.debian.org Release.gpg [835 B]
+Ign http://backports-master.debian.org/buildd/squeeze-backports/ Translation-en
+Get:5 http://backports-master.debian.org squeeze-backports Release [61.2 kB]
+Get:6 http://spohr.debian.org squeeze/non-free Sources [61.7 kB]
+Hit http://spohr.debian.org squeeze/main ia64 Packages
+Hit http://spohr.debian.org squeeze/contrib ia64 Packages
+Get:7 http://spohr.debian.org squeeze-proposed-updates/main Sources [37.0 kB]
+Get:8 http://spohr.debian.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:9 http://spohr.debian.org squeeze-proposed-updates/non-free Sources [926 B]
+Get:10 http://spohr.debian.org squeeze-proposed-updates/main ia64 Packages [106 kB]
+Get:11 http://spohr.debian.org squeeze-proposed-updates/contrib ia64 Packages [14 B]
+Get:12 http://ftp.debian.org squeeze Release.gpg [1671 B]
+Ign http://ftp.debian.org/debian/ squeeze/contrib Translation-en
+Get:13 http://backports-master.debian.org Release [1644 B]
+Get:14 http://backports-master.debian.org squeeze-backports/main Sources [9340 B]
+Ign http://ftp.debian.org/debian/ squeeze/main Translation-en
+Get:15 http://ftp.debian.org squeeze-proposed-updates Release.gpg [835 B]
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/main Translation-en
+Get:16 http://ftp.debian.org squeeze Release [69.3 kB]
+Get:17 http://backports-master.debian.org squeeze-backports/contrib Sources [14 B]
+Get:18 http://backports-master.debian.org squeeze-backports/non-free Sources [14 B]
+Get:19 http://backports-master.debian.org squeeze-backports/main ia64 Packages [20.1 kB]
+Get:20 http://backports-master.debian.org squeeze-backports/contrib ia64 Packages [14 B]
+Get:21 http://backports-master.debian.org Sources [605 B]
+Get:22 http://backports-master.debian.org Packages [12.1 kB]
+Get:23 http://ftp.debian.org squeeze-proposed-updates Release [59.0 kB]
+Get:24 http://ftp.debian.org squeeze/main Sources [3720 kB]
+Get:25 http://ftp.debian.org squeeze/contrib Sources [33.9 kB]
+Get:26 http://ftp.debian.org squeeze/non-free Sources [61.7 kB]
+Get:27 http://ftp.debian.org squeeze/main ia64 Packages [6381 kB]
+Get:28 http://ftp.debian.org squeeze/contrib ia64 Packages [45.4 kB]
+Get:29 http://ftp.debian.org squeeze-proposed-updates/main Sources [37.0 kB]
+Get:30 http://ftp.debian.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:31 http://ftp.debian.org squeeze-proposed-updates/non-free Sources [926 B]
+Get:32 http://ftp.debian.org squeeze-proposed-updates/main ia64 Packages [106 kB]
+Get:33 http://ftp.debian.org squeeze-proposed-updates/contrib ia64 Packages [14 B]
+Fetched 10.9 MB in 10s (1014 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -64,108 +108,209 @@ 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:
+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://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
-Fetched 364 kB in 0s (445 kB/s)
+Need to get 363 kB of source archives.
+Get:1 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (dsc) [1338 B]
+Get:2 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (tar) [356 kB]
+Get:3 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (diff) [6406 B]
+Fetched 363 kB in 1s (362 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
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install build dependencies (aptitude-based 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:
- gettext gettext-base groff-base html2text intltool-debian libcroco3
- libglib2.0-0 libpcre3 libunistring0 libxml2 man-db po-debconf
+ libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5 libsigc++-2.0-0c2a
+ libsqlite3-0 libxapian22
Suggested packages:
- devscripts doc-base dh-make gettext-doc groff less www-browser
- libmail-box-perl
+ tasksel debtags libcwidget-dev xapian-tools
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ aptitude-doc-en aptitude-doc apt-xapian-index libparse-debianchangelog-perl
+ libgpm2
The following NEW packages will be installed:
- cdbs debhelper gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libncurses5-dev libpcre3 libunistring0 libxml2 man-db
- po-debconf zlib1g-dev
+ aptitude libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5
+ libsigc++-2.0-0c2a libsqlite3-0 libxapian22
+0 upgraded, 8 newly installed, 0 to remove and 6 not upgraded.
+Need to get 7808 kB of archives.
+After this operation, 26.1 MB of additional disk space will be used.
+Get:1 http://spohr.debian.org/debian/ squeeze/main libboost-iostreams1.42.0 ia64 1.42.0-4 [68.9 kB]
+Get:2 http://spohr.debian.org/debian/ squeeze/main libncursesw5 ia64 5.7+20100313-5 [484 kB]
+Get:3 http://spohr.debian.org/debian/ squeeze/main libsigc++-2.0-0c2a ia64 2.2.4.2-1 [41.2 kB]
+Get:4 http://spohr.debian.org/debian/ squeeze/main libcwidget3 ia64 0.5.16-3 [402 kB]
+Get:5 http://spohr.debian.org/debian/ squeeze/main libxapian22 ia64 1.2.3-2 [1468 kB]
+Get:6 http://spohr.debian.org/debian/ squeeze/main libept1 ia64 1.0.4 [191 kB]
+Get:7 http://spohr.debian.org/debian/ squeeze/main libsqlite3-0 ia64 3.7.3-1 [595 kB]
+Get:8 http://spohr.debian.org/debian/ squeeze/main aptitude ia64 0.6.3-3.2 [4557 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 16 newly installed, 0 to remove and 35 not upgraded.
-Need to get 0 B/13.5 MB of archives.
-After this operation, 49.0 MB of additional disk space will be used.
-Selecting previously deselected package groff-base.
-(Reading database ... 10388 files and directories currently installed.)
-Unpacking groff-base (from .../groff-base_1.20.1-10_ia64.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_ia64.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_ia64.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_ia64.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_ia64.deb) ...
+Fetched 7808 kB in 5s (1301 kB/s)
+Selecting previously deselected package libboost-iostreams1.42.0.
+(Reading database ... 10096 files and directories currently installed.)
+Unpacking libboost-iostreams1.42.0 (from .../libboost-iostreams1.42.0_1.42.0-4_ia64.deb) ...
+Selecting previously deselected package libncursesw5.
+Unpacking libncursesw5 (from .../libncursesw5_5.7+20100313-5_ia64.deb) ...
+Selecting previously deselected package libsigc++-2.0-0c2a.
+Unpacking libsigc++-2.0-0c2a (from .../libsigc++-2.0-0c2a_2.2.4.2-1_ia64.deb) ...
+Selecting previously deselected package libcwidget3.
+Unpacking libcwidget3 (from .../libcwidget3_0.5.16-3_ia64.deb) ...
+Selecting previously deselected package libxapian22.
+Unpacking libxapian22 (from .../libxapian22_1.2.3-2_ia64.deb) ...
+Selecting previously deselected package libept1.
+Unpacking libept1 (from .../libept1_1.0.4_ia64.deb) ...
+Selecting previously deselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.3-1_ia64.deb) ...
+Selecting previously deselected package aptitude.
+Unpacking aptitude (from .../aptitude_0.6.3-3.2_ia64.deb) ...
+Setting up libboost-iostreams1.42.0 (1.42.0-4) ...
+Setting up libncursesw5 (5.7+20100313-5) ...
+Setting up libsigc++-2.0-0c2a (2.2.4.2-1) ...
+Setting up libcwidget3 (0.5.16-3) ...
+Setting up libxapian22 (1.2.3-2) ...
+Setting up libept1 (1.0.4) ...
+Setting up libsqlite3-0 (3.7.3-1) ...
+Setting up aptitude (0.6.3-3.2) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode.
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/buildd-samtools-ia64-ZRPzW7/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously deselected package sbuild-build-depends-samtools-dummy.
+(Reading database ... 10304 files and directories currently installed.)
+Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
+dpkg: dependency problems prevent configuration of sbuild-build-depends-samtools-dummy:
+ sbuild-build-depends-samtools-dummy depends on debhelper (>= 8); however:
+ Package debhelper is not installed.
+ sbuild-build-depends-samtools-dummy depends on cdbs; however:
+ Package cdbs is not installed.
+ sbuild-build-depends-samtools-dummy depends on libncurses5-dev; however:
+ Package libncurses5-dev is not installed.
+ sbuild-build-depends-samtools-dummy depends on zlib1g-dev; however:
+ Package zlib1g-dev is not installed.
+dpkg: error processing sbuild-build-depends-samtools-dummy (--install):
+ dependency problems - leaving unconfigured
+Errors were encountered while processing:
+ sbuild-build-depends-samtools-dummy
+aptitude -y --without-recommends -o APT::Install-Recommends=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-samtools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Tier=55000 -o Aptitude::ProblemResolver::Remove-Essential-Tier=maximum install sbuild-build-depends-samtools-dummy
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
+The following NEW packages will be installed:
+ bsdmainutils{a} cdbs{a} debhelper{a} file{a} gettext{a} gettext-base{a}
+ groff-base{a} html2text{a} intltool-debian{a} libcroco3{a}
+ libglib2.0-0{a} libmagic1{a} libncurses5-dev{a} libpcre3{a}
+ libunistring0{a} libxml2{a} man-db{a} po-debconf{a} zlib1g-dev{a}
+The following partially installed packages will be configured:
+ sbuild-build-depends-samtools-dummy
+0 packages upgraded, 19 newly installed, 0 to remove and 6 not upgraded.
+Need to get 14.0 MB of archives. After unpacking 48.2 MB will be used.
+Writing extended state information...
+Get:1 http://spohr.debian.org/debian/ squeeze/main libmagic1 ia64 5.04-5 [263 kB]
+Get:2 http://spohr.debian.org/debian/ squeeze/main file ia64 5.04-5 [51.9 kB]
+Get:3 http://spohr.debian.org/debian/ squeeze/main html2text ia64 1.3.2a-15 [134 kB]
+Get:4 http://spohr.debian.org/debian/ squeeze/main libpcre3 ia64 8.02-1.1 [286 kB]
+Get:5 http://spohr.debian.org/debian/ squeeze/main libglib2.0-0 ia64 2.24.2-1 [1395 kB]
+Get:6 http://spohr.debian.org/debian/ squeeze/main libxml2 ia64 2.7.8.dfsg-2 [1181 kB]
+Get:7 http://spohr.debian.org/debian/ squeeze/main libcroco3 ia64 0.6.2-1 [155 kB]
+Get:8 http://spohr.debian.org/debian/ squeeze/main libunistring0 ia64 0.9.3-3 [469 kB]
+Get:9 http://spohr.debian.org/debian/ squeeze/main gettext-base ia64 0.18.1.1-3 [174 kB]
+Get:10 http://spohr.debian.org/debian/ squeeze/main gettext ia64 0.18.1.1-3 [2453 kB]
+Get:11 http://spohr.debian.org/debian/ squeeze/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:12 http://spohr.debian.org/debian/ squeeze/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:13 http://spohr.debian.org/debian/ squeeze/main groff-base ia64 1.20.1-10 [1387 kB]
+Get:14 http://spohr.debian.org/debian/ squeeze/main bsdmainutils ia64 8.0.13 [236 kB]
+Get:15 http://spohr.debian.org/debian/ squeeze/main man-db ia64 2.5.7-8 [1952 kB]
+Get:16 http://spohr.debian.org/debian/ squeeze/main debhelper all 8.0.0 [454 kB]
+Get:17 http://spohr.debian.org/debian/ squeeze/main cdbs all 0.4.89 [1240 kB]
+Get:18 http://spohr.debian.org/debian/ squeeze/main libncurses5-dev ia64 5.7+20100313-5 [1716 kB]
+Get:19 http://spohr.debian.org/debian/ squeeze/main zlib1g-dev ia64 1:1.2.3.4.dfsg-3 [224 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 14.0 MB in 6s (2032 kB/s)
+Selecting previously deselected package libmagic1.
+(Reading database ... 10304 files and directories currently installed.)
+Unpacking libmagic1 (from .../libmagic1_5.04-5_ia64.deb) ...
+Selecting previously deselected package file.
+Unpacking file (from .../archives/file_5.04-5_ia64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_ia64.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.02-1.1_ia64.deb) ...
Selecting previously deselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_ia64.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_ia64.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_ia64.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-3_ia64.deb) ...
+Selecting previously deselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_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_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously deselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.20.1-10_ia64.deb) ...
+Selecting previously deselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_ia64.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.5.7-8_ia64.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_ia64.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_ia64.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_ia64.deb) ...
-Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
-Building database of manual pages ...
-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 libmagic1 (5.04-5) ...
+Setting up file (5.04-5) ...
Setting up html2text (1.3.2a-15) ...
+Setting up libpcre3 (8.02-1.1) ...
Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
+Setting up gettext-base (0.18.1.1-3) ...
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 groff-base (1.20.1-10) ...
+Setting up bsdmainutils (8.0.13) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
+Setting up man-db (2.5.7-8) ...
+debconf: unable to initialize frontend: Dialog
+debconf: (TERM is not set, so the dialog frontend is not usable.)
+debconf: falling back to frontend: Readline
+debconf: unable to initialize frontend: Readline
+debconf: (This frontend requires a controlling tty.)
+debconf: falling back to frontend: Teletype
+Building database of manual pages ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
-Setting up libncurses5-dev (5.7+20100313-4) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Removing negative dependencies:
-Checking correctness of source dependencies...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
Kernel: Linux 2.6.32-bpo.5-mckinley ia64 (ia64)
-Toolchain package versions: libc6.1-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 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
-Package versions: apt_0.8.8 autoconf_2.67-2 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-10 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 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 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-1 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_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 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 libc6.1_2.11.2-7 libc6.1-dev_2.11.2-7 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-3 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 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 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 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 libunwind7_0.99-0.2 libunwind7-dev_0.99-0.2 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-26 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-24 lzma_4.43-14 m4_1.4.14-3 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-1 patch_2.6-2 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-2.1 tzdata_2010o-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6.1-dev_2.11.2-10 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-8 g++-4.4_4.4.5-8 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-8 libstdc++6_4.4.5-8
+Package versions: apt_0.8.10.3 aptitude_0.6.3-3.2 base-files_6.0 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.0.13 bsdutils_1:2.17.2-9 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-8 dash_0.5.5.1-7.4 debconf_1.5.36.1 debconf-i18n_1.5.36.1 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 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_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-8 gcc_4:4.4.5-1 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 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-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 libboost-iostreams1.42.0_1.42.0-4 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-10 libc-dev-bin_2.11.2-10 libc6.1_2.11.2-10 libc6.1-dev_2.11.2-10 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcwidget3_0.5.16-3 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.10 libept1_1.0.4 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-8 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-8 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 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 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libsigc++-2.0-0c2a_2.2.4.2-1 libslang2_2.2.2-4 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libstdc++6_4.4.5-8 libstdc++6-4.4-dev_4.4.5-8 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 libunwind7_0.99-0.2 libunwind7-dev_0.99-0.2 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-9 libxapian22_1.2.3-2 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-30 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-23.2squeeze1 lzma_4.43-14 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 mount_2.17.2-9 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6-2 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 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2.squeeze.1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.23-3 tzdata_2010o-1 util-linux_2.17.2-9 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -176,13 +321,13 @@ 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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Thu Feb 17 08:40:32 2011 UTC using DSA key ID BAFEC7F2
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1~bpo60+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
+dpkg-source: info: unpacking samtools_0.1.12a-1~bpo60+1.debian.tar.gz
Check disc space
────────────────
@@ -197,35 +342,35 @@ 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-buildpackage: source version 0.1.12a-1~bpo60+1
dpkg-source --before-build samtools-0.1.12a
dpkg-buildpackage: host architecture ia64
/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-ia64-gr6cnc/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
+/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~bpo60+1-ia64-agwae5/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/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-ia64-gr6cnc/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/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-ia64-gr6cnc/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/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-ia64-gr6cnc/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/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 "."
+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-ia64-gr6cnc/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
+/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~bpo60+1-ia64-agwae5/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/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
@@ -245,8 +390,8 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-ia64-gr6cnc/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/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
@@ -257,10 +402,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-ia64-gr6cnc/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/samtools-0.1.12a/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/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
@@ -277,24 +422,24 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-ia64-gr6cnc/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/misc'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/samtools-0.1.12a'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/samtools-0.1.12a/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/samtools-0.1.12a/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/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-ia64-gr6cnc/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/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-ia64-gr6cnc/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/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
@@ -304,50 +449,50 @@ 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-ia64-gr6cnc/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/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-ia64-gr6cnc/samtools-0.1.12a'
+make[1]: Nothing to be done for `lib'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/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-ia64-gr6cnc/samtools-0.1.12a/examples'
+/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~bpo60+1-ia64-agwae5/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 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
+../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
+../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
+(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'
+[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
+[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
+<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'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/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 "."
+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
@@ -373,8 +518,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/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
@@ -398,7 +543,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -413,69 +558,66 @@ 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_ia64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1~bpo60+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_0.1.12a-1_ia64.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1~bpo60+1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org> >../samtools_0.1.12a-1~bpo60+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-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0924
+Build finished at 20110314-2338
-samtools_0.1.12a-1_ia64.changes:
+samtools_0.1.12a-1~bpo60+1_ia64.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Thu, 17 Feb 2011 13:13:09 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: ia64
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.12a-1~bpo60+1
+Distribution: squeeze-backports
Urgency: low
-Maintainer: ia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+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 (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.12a-1~bpo60+1) squeeze-backports; 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).
+ * Backported for Squeeze (no changes needed).
Checksums-Sha1:
- a3f0377809cbc0f8d1f1f8218392d666dbca7257 691894 samtools_0.1.12a-1_ia64.deb
- c650b494bdef80cf7bcdb93d5b2bf550ecdd1022 207066 libbam-dev_0.1.12a-1_ia64.deb
+ 21c1a43774b10e08209c618b519b664d6c9e3729 680702 samtools_0.1.12a-1~bpo60+1_ia64.deb
+ 35dbf9d2cebc2e52c83d8eff1a407764305d7e9c 207076 libbam-dev_0.1.12a-1~bpo60+1_ia64.deb
Checksums-Sha256:
- a9e74b2485999044dbf3025354617b13e5844054a013f840d37ee0f6a1c302fa 691894 samtools_0.1.12a-1_ia64.deb
- c3033101dbd1ae9b7da5b6996a0894fad18ed3a41809e685e998a124e89e2f57 207066 libbam-dev_0.1.12a-1_ia64.deb
+ e298f15689e5a31ac95a74754a34f9dc2c2761f83992411beb8ec020d2904946 680702 samtools_0.1.12a-1~bpo60+1_ia64.deb
+ 6e0414c90a890eee3aa98a4e376d63ee8dcec7c922aacc5b3229beb3fc0487db 207076 libbam-dev_0.1.12a-1~bpo60+1_ia64.deb
Files:
- 3c80dbac2bcc0a5e51eafb62fdb31c86 691894 science optional samtools_0.1.12a-1_ia64.deb
- 8615cef0efb0fbe67b778596950e8533 207066 libdevel optional libbam-dev_0.1.12a-1_ia64.deb
+ 53d7c2bd2bf8b2f0f1831ed721c687ff 680702 science optional samtools_0.1.12a-1~bpo60+1_ia64.deb
+ ef1db570163bf43d00531429a5c55714 207076 libdevel optional libbam-dev_0.1.12a-1~bpo60+1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_ia64.deb
-───────────────────────────
+samtools_0.1.12a-1~bpo60+1_ia64.deb
+───────────────────────────────────
new debian package, version 2.0.
- size 691894 bytes: control archive= 1791 bytes.
- 794 bytes, 16 lines control
+ size 680702 bytes: control archive= 1796 bytes.
+ 802 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.12a-1~bpo60+1
Architecture: ia64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1564
- Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -487,71 +629,71 @@ samtools_0.1.12a-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 2010-12-03 09:24 ./
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./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 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 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./usr/
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1966 2011-03-14 23:38 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 592 2011-02-15 05:37 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-02-15 05:37 ./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 2011-03-14 23:38 ./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 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 2010-12-03 09:23 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2010-12-03 09:24 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 126609 2011-03-14 23:38 ./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 4927 2011-02-15 05:37 ./usr/share/doc/samtools/copyright
-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
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-12-03 09:24 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7546 2010-12-03 09:24 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/samtools/
--rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2011-03-14 23:38 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
-rwxr-xr-x root/root 12567 2010-12-02 16:41 ./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 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.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
-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 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 5778 2010-12-03 09:24 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/bin/
--rwxr-xr-x root/root 206648 2010-12-03 09:24 ./usr/bin/bcftools
--rwxr-xr-x root/root 52520 2010-12-03 09:24 ./usr/bin/razip
--rwxr-xr-x root/root 707816 2010-12-03 09:24 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/lib/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/lib/samtools/
--rwxr-xr-x root/root 30712 2010-12-03 09:24 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 13360 2010-12-03 09:24 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 13296 2010-12-03 09:24 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 22384 2010-12-03 09:24 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 14944 2010-12-03 09:24 ./usr/lib/samtools/md5sum-lite
-lrwxrwxrwx root/root 0 2010-12-03 09:24 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.12a-1_ia64.deb
-─────────────────────────────
+-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
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./usr/share/man/man1/
+-rw-r--r-- root/root 7546 2011-03-14 23:38 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-03-14 23:38 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./usr/bin/
+-rwxr-xr-x root/root 707816 2011-03-14 23:38 ./usr/bin/samtools
+-rwxr-xr-x root/root 52520 2011-03-14 23:38 ./usr/bin/razip
+-rwxr-xr-x root/root 206648 2011-03-14 23:38 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./usr/lib/samtools/
+-rwxr-xr-x root/root 13296 2011-03-14 23:38 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 13360 2011-03-14 23:38 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 14944 2011-03-14 23:38 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 30712 2011-03-14 23:38 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 22384 2011-03-14 23:38 ./usr/lib/samtools/md5fa
+lrwxrwxrwx root/root 0 2011-03-14 23:38 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1~bpo60+1_ia64.deb
+─────────────────────────────────────
new debian package, version 2.0.
- size 207066 bytes: control archive= 894 bytes.
- 674 bytes, 15 lines control
+ size 207076 bytes: control archive= 901 bytes.
+ 682 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.12a-1~bpo60+1
Architecture: ia64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 660
Section: libdevel
Priority: optional
@@ -563,23 +705,23 @@ libbam-dev_0.1.12a-1_ia64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./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 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./usr/
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./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 2011-02-15 05:37 ./usr/share/doc/libbam-dev/copyright
-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 09:24 ./usr/lib/
--rw-r--r-- root/root 521254 2010-12-03 09:24 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/include/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-14 23:38 ./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
--rw-r--r-- root/root 16522 2010-11-17 04:16 ./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 2011-03-14 23:38 ./usr/lib/
+-rw-r--r-- root/root 521238 2011-03-14 23:38 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -588,34 +730,9 @@ drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-ec894d00-3834-4b0f-8e8c-e53553a07378/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc
-(Reading database ... 12621 files and directories currently installed.)
-Removing libncurses5-dev ...
-Removing zlib1g-dev ...
-Removing cdbs ...
-Removing debhelper ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing gettext-base ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-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 ...
+Purging /var/lib/schroot/mount/squeeze-backports-ia64-sbuild-64a0aa24-b2e0-414c-b874-7d59927d70a8/build/buildd-samtools_0.1.12a-1~bpo60+1-ia64-agwae5
+Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0924
-Build needed 00:02:10, 12688k disc space
+Finished at 20110314-2338
+Build needed 00:03:45, 12680k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/info b/info
new file mode 100644
index 0000000..eedc188
--- /dev/null
+++ b/info
@@ -0,0 +1,10 @@
+i386~1298046650~squeeze-backports~successful
+sparc~1298051223~squeeze-backports~failed
+s390~1298575078~squeeze-backports~successful
+powerpc~1300116722~squeeze-backports~successful
+ia64~1300145955~squeeze-backports~successful
+armel~1300168559~squeeze-backports~failed
+kfreebsd-i386~1300239669~squeeze-backports~successful
+kfreebsd-amd64~1300247943~squeeze-backports~successful
+mipsel~1300307176~squeeze-backports~successful
+mips~1300662528~squeeze-backports~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index 78c9c3c..5173701 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,46 +1,67 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/kfreebsd-amd64 received Fri Dec 3 10:18:06 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=kfreebsd-amd64">kfreebsd-amd64</a> >> Fri Dec 3 10:18:06 2010<pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on fasch.debian.org
+From buildd at fano.debian.org Wed Mar 16 03:59:03 2011
+Return-path: <buildd at fano.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 fano.debian.org>)
+ id 1Pzht0-0005is-Ty
+ for logs at buildd.debian.org; Wed, 16 Mar 2011 03:59:03 +0000
+Received: from fano.debian.org ([206.12.19.110])
+ 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 1Pzhsx-0005JY-Ue; Wed, 16 Mar 2011 03:59:01 +0000
+Received: from buildd by fano.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at fano.debian.org>)
+ id 1Pzhsv-0008MV-Mi; Wed, 16 Mar 2011 03:58:57 +0000
+Date: Wed, 16 Mar 2011 03:58:57 +0000
+Message-Id: <E1Pzhsv-0008MV-Mi at fano.debian.org>
+From: buildd on fano <buildd at fano.debian.org>
+To: logs at buildd.debian.org,aurelien at aurel32.net,kibi at debian-ports.org
+Subject: Log for successful build of samtools_0.1.12a-1~bpo60+1 on
+ kfreebsd-amd64 (dist=squeeze-backports)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (kfreebsd-amd64) 03 Dec 2010 10:14 ║
+║ samtools 0.1.12a-1~bpo60+1 (kfreebsd-amd64) 16 Mar 2011 03:57 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.12a-1~bpo60+1
Architecture: kfreebsd-amd64
-Chroot Build Dir: /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2
-Start Time: 20101203-1014
-Hit http://ftp.gr.debian.org sid Release.gpg
-Ign http://ftp.gr.debian.org/debian/ sid/contrib Translation-en
-Ign http://ftp.gr.debian.org/debian/ sid/main Translation-en
-Ign http://ftp.gr.debian.org/debian/ sid/non-free Translation-en
-Hit http://ftp.gr.debian.org sid Release
-Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
-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://incoming.debian.org sid Release.gpg
-Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
-Ign http://incoming.debian.org/debian/ sid/main Translation-en
-Ign http://incoming.debian.org/debian/ sid/non-free Translation-en
-Hit http://incoming.debian.org Release.gpg
-Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
-Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages
-Hit http://incoming.debian.org sid Release
-Hit http://incoming.debian.org Release
-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
-Hit http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
-Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
-Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages
+Chroot Build Dir: /var/lib/schroot/mount/squeeze-backports-ka-sbuild-1300247827-30312/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d
+Start Time: 20110316-0357
+Hit http://mirror-ubc.debian.org squeeze Release.gpg
+Ign http://mirror-ubc.debian.org/debian/ squeeze/contrib Translation-en
+Ign http://mirror-ubc.debian.org/debian/ squeeze/main Translation-en
+Ign http://mirror-ubc.debian.org/debian/ squeeze/non-free Translation-en
+Hit http://mirror-ubc.debian.org squeeze Release
+Hit http://mirror-ubc.debian.org squeeze/main Sources
+Hit http://mirror-ubc.debian.org squeeze/contrib Sources
+Hit http://mirror-ubc.debian.org squeeze/non-free Sources
+Hit http://mirror-ubc.debian.org squeeze/main kfreebsd-amd64 Packages
+Hit http://mirror-ubc.debian.org squeeze/contrib kfreebsd-amd64 Packages
+Hit http://mirror-ubc.debian.org squeeze/non-free kfreebsd-amd64 Packages
+Get:1 http://www.backports.org squeeze-backports Release.gpg [835 B]
+Ign http://www.backports.org/buildd/ squeeze-backports/contrib Translation-en
+Ign http://www.backports.org/buildd/ squeeze-backports/main Translation-en
+Ign http://www.backports.org/buildd/ squeeze-backports/non-free Translation-en
+Get:2 http://www.backports.org squeeze-backports Release [61.2 kB]
+Hit http://www.backports.org squeeze-backports/main Sources/DiffIndex
+Hit http://www.backports.org squeeze-backports/contrib Sources
+Hit http://www.backports.org squeeze-backports/non-free Sources
+Get:3 http://www.backports.org squeeze-backports/main kfreebsd-amd64 Packages/DiffIndex [6577 B]
+Hit http://www.backports.org squeeze-backports/contrib kfreebsd-amd64 Packages
+Hit http://www.backports.org squeeze-backports/non-free kfreebsd-amd64 Packages
+Get:4 http://www.backports.org squeeze-backports/main kfreebsd-amd64 Packages [11.4 kB]
+Fetched 80.0 kB in 2s (35.1 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -59,76 +80,125 @@ 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:
+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://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
-Fetched 364 kB in 1s (194 kB/s)
+Need to get 363 kB of source archives.
+Get:1 http://www.backports.org/buildd/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (dsc) [1338 B]
+Get:2 http://www.backports.org/buildd/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (tar) [356 kB]
+Get:3 http://www.backports.org/buildd/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (diff) [6406 B]
+Fetched 363 kB in 1s (195 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
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install build dependencies (aptitude-based 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 packages were automatically installed and are no longer required:
+ libwrap0 libpcre3 groff-base adduser libssl0.9.8 man-db
+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 libunistring0 libxml2 man-db po-debconf
+ libboost-iostreams1.42.0 libcwidget3 libept1 libsigc++-2.0-0c2a libsqlite3-0
+ libxapian22
Suggested packages:
- devscripts doc-base dh-make gettext-doc groff less www-browser
- libmail-box-perl
+ tasksel debtags libcwidget-dev xapian-tools
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ aptitude-doc-en aptitude-doc apt-xapian-index libparse-debianchangelog-perl
+debconf: delaying package configuration, since apt-utils is not installed
+The following NEW packages will be installed:
+ aptitude libboost-iostreams1.42.0 libcwidget3 libept1 libsigc++-2.0-0c2a
+ libsqlite3-0 libxapian22
+0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/5948 kB of archives.
+After this operation, 16.5 MB of additional disk space will be used.
+Selecting previously deselected package libboost-iostreams1.42.0.
+(Reading database ... 12241 files and directories currently installed.)
+Unpacking libboost-iostreams1.42.0 (from .../libboost-iostreams1.42.0_1.42.0-4_kfreebsd-amd64.deb) ...
+Selecting previously deselected package libsigc++-2.0-0c2a.
+Unpacking libsigc++-2.0-0c2a (from .../libsigc++-2.0-0c2a_2.2.4.2-1_kfreebsd-amd64.deb) ...
+Selecting previously deselected package libcwidget3.
+Unpacking libcwidget3 (from .../libcwidget3_0.5.16-3_kfreebsd-amd64.deb) ...
+Selecting previously deselected package libxapian22.
+Unpacking libxapian22 (from .../libxapian22_1.2.3-2_kfreebsd-amd64.deb) ...
+Selecting previously deselected package libept1.
+Unpacking libept1 (from .../libept1_1.0.4_kfreebsd-amd64.deb) ...
+Selecting previously deselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.3-1_kfreebsd-amd64.deb) ...
+Selecting previously deselected package aptitude.
+Unpacking aptitude (from .../aptitude_0.6.3-3.2_kfreebsd-amd64.deb) ...
+Processing triggers for man-db ...
+Setting up libboost-iostreams1.42.0 (1.42.0-4) ...
+Setting up libsigc++-2.0-0c2a (2.2.4.2-1) ...
+Setting up libcwidget3 (0.5.16-3) ...
+Setting up libxapian22 (1.2.3-2) ...
+Setting up libept1 (1.0.4) ...
+Setting up libsqlite3-0 (3.7.3-1) ...
+Setting up aptitude (0.6.3-3.2) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode.
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/buildd-samtools-kfreebsd-amd64-TgxuOJ/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously deselected package sbuild-build-depends-samtools-dummy.
+(Reading database ... 12435 files and directories currently installed.)
+Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
+dpkg: dependency problems prevent configuration of sbuild-build-depends-samtools-dummy:
+ sbuild-build-depends-samtools-dummy depends on debhelper (>= 8); however:
+ Package debhelper is not installed.
+ sbuild-build-depends-samtools-dummy depends on cdbs; however:
+ Package cdbs is not installed.
+ sbuild-build-depends-samtools-dummy depends on libncurses5-dev; however:
+ Package libncurses5-dev is not installed.
+ sbuild-build-depends-samtools-dummy depends on zlib1g-dev; however:
+ Package zlib1g-dev is not installed.
+dpkg: error processing sbuild-build-depends-samtools-dummy (--install):
+ dependency problems - leaving unconfigured
+Errors were encountered while processing:
+ sbuild-build-depends-samtools-dummy
+aptitude -y --without-recommends -o APT::Install-Recommends=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-samtools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Tier=55000 -o Aptitude::ProblemResolver::Remove-Essential-Tier=maximum install sbuild-build-depends-samtools-dummy
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
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
+ cdbs{a} debhelper{a} file{a} gettext{a} gettext-base{a} html2text{a}
+ intltool-debian{a} libcroco3{a} libglib2.0-0{a} libmagic1{a}
+ libncurses5-dev{a} libunistring0{a} libxml2{a} po-debconf{a}
+ zlib1g-dev{a}
+The following packages will be REMOVED:
+ adduser{u} libssl0.9.8{u} libwrap0{u}
+The following partially installed packages will be configured:
+ sbuild-build-depends-samtools-dummy
+0 packages upgraded, 15 newly installed, 3 to remove and 0 not upgraded.
+Need to get 2848 kB/8915 kB of archives. After unpacking 22.8 MB will be used.
+Writing extended state information...
+Get:1 http://mirror-ubc.debian.org/debian/ squeeze/main cdbs all 0.4.89 [1240 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ squeeze/main libncurses5-dev kfreebsd-amd64 5.7+20100313-5 [1608 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 18 newly installed, 0 to remove and 3 not upgraded.
-Need to get 0 B/11.8 MB of archives.
-After this operation, 33.4 MB of additional disk space will be used.
-Selecting previously deselected package groff-base.
-(Reading database ... 13308 files and directories currently installed.)
-Unpacking groff-base (from .../groff-base_1.20.1-10_kfreebsd-amd64.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_kfreebsd-amd64.deb) ...
+Fetched 2848 kB in 0s (6153 kB/s)
Selecting previously deselected package libmagic1.
+(Reading database ... 12435 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_8.02-1.1_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_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_2.24.2-1_kfreebsd-amd64.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_kfreebsd-amd64.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-3_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 gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_kfreebsd-amd64.deb) ...
Selecting previously deselected package intltool-debian.
@@ -140,33 +210,53 @@ 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_kfreebsd-amd64.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_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 (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
-Building database of manual pages ...
+Processing triggers for man-db ...
+debconf: unable to initialize frontend: Dialog
+debconf: (TERM is not set, so the dialog frontend is not usable.)
+debconf: falling back to frontend: Readline
+debconf: unable to initialize frontend: Readline
+debconf: (This frontend requires a controlling tty.)
+debconf: falling back to frontend: Teletype
+Processing triggers for install-info ...
+(Reading database ... 14322 files and directories currently installed.)
+Removing adduser ...
+Removing libssl0.9.8 ...
+Removing libwrap0 ...
+Processing triggers for man-db ...
+debconf: unable to initialize frontend: Dialog
+debconf: (TERM is not set, so the dialog frontend is not usable.)
+debconf: falling back to frontend: Readline
+debconf: unable to initialize frontend: Readline
+debconf: (This frontend requires a controlling tty.)
+debconf: falling back to frontend: Teletype
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 libxml2 (2.7.8.dfsg-2) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
+Setting up gettext-base (0.18.1.1-3) ...
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 libncurses5-dev (5.7+20100313-5) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Removing negative dependencies:
-Checking correctness of source dependencies...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.6 libstdc++6_4.4.5-9 gcc-4.4_4.4.5-9 g++-4.4_4.4.5-9 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-9 libc0.1-dev_2.11.2-7 kfreebsd-kernel-headers_0.53
-Package versions: apt_0.8.9 base-files_5.10 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.17 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 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 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.2 diffutils_1:3.0-1 dpkg_1.15.8.6 dpkg-dev_1.15.8.6 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-2+b1 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_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 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 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc0.1_2.11.2-7 libc0.1-dev_2.11.2-7 libcam0_8.1-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-10 libdb4.8_4.8.30-3 libdpkg-perl_1.15.8.6 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-9 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-9 libgpg-error0_1.6-1 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 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 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-6 libsbuf0_8.1-5 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-9 libstdc++6-4.4-dev_4.4.5-9 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 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 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 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 sudo_1.7.4p4-4 sysv-rc_2.88dsf-13 sysvinit_2.88dsf-13 sysvinit-utils_2.88dsf-13 tar_1.23-3 type-handling_0.2.23 tzdata_2010o-1 ufsutils_7.3-1+b1 util-linux_2.17.2-3.3 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
+Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.10 libstdc++6_4.4.5-8 gcc-4.4_4.4.5-8 g++-4.4_4.4.5-8 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-8 libc0.1-dev_2.11.2-10 kfreebsd-kernel-headers_0.53
+Package versions: apt_0.8.10.3 aptitude_0.6.3-3.2 base-files_6.0 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.0.13 bsdutils_1:2.17.2-9 build-essential_11.5 bzip2_1.0.5-6 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_0.5.5.1-7.4 debconf_1.5.36.1 debconf-i18n_1.5.36.1 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 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_1.14.4-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-4+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-8 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 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-13.1 insserv_1.14.0-2 install-info_4.13a.dfsg.1-6 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 libboost-iostreams1.42.0_1.42.0-4 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-10 libc-dev-bin_2.11.2-10 libc0.1_2.11.2-10 libc0.1-dev_2.11.2-10 libcam0_8.1-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcwidget3_0.5.16-3 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.10 libedit2_2.11-20080614-2 libept1_1.0.4 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 libgeom0_8.1-5 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 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 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 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.dfsg1-7 libsbuf0_8.1-5 libsigc++-2.0-0c2a_2.2.4.2-1 libslang2_2.2.2-4 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 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 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-9 libxapian22_1.2.3-2 libxml2_2.7.8.dfsg-2 login_1:4.1.4.2+svn3283-2+squeeze1 lsb-base_3.2-23.2squeeze1 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2+squeeze1 patch_2.6-2 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-9 readline-common_6.1-3 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2.squeeze.1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.23-3 type-handling_0.2.23 tzdata_2010o-1 ufsutils_7.3-1+b1 util-linux_2.17.2-9 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -177,13 +267,13 @@ 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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Thu Feb 17 08:40:32 2011 UTC using DSA key ID BAFEC7F2
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1~bpo60+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
+dpkg-source: info: unpacking samtools_0.1.12a-1~bpo60+1.debian.tar.gz
Check disc space
────────────────
@@ -198,35 +288,35 @@ 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-buildpackage: source version 0.1.12a-1~bpo60+1
dpkg-source --before-build samtools-0.1.12a
dpkg-buildpackage: host architecture kfreebsd-amd64
/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-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
+/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~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/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-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/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-kfreebsd-amd64-RqAos2/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/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-kfreebsd-amd64-RqAos2/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/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 "."
+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-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
+/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~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/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
@@ -246,8 +336,8 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/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
@@ -258,10 +348,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-kfreebsd-amd64-RqAos2/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/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
@@ -278,24 +368,24 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/misc'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/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-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/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-kfreebsd-amd64-RqAos2/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/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
@@ -305,50 +395,50 @@ 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-kfreebsd-amd64-RqAos2/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/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-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
+make[1]: Nothing to be done for `lib'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/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-kfreebsd-amd64-RqAos2/samtools-0.1.12a/examples'
+/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~bpo60+1-kfreebsd-amd64-A6mf5d/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 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
+../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
+../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
+(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'
+[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
+[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
+<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'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/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 "."
+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
@@ -374,8 +464,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/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
@@ -399,7 +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_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -414,69 +504,66 @@ 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_kfreebsd-amd64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1~bpo60+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_0.1.12a-1_kfreebsd-amd64.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1~bpo60+1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_0.1.12a-1~bpo60+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-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-1017
+Build finished at 20110316-0358
-samtools_0.1.12a-1_kfreebsd-amd64.changes:
+samtools_0.1.12a-1~bpo60+1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Thu, 17 Feb 2011 13:13:09 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-amd64
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.12a-1~bpo60+1
+Distribution: squeeze-backports
Urgency: low
-Maintainer: kfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano 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 (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.12a-1~bpo60+1) squeeze-backports; 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).
+ * Backported for Squeeze (no changes needed).
Checksums-Sha1:
- e9571bc72c8ddd5a2972a340e923f3def5591768 553904 samtools_0.1.12a-1_kfreebsd-amd64.deb
- cbd8d3ca435ec22efad48117cbc24b09e7d9efe9 155700 libbam-dev_0.1.12a-1_kfreebsd-amd64.deb
+ 48e1ed6d6fd6fc8c48262037edc4d0e4c13f004a 553946 samtools_0.1.12a-1~bpo60+1_kfreebsd-amd64.deb
+ c63cd2a5a9ac866254b4aa02e80cd4863132375d 155680 libbam-dev_0.1.12a-1~bpo60+1_kfreebsd-amd64.deb
Checksums-Sha256:
- 2baa21df0016f17cb370b589b73a3ea3d85113fdf97ed83de975a1c33e04ea35 553904 samtools_0.1.12a-1_kfreebsd-amd64.deb
- ee66327cf310e59d1a5430ef2be8591b0c9fe481c705a96b80b86567fd57bc8b 155700 libbam-dev_0.1.12a-1_kfreebsd-amd64.deb
+ d01b82ec198f8c3b74515bcbbb09ac715275d90188776dd9d73dde0e5ae45600 553946 samtools_0.1.12a-1~bpo60+1_kfreebsd-amd64.deb
+ 5ce9e952493dc206124e9fa61145b5f77d16d780d3572c6f9a552e4b8df50ed4 155680 libbam-dev_0.1.12a-1~bpo60+1_kfreebsd-amd64.deb
Files:
- e9cc7f82a9df7d162d8c21a1f88c5cbb 553904 science optional samtools_0.1.12a-1_kfreebsd-amd64.deb
- 8f0652d453338d28eff781fcc85ee532 155700 libdevel optional libbam-dev_0.1.12a-1_kfreebsd-amd64.deb
+ 6c792e29b447c1cfe134bcb9ddd6fb83 553946 science optional samtools_0.1.12a-1~bpo60+1_kfreebsd-amd64.deb
+ 67e9f5b850edc64a15a75dca27c761a0 155680 libdevel optional libbam-dev_0.1.12a-1~bpo60+1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_kfreebsd-amd64.deb
-─────────────────────────────────────
+samtools_0.1.12a-1~bpo60+1_kfreebsd-amd64.deb
+─────────────────────────────────────────────
new debian package, version 2.0.
- size 553904 bytes: control archive= 1800 bytes.
- 803 bytes, 16 lines control
+ size 553946 bytes: control archive= 1807 bytes.
+ 811 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.12a-1~bpo60+1
Architecture: kfreebsd-amd64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 942
- Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -488,31 +575,31 @@ samtools_0.1.12a-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 2010-12-03 10:17 ./
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./usr/
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./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 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 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-02-15 05:37 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-02-15 05:37 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 4927 2011-02-15 05:37 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./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 2010-12-03 10:16 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-03-16 03:58 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2010-12-03 10:17 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1966 2011-03-16 03:58 ./usr/share/doc/samtools/README.bcftools
-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
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-12-03 10:17 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7546 2010-12-03 10:17 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/samtools/
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-16 03:58 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7546 2011-03-16 03:58 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./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 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
@@ -526,33 +613,33 @@ drwxr-xr-x root/root 0 2010-12-03 10:17 ./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 2010-12-03 10:17 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/bin/
--rwxr-xr-x root/root 85384 2010-12-03 10:17 ./usr/bin/bcftools
--rwxr-xr-x root/root 24864 2010-12-03 10:17 ./usr/bin/razip
--rwxr-xr-x root/root 318672 2010-12-03 10:17 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/lib/
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/lib/samtools/
--rwxr-xr-x root/root 19248 2010-12-03 10:17 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8248 2010-12-03 10:17 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 8200 2010-12-03 10:17 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 11712 2010-12-03 10:17 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 8520 2010-12-03 10:17 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.12a-1_kfreebsd-amd64.deb
-───────────────────────────────────────
+-rwxr-xr-x root/root 5778 2011-03-16 03:58 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./usr/bin/
+-rwxr-xr-x root/root 85384 2011-03-16 03:58 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24864 2011-03-16 03:58 ./usr/bin/razip
+-rwxr-xr-x root/root 318672 2011-03-16 03:58 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19248 2011-03-16 03:58 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8248 2011-03-16 03:58 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8200 2011-03-16 03:58 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 11712 2011-03-16 03:58 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 8520 2011-03-16 03:58 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2011-03-16 03:58 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1~bpo60+1_kfreebsd-amd64.deb
+───────────────────────────────────────────────
new debian package, version 2.0.
- size 155700 bytes: control archive= 902 bytes.
- 684 bytes, 15 lines control
+ size 155680 bytes: control archive= 910 bytes.
+ 692 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.12a-1~bpo60+1
Architecture: kfreebsd-amd64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 438
Section: libdevel
Priority: optional
@@ -564,19 +651,19 @@ libbam-dev_0.1.12a-1_kfreebsd-amd64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./usr/
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./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 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 4927 2011-02-15 05:37 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
-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 10:17 ./usr/lib/
--rw-r--r-- root/root 295222 2010-12-03 10:17 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/include/
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./usr/lib/
+-rw-r--r-- root/root 295222 2011-03-16 03:58 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-16 03:58 ./usr/include/
-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
-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
@@ -589,18 +676,55 @@ drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2
-(Reading database ... 15570 files and directories currently installed.)
+Purging /var/lib/schroot/mount/squeeze-backports-ka-sbuild-1300247827-30312/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-amd64-A6mf5d
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Recommended packages:
+ tcpd
+The following NEW packages will be installed:
+ adduser libssl0.9.8 libwrap0
+0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded.
+Need to get 1297 kB of archives.
+After this operation, 3838 kB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ squeeze/main adduser all 3.112+nmu2 [250 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ squeeze/main libssl0.9.8 kfreebsd-amd64 0.9.8o-4 [996 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ squeeze/main libwrap0 kfreebsd-amd64 7.6.q-19 [50.7 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 1297 kB in 0s (11.1 MB/s)
+Selecting previously deselected package adduser.
+(Reading database ... 14192 files and directories currently installed.)
+Unpacking adduser (from .../adduser_3.112+nmu2_all.deb) ...
+Selecting previously deselected package libssl0.9.8.
+Unpacking libssl0.9.8 (from .../libssl0.9.8_0.9.8o-4_kfreebsd-amd64.deb) ...
+Selecting previously deselected package libwrap0.
+Unpacking libwrap0 (from .../libwrap0_7.6.q-19_kfreebsd-amd64.deb) ...
+Processing triggers for man-db ...
+Setting up adduser (3.112+nmu2) ...
+Setting up libssl0.9.8 (0.9.8o-4) ...
+Setting up libwrap0 (7.6.q-19) ...
+(Reading database ... 14322 files and directories currently installed.)
+Removing aptitude ...
+Purging configuration files for aptitude ...
+Removing sbuild-build-depends-samtools-dummy ...
+Removing libncurses5-dev ...
+Removing libsqlite3-0 ...
+Purging configuration files for libsqlite3-0 ...
+Removing libept1 ...
+Purging configuration files for libept1 ...
+Removing libcwidget3 ...
+Purging configuration files for libcwidget3 ...
Removing zlib1g-dev ...
+Removing libboost-iostreams1.42.0 ...
+Purging configuration files for libboost-iostreams1.42.0 ...
+Removing libxapian22 ...
+Purging configuration files for libxapian22 ...
Removing cdbs ...
+Removing libsigc++-2.0-0c2a ...
+Purging configuration files for libsigc++-2.0-0c2a ...
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 ...
@@ -616,10 +740,9 @@ 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 man-db ...
+Processing triggers for install-info ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-1017
-Build needed 00:02:21, 9698k disc space
+Finished at 20110316-0358
+Build needed 00:01:28, 9698k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index 847b191..c6d4ee4 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,117 +1,70 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/kfreebsd-i386 received Fri Dec 3 09:27:05 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=kfreebsd-i386">kfreebsd-i386</a> >> Fri Dec 3 09:27:05 2010<pre>
+From buildd at field.debian.org Wed Mar 16 01:41:09 2011
+Return-path: <buildd at field.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 field.debian.org>)
+ id 1PzfjY-0001Ch-MN
+ for logs at buildd.debian.org; Wed, 16 Mar 2011 01:41:09 +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=field.debian.org, EMAIL=hostmaster at field.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at field.debian.org>)
+ id 1PzfjU-0007lc-SF; Wed, 16 Mar 2011 01:41:05 +0000
+Received: from buildd by field.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at field.debian.org>)
+ id 1PzfjT-000Fu3-Jl; Wed, 16 Mar 2011 01:41:03 +0000
+Date: Wed, 16 Mar 2011 01:41:03 +0000
+Message-Id: <E1PzfjT-000Fu3-Jl 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_0.1.12a-1~bpo60+1 on
+ kfreebsd-i386 (dist=squeeze-backports)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Delivered-To: logs at buildd.debian.org
+
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on field.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (kfreebsd-i386) 03 Dec 2010 09:23 ║
+║ samtools 0.1.12a-1~bpo60+1 (kfreebsd-i386) 16 Mar 2011 01:37 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.12a-1~bpo60+1
Architecture: kfreebsd-i386
-Chroot Build Dir: /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx
-Start Time: 20101203-0923
-Get:1 http://ftp.gr.debian.org sid Release.gpg [835 B]
-Ign http://ftp.gr.debian.org/debian/ sid/contrib Translation-en
-Ign http://ftp.gr.debian.org/debian/ sid/main Translation-en
-Ign http://ftp.gr.debian.org/debian/ sid/non-free Translation-en
-Get:2 http://ftp.gr.debian.org sid Release [104 kB]
-Get:3 http://ftp.gr.debian.org sid/main Sources/DiffIndex [2038 B]
-Get:4 http://incoming.debian.org sid Release.gpg [835 B]
-Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
-Ign http://incoming.debian.org/debian/ sid/main Translation-en
-Ign http://incoming.debian.org/debian/ sid/non-free Translation-en
-Get:5 http://incoming.debian.org Release.gpg [835 B]
-Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:6 http://ftp.gr.debian.org sid/contrib Sources/DiffIndex [2023 B]
-Get:7 http://ftp.gr.debian.org sid/non-free Sources/DiffIndex [2023 B]
-Get:8 http://ftp.gr.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
-Hit http://ftp.gr.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
-Get:9 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex [2023 B]
-Get:10 http://ftp.gr.debian.org sid/main 2010-12-01-1412.04.pdiff [2285 B]
-Get:11 http://ftp.gr.debian.org sid/contrib 2010-12-01-2014.11.pdiff [31 B]
-Get:12 http://incoming.debian.org sid Release [104 kB]
-Get:13 http://ftp.gr.debian.org sid/main 2010-12-01-1412.04.pdiff [2285 B]
-Get:14 http://ftp.gr.debian.org sid/non-free 2010-12-01-1412.04.pdiff [329 B]
-Get:15 http://ftp.gr.debian.org sid/contrib 2010-12-01-2014.11.pdiff [31 B]
-Get:16 http://ftp.gr.debian.org sid/main 2010-12-01-1412.04.pdiff [2285 B]
-Get:17 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-01-1412.04.pdiff [500 B]
-Get:18 http://ftp.gr.debian.org sid/non-free 2010-12-01-1412.04.pdiff [329 B]
-Get:19 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2010-12-01-1412.04.pdiff [257 B]
-Get:20 http://incoming.debian.org Release [1604 B]
-Get:21 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-01-1412.04.pdiff [500 B]
-Get:22 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2010-12-01-1412.04.pdiff [257 B]
-Get:23 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Get:24 http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
-Hit http://incoming.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
-Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Get:25 http://incoming.debian.org Sources [8014 B]
-Get:26 http://ftp.gr.debian.org sid/contrib 2010-12-01-2014.11.pdiff [31 B]
-Get:27 http://ftp.gr.debian.org sid/main 2010-12-01-2014.11.pdiff [10.4 kB]
-Get:28 http://ftp.gr.debian.org sid/main 2010-12-01-2014.11.pdiff [10.4 kB]
-Get:29 http://ftp.gr.debian.org sid/non-free 2010-12-01-1412.04.pdiff [329 B]
-Get:30 http://incoming.debian.org Packages [169 kB]
-Get:31 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-01-1412.04.pdiff [500 B]
-Get:32 http://ftp.gr.debian.org sid/non-free 2010-12-02-0815.49.pdiff [238 B]
-Get:33 http://ftp.gr.debian.org sid/non-free 2010-12-02-0815.49.pdiff [238 B]
-Get:34 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:35 http://incoming.debian.org sid/main kfreebsd-i386 2010-12-03-0810.19.pdiff [796 B]
-Get:36 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:37 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2010-12-01-1412.04.pdiff [257 B]
-Get:38 http://incoming.debian.org sid/main kfreebsd-i386 2010-12-03-0810.19.pdiff [796 B]
-Get:39 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-01-2014.11.pdiff [20.5 kB]
-Get:40 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-01-2014.11.pdiff [20.5 kB]
-Get:41 http://ftp.gr.debian.org sid/main 2010-12-01-2014.11.pdiff [10.4 kB]
-Get:42 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2010-12-02-2015.37.pdiff [529 B]
-Get:43 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2010-12-02-2015.37.pdiff [529 B]
-Get:44 http://ftp.gr.debian.org sid/non-free 2010-12-02-0815.49.pdiff [238 B]
-Get:45 http://ftp.gr.debian.org sid/main 2010-12-02-0209.58.pdiff [5265 B]
-Get:46 http://ftp.gr.debian.org sid/main 2010-12-02-0209.58.pdiff [5265 B]
-Get:47 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:48 http://ftp.gr.debian.org sid/non-free 2010-12-02-2015.37.pdiff [394 B]
-Get:49 http://ftp.gr.debian.org sid/non-free 2010-12-02-2015.37.pdiff [394 B]
-Get:50 http://incoming.debian.org sid/main kfreebsd-i386 2010-12-03-0810.19.pdiff [796 B]
-Get:51 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-01-2014.11.pdiff [20.5 kB]
-Get:52 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2010-12-02-2015.37.pdiff [529 B]
-Get:53 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-0209.58.pdiff [28.1 kB]
-Get:54 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-0209.58.pdiff [28.1 kB]
-Get:55 http://ftp.gr.debian.org sid/main 2010-12-02-0209.58.pdiff [5265 B]
-Get:56 http://ftp.gr.debian.org sid/non-free 2010-12-02-2015.37.pdiff [394 B]
-Get:57 http://ftp.gr.debian.org sid/main 2010-12-02-0815.49.pdiff [2245 B]
-Get:58 http://ftp.gr.debian.org sid/main 2010-12-02-0815.49.pdiff [2245 B]
-Get:59 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-0209.58.pdiff [28.1 kB]
-Get:60 http://ftp.gr.debian.org sid/main 2010-12-02-0815.49.pdiff [2245 B]
-Get:61 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-0815.49.pdiff [226 B]
-Get:62 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-0815.49.pdiff [226 B]
-Get:63 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-0815.49.pdiff [226 B]
-Get:64 http://ftp.gr.debian.org sid/main 2010-12-02-1418.14.pdiff [2470 B]
-Get:65 http://ftp.gr.debian.org sid/main 2010-12-02-1418.14.pdiff [2470 B]
-Get:66 http://ftp.gr.debian.org sid/main 2010-12-02-1418.14.pdiff [2470 B]
-Get:67 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-1418.14.pdiff [9688 B]
-Get:68 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-1418.14.pdiff [9688 B]
-Get:69 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-1418.14.pdiff [9688 B]
-Get:70 http://ftp.gr.debian.org sid/main 2010-12-02-2015.37.pdiff [2371 B]
-Get:71 http://ftp.gr.debian.org sid/main 2010-12-02-2015.37.pdiff [2371 B]
-Get:72 http://ftp.gr.debian.org sid/main 2010-12-02-2015.37.pdiff [2371 B]
-Get:73 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-2015.37.pdiff [406 B]
-Get:74 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-2015.37.pdiff [406 B]
-Get:75 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-2015.37.pdiff [406 B]
-Get:76 http://ftp.gr.debian.org sid/main 2010-12-03-0208.36.pdiff [3044 B]
-Get:77 http://ftp.gr.debian.org sid/main 2010-12-03-0208.36.pdiff [3044 B]
-Get:78 http://ftp.gr.debian.org sid/main 2010-12-03-0208.36.pdiff [3044 B]
-Get:79 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-03-0208.36.pdiff [402 B]
-Get:80 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-03-0208.36.pdiff [402 B]
-Get:81 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-03-0208.36.pdiff [402 B]
-Get:82 http://ftp.gr.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:83 http://ftp.gr.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:84 http://ftp.gr.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
-Get:85 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-03-0810.19.pdiff [796 B]
-Get:86 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-03-0810.19.pdiff [796 B]
-Get:87 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-03-0810.19.pdiff [796 B]
-Fetched 495 kB in 25s (19.1 kB/s)
+Chroot Build Dir: /var/lib/schroot/mount/squeeze-backports-ki-sbuild-1300239453-58969/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218
+Start Time: 20110316-0137
+Hit http://ftp.gr.debian.org squeeze Release.gpg
+Ign http://ftp.gr.debian.org/debian/ squeeze/contrib Translation-en
+Ign http://ftp.gr.debian.org/debian/ squeeze/main Translation-en
+Ign http://ftp.gr.debian.org/debian/ squeeze/non-free Translation-en
+Hit http://ftp.gr.debian.org squeeze Release
+Hit http://ftp.gr.debian.org squeeze/main Sources
+Hit http://ftp.gr.debian.org squeeze/contrib Sources
+Hit http://ftp.gr.debian.org squeeze/non-free Sources
+Hit http://ftp.gr.debian.org squeeze/main kfreebsd-i386 Packages
+Hit http://ftp.gr.debian.org squeeze/contrib kfreebsd-i386 Packages
+Hit http://ftp.gr.debian.org squeeze/non-free kfreebsd-i386 Packages
+Get:1 http://www.backports.org squeeze-backports Release.gpg [835 B]
+Ign http://www.backports.org/buildd/ squeeze-backports/contrib Translation-en
+Ign http://www.backports.org/buildd/ squeeze-backports/main Translation-en
+Ign http://www.backports.org/buildd/ squeeze-backports/non-free Translation-en
+Get:2 http://www.backports.org squeeze-backports Release [61.2 kB]
+Hit http://www.backports.org squeeze-backports/main Sources/DiffIndex
+Hit http://www.backports.org squeeze-backports/contrib Sources
+Hit http://www.backports.org squeeze-backports/non-free Sources
+Get:3 http://www.backports.org squeeze-backports/main kfreebsd-i386 Packages/DiffIndex [6301 B]
+Hit http://www.backports.org squeeze-backports/contrib kfreebsd-i386 Packages
+Hit http://www.backports.org squeeze-backports/non-free kfreebsd-i386 Packages
+Get:4 http://www.backports.org squeeze-backports/main kfreebsd-i386 2011-03-14-1735.30.pdiff [1539 B]
+Get:5 http://www.backports.org squeeze-backports/main kfreebsd-i386 2011-03-14-1735.30.pdiff [1539 B]
+Get:6 http://www.backports.org squeeze-backports/main kfreebsd-i386 2011-03-14-1735.30.pdiff [1539 B]
+Get:7 http://www.backports.org squeeze-backports/main kfreebsd-i386 [13.3 kB]
+Fetched 83.2 kB in 1s (57.9 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -130,114 +83,179 @@ 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:
+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://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
-Fetched 364 kB in 1s (210 kB/s)
+Need to get 363 kB of source archives.
+Get:1 http://www.backports.org/buildd/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (dsc) [1338 B]
+Get:2 http://www.backports.org/buildd/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (tar) [356 kB]
+Get:3 http://www.backports.org/buildd/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (diff) [6406 B]
+Fetched 363 kB in 0s (406 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
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install build dependencies (aptitude-based 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:
- file gettext gettext-base groff-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libpcre3 libunistring0 libxml2 man-db po-debconf
+ libboost-iostreams1.42.0 libcwidget3 libept1 libsigc++-2.0-0c2a libsqlite3-0
+ libxapian22
Suggested packages:
- devscripts doc-base dh-make gettext-doc groff less www-browser
- libmail-box-perl
+ tasksel debtags libcwidget-dev xapian-tools
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ aptitude-doc-en aptitude-doc apt-xapian-index libparse-debianchangelog-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
+ aptitude libboost-iostreams1.42.0 libcwidget3 libept1 libsigc++-2.0-0c2a
+ libsqlite3-0 libxapian22
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 18 newly installed, 0 to remove and 33 not upgraded.
-Need to get 0 B/11.1 MB of archives.
-After this operation, 31.3 MB of additional disk space will be used.
-Selecting previously deselected package groff-base.
-(Reading database ... 11720 files and directories currently installed.)
-Unpacking groff-base (from .../groff-base_1.20.1-10_kfreebsd-i386.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_kfreebsd-i386.deb) ...
+0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/6667 kB of archives.
+After this operation, 18.1 MB of additional disk space will be used.
+Selecting previously deselected package libboost-iostreams1.42.0.
+(Reading database ... 11412 files and directories currently installed.)
+Unpacking libboost-iostreams1.42.0 (from .../libboost-iostreams1.42.0_1.42.0-4_kfreebsd-i386.deb) ...
+Selecting previously deselected package libsigc++-2.0-0c2a.
+Unpacking libsigc++-2.0-0c2a (from .../libsigc++-2.0-0c2a_2.2.4.2-1_kfreebsd-i386.deb) ...
+Selecting previously deselected package libcwidget3.
+Unpacking libcwidget3 (from .../libcwidget3_0.5.16-3_kfreebsd-i386.deb) ...
+Selecting previously deselected package libxapian22.
+Unpacking libxapian22 (from .../libxapian22_1.2.3-2_kfreebsd-i386.deb) ...
+Selecting previously deselected package libept1.
+Unpacking libept1 (from .../libept1_1.0.4_kfreebsd-i386.deb) ...
+Selecting previously deselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.3-1_kfreebsd-i386.deb) ...
+Selecting previously deselected package aptitude.
+Unpacking aptitude (from .../aptitude_0.6.3-3.2_kfreebsd-i386.deb) ...
+Setting up libboost-iostreams1.42.0 (1.42.0-4) ...
+Setting up libsigc++-2.0-0c2a (2.2.4.2-1) ...
+Setting up libcwidget3 (0.5.16-3) ...
+Setting up libxapian22 (1.2.3-2) ...
+Setting up libept1 (1.0.4) ...
+Setting up libsqlite3-0 (3.7.3-1) ...
+Setting up aptitude (0.6.3-3.2) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode.
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/buildd-samtools-kfreebsd-i386-Vn5kcJ/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously deselected package sbuild-build-depends-samtools-dummy.
+(Reading database ... 11609 files and directories currently installed.)
+Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
+dpkg: dependency problems prevent configuration of sbuild-build-depends-samtools-dummy:
+ sbuild-build-depends-samtools-dummy depends on debhelper (>= 8); however:
+ Package debhelper is not installed.
+ sbuild-build-depends-samtools-dummy depends on cdbs; however:
+ Package cdbs is not installed.
+ sbuild-build-depends-samtools-dummy depends on libncurses5-dev; however:
+ Package libncurses5-dev is not installed.
+ sbuild-build-depends-samtools-dummy depends on zlib1g-dev; however:
+ Package zlib1g-dev is not installed.
+dpkg: error processing sbuild-build-depends-samtools-dummy (--install):
+ dependency problems - leaving unconfigured
+Errors were encountered while processing:
+ sbuild-build-depends-samtools-dummy
+aptitude -y --without-recommends -o APT::Install-Recommends=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-samtools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Tier=55000 -o Aptitude::ProblemResolver::Remove-Essential-Tier=maximum install sbuild-build-depends-samtools-dummy
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
+The following NEW packages will be installed:
+ bsdmainutils{a} cdbs{a} debhelper{a} file{a} gettext{a} gettext-base{a}
+ groff-base{a} html2text{a} intltool-debian{a} libcroco3{a}
+ libglib2.0-0{a} libmagic1{a} libncurses5-dev{a} libpcre3{a}
+ libunistring0{a} libxml2{a} man-db{a} po-debconf{a} zlib1g-dev{a}
+The following partially installed packages will be configured:
+ sbuild-build-depends-samtools-dummy
+0 packages upgraded, 19 newly installed, 0 to remove and 0 not upgraded.
+Need to get 2811 kB/11.3 MB of archives. After unpacking 31.8 MB will be used.
+Writing extended state information...
+Get:1 http://ftp.gr.debian.org/debian/ squeeze/main cdbs all 0.4.89 [1240 kB]
+Get:2 http://ftp.gr.debian.org/debian/ squeeze/main libncurses5-dev kfreebsd-i386 5.7+20100313-5 [1570 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 2811 kB in 0s (11.8 MB/s)
Selecting previously deselected package libmagic1.
+(Reading database ... 11609 files and directories currently installed.)
Unpacking libmagic1 (from .../libmagic1_5.04-5_kfreebsd-i386.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5_kfreebsd-i386.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-i386.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_kfreebsd-i386.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_kfreebsd-i386.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-i386.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.02-1.1_kfreebsd-i386.deb) ...
Selecting previously deselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_kfreebsd-i386.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_kfreebsd-i386.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-i386.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-3_kfreebsd-i386.deb) ...
+Selecting previously deselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-i386.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_kfreebsd-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 groff-base.
+Unpacking groff-base (from .../groff-base_1.20.1-10_kfreebsd-i386.deb) ...
+Selecting previously deselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_kfreebsd-i386.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.5.7-8_kfreebsd-i386.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_kfreebsd-i386.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_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 (1.20.1-10) ...
-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 libpcre3 (8.02-1.1) ...
Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
+Setting up gettext-base (0.18.1.1-3) ...
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 groff-base (1.20.1-10) ...
+Setting up bsdmainutils (8.0.13) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
+Setting up man-db (2.5.7-8) ...
+debconf: unable to initialize frontend: Dialog
+debconf: (TERM is not set, so the dialog frontend is not usable.)
+debconf: falling back to frontend: Readline
+debconf: unable to initialize frontend: Readline
+debconf: (This frontend requires a controlling tty.)
+debconf: falling back to frontend: Teletype
+Building database of manual pages ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
-Setting up libncurses5-dev (5.7+20100313-4) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Removing negative dependencies:
-Checking correctness of source dependencies...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
-Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.5 libstdc++6_4.4.5-10 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-10 libc0.1-dev_2.11.2-6 kfreebsd-kernel-headers_0.53
-Package versions: apt_0.8.7 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 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-10 dash_0.5.5.1-7 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 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 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-2+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-10 gcc_4:4.4.5-1 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_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc0.1_2.11.2-6 libc0.1-dev_2.11.2-6 libcam0_8.1-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-3 libdpkg-perl_1.15.8.5 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-10 libgpg-error0_1.6-1 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 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 libpam-runtime_1.1.1-6 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 libsbuf0_8.1-5 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 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 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 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 netbase_4.42 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16+nmu1 procps_1:3.2.8-9 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 type-handling_0.2.23 tzdata_2010m-1 ufsutils_7.3-1+b1 util-linux_2.17.2-3.3 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: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.10 libstdc++6_4.4.5-8 gcc-4.4_4.4.5-8 g++-4.4_4.4.5-8 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-8 libc0.1-dev_2.11.2-10+b1 kfreebsd-kernel-headers_0.53
+Package versions: apt_0.8.10.3 aptitude_0.6.3-3.2 base-files_6.0 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.0.13 bsdutils_1:2.17.2-9 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-8 dash_0.5.5.1-7.4 debconf_1.5.36.1 debconf-i18n_1.5.36.1 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 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_1.14.4-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-4 g++_4:4.4.5-1 g++-4.4_4.4.5-8 gcc_4:4.4.5-1 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 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-13.1 insserv_1.14.0-2 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 libboost-iostreams1.42.0_1.42.0-4 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-10+b1 libc-dev-bin_2.11.2-10+b1 libc0.1_2.11.2-10+b1 libc0.1-dev_2.11.2-10+b1 libcam0_8.1-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcwidget3_0.5.16-3 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.10 libedit2_2.11-20080614-2 libept1_1.0.4 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-8 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-8 libkiconv4_8.1-5 libkvm0_8.1-5 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 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 libreadline6_6.1-3 libsbuf0_8.1-5 libsigc++-2.0-0c2a_2.2.4.2-1 libslang2_2.2.2-4 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libstdc++6_4.4.5-8 libstdc++6-4.4-dev_4.4.5-8 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_2:0.1.12-16 libuuid1_2.17.2-9 libxapian22_1.2.3-2 libxml2_2.7.8.dfsg-2 login_1:4.1.4.2+svn3283-2+squeeze1 lsb-base_3.2-23.2squeeze1 lzma_4.43-14 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2+squeeze1 patch_2.6-2 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-9 readline-common_6.1-3 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-7 sensible-utils_0.0.4 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.23-3 type-handling_0.2.23 tzdata_2010o-1 ufsutils_7.3-1+b1 util-linux_2.17.2-9 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -248,13 +266,13 @@ 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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Thu Feb 17 08:40:32 2011 UTC using DSA key ID BAFEC7F2
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1~bpo60+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
+dpkg-source: info: unpacking samtools_0.1.12a-1~bpo60+1.debian.tar.gz
Check disc space
────────────────
@@ -269,46 +287,46 @@ 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-buildpackage: source version 0.1.12a-1~bpo60+1
dpkg-source --before-build samtools-0.1.12a
dpkg-buildpackage: host architecture kfreebsd-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 -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
+/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~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/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-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/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-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/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-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/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 "."
+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-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
+/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~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/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'
+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
@@ -323,8 +341,8 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/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
@@ -335,10 +353,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/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
@@ -355,24 +373,24 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/misc'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/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-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/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-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/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
@@ -382,50 +400,50 @@ 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-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/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-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
+make[1]: Nothing to be done for `lib'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/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-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/examples'
+/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~bpo60+1-kfreebsd-i386-jMp218/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 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
+../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
+../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
+(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'
+[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
+[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
+<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'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/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 "."
+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
@@ -451,8 +469,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/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
@@ -476,7 +494,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -491,69 +509,66 @@ 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_kfreebsd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1~bpo60+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_0.1.12a-1_kfreebsd-i386.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1~bpo60+1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../samtools_0.1.12a-1~bpo60+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-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0926
+Build finished at 20110316-0140
-samtools_0.1.12a-1_kfreebsd-i386.changes:
+samtools_0.1.12a-1~bpo60+1_kfreebsd-i386.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Thu, 17 Feb 2011 13:13:09 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-i386
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.12a-1~bpo60+1
+Distribution: squeeze-backports
Urgency: low
-Maintainer: kfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+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 (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.12a-1~bpo60+1) squeeze-backports; 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).
+ * Backported for Squeeze (no changes needed).
Checksums-Sha1:
- 164adcd56b82ee0bcf67f213f6b768cda0e37c87 546952 samtools_0.1.12a-1_kfreebsd-i386.deb
- 35fd1a19555c60c04ccd6bc7415a68191b52fa0b 157656 libbam-dev_0.1.12a-1_kfreebsd-i386.deb
+ 8ac0d0a250665a65b0fa28d2494cc6484c067b4c 546948 samtools_0.1.12a-1~bpo60+1_kfreebsd-i386.deb
+ 298d9b2395a8557c550f6f2425fcd991603a3776 157696 libbam-dev_0.1.12a-1~bpo60+1_kfreebsd-i386.deb
Checksums-Sha256:
- ed916c3a9eb8d0ede51fd39e93624daea4f232f64648a850c6272d9a16b62a0a 546952 samtools_0.1.12a-1_kfreebsd-i386.deb
- 2bc39a07a79e3115a616b805723e76262773dca29dea0bf8565792dd2fe68456 157656 libbam-dev_0.1.12a-1_kfreebsd-i386.deb
+ 766e25f635048a89863307a24f673a85be9437c390203ff2f86ab1b153d1d20b 546948 samtools_0.1.12a-1~bpo60+1_kfreebsd-i386.deb
+ db849cc5dd54a1a7abaf99cf40b18c36349c64e90bfe9912d151465cae542243 157696 libbam-dev_0.1.12a-1~bpo60+1_kfreebsd-i386.deb
Files:
- b69ec10fef8c78f148be3c40055c42bd 546952 science optional samtools_0.1.12a-1_kfreebsd-i386.deb
- 28a03f293b4a554282d54e4738f1361e 157656 libdevel optional libbam-dev_0.1.12a-1_kfreebsd-i386.deb
+ 7d045c50d7d3c944505e3b7c948b2cb0 546948 science optional samtools_0.1.12a-1~bpo60+1_kfreebsd-i386.deb
+ 81332204b80757c4df74f9fa696286d9 157696 libdevel optional libbam-dev_0.1.12a-1~bpo60+1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_kfreebsd-i386.deb
-────────────────────────────────────
+samtools_0.1.12a-1~bpo60+1_kfreebsd-i386.deb
+────────────────────────────────────────────
new debian package, version 2.0.
- size 546952 bytes: control archive= 1795 bytes.
- 802 bytes, 16 lines control
+ size 546948 bytes: control archive= 1809 bytes.
+ 810 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.12a-1~bpo60+1
Architecture: kfreebsd-i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 924
- Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -565,31 +580,31 @@ samtools_0.1.12a-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 2010-12-03 09:26 ./
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./usr/
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./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 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 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-02-15 05:37 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-02-15 05:37 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 4927 2011-02-15 05:37 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./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 2010-12-03 09:26 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-03-16 01:40 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2010-12-03 09:26 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1966 2011-03-16 01:40 ./usr/share/doc/samtools/README.bcftools
-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
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-12-03 09:26 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7546 2010-12-03 09:26 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/samtools/
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-16 01:40 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7546 2011-03-16 01:40 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./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 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
@@ -603,33 +618,33 @@ drwxr-xr-x root/root 0 2010-12-03 09:26 ./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 2010-12-03 09:26 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/bin/
--rwxr-xr-x root/root 80068 2010-12-03 09:26 ./usr/bin/bcftools
--rwxr-xr-x root/root 23612 2010-12-03 09:26 ./usr/bin/razip
--rwxr-xr-x root/root 313868 2010-12-03 09:26 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/lib/
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/lib/samtools/
--rwxr-xr-x root/root 17296 2010-12-03 09:26 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6160 2010-12-03 09:26 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6144 2010-12-03 09:26 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 9876 2010-12-03 09:26 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6632 2010-12-03 09:26 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.12a-1_kfreebsd-i386.deb
-──────────────────────────────────────
+-rwxr-xr-x root/root 5778 2011-03-16 01:40 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./usr/bin/
+-rwxr-xr-x root/root 80068 2011-03-16 01:40 ./usr/bin/bcftools
+-rwxr-xr-x root/root 23612 2011-03-16 01:40 ./usr/bin/razip
+-rwxr-xr-x root/root 313868 2011-03-16 01:40 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17296 2011-03-16 01:40 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6160 2011-03-16 01:40 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6144 2011-03-16 01:40 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9876 2011-03-16 01:40 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6632 2011-03-16 01:40 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2011-03-16 01:40 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1~bpo60+1_kfreebsd-i386.deb
+──────────────────────────────────────────────
new debian package, version 2.0.
- size 157656 bytes: control archive= 902 bytes.
- 683 bytes, 15 lines control
+ size 157696 bytes: control archive= 909 bytes.
+ 691 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.12a-1~bpo60+1
Architecture: kfreebsd-i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 374
Section: libdevel
Priority: optional
@@ -641,19 +656,19 @@ libbam-dev_0.1.12a-1_kfreebsd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./usr/
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./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 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 4927 2011-02-15 05:37 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
-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 09:26 ./usr/lib/
--rw-r--r-- root/root 243644 2010-12-03 09:26 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/include/
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./usr/lib/
+-rw-r--r-- root/root 243624 2011-03-16 01:40 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-16 01:40 ./usr/include/
-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
-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
@@ -666,13 +681,28 @@ drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx
-(Reading database ... 13982 files and directories currently installed.)
+Purging /var/lib/schroot/mount/squeeze-backports-ki-sbuild-1300239453-58969/build/buildd-samtools_0.1.12a-1~bpo60+1-kfreebsd-i386-jMp218
+(Reading database ... 13985 files and directories currently installed.)
+Removing aptitude ...
+Purging configuration files for aptitude ...
+Removing sbuild-build-depends-samtools-dummy ...
+Removing libncurses5-dev ...
+Removing libsqlite3-0 ...
+Purging configuration files for libsqlite3-0 ...
+Removing libept1 ...
+Purging configuration files for libept1 ...
+Removing libcwidget3 ...
+Purging configuration files for libcwidget3 ...
Removing zlib1g-dev ...
+Removing libboost-iostreams1.42.0 ...
+Purging configuration files for libboost-iostreams1.42.0 ...
+Removing libxapian22 ...
+Purging configuration files for libxapian22 ...
Removing cdbs ...
+Removing libsigc++-2.0-0c2a ...
+Purging configuration files for libsigc++-2.0-0c2a ...
Removing debhelper ...
Removing po-debconf ...
-Removing libncurses5-dev ...
Removing man-db ...
Purging configuration files for man-db ...
Removing intltool-debian ...
@@ -691,12 +721,13 @@ 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 20101203-0926
-Build needed 00:02:38, 8120k disc space
+Finished at 20110316-0140
+Build needed 00:02:48, 8120k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/mips.log b/mips.log
index 946901a..8ee14a6 100644
--- a/mips.log
+++ b/mips.log
@@ -1,41 +1,94 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/mips received Sat Dec 4 07:50:05 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=mips">mips</a> >> Sat Dec 4 07:50:05 2010<pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on ball.debian.org
+From buildd at corelli.debian.org Sun Mar 20 23:08:47 2011
+Return-path: <buildd at corelli.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 corelli.debian.org>)
+ id 1Q1Rjr-0006Oy-Ah
+ for logs at buildd.debian.org; Sun, 20 Mar 2011 23:08:47 +0000
+Received: from corelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4489])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=corelli.debian.org, EMAIL=hostmaster at corelli.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at corelli.debian.org>)
+ id 1Q1Rjo-0002Jj-TY; Sun, 20 Mar 2011 23:08:45 +0000
+Received: from buildd by corelli.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at corelli.debian.org>)
+ id 1Q1Rjk-0006i2-ON; Sun, 20 Mar 2011 23:08:40 +0000
+From: buildd on corelli <buildd at corelli.debian.org>
+To: aba at debian.org,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.12a-1~bpo60+1 on mips
+ (dist=squeeze-backports)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1Q1Rjk-0006i2-ON at corelli.debian.org>
+Date: Sun, 20 Mar 2011 23:08:40 +0000
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.5 (14 Nov 2010) on corelli.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (mips) 04 Dec 2010 07:42 ║
+║ samtools 0.1.12a-1~bpo60+1 (mips) 20 Mar 2011 22:25 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.12a-1~bpo60+1
Architecture: mips
-Chroot Build Dir: /var/lib/schroot/mount/sid-mips-sbuild-f75c9a7d-199d-45ad-ba56-a30973cbabf2/build/buildd-samtools_0.1.12a-1-mips-QwKHhy
-Start Time: 20101204-0742
-Get:1 http://debian.netcologne.de unstable Release.gpg [835B]
-Ign http://debian.netcologne.de/debian/ unstable/contrib Translation-en
-Ign http://debian.netcologne.de/debian/ unstable/main Translation-en
-Get:2 http://debian.netcologne.de unstable Release [104kB]
-Get:3 http://incoming.debian.org unstable Release.gpg [835B]
-Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
-Ign http://incoming.debian.org/debian/ unstable/main Translation-en
-Get:4 http://incoming.debian.org Release.gpg [835B]
-Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:5 http://incoming.debian.org unstable Release [104kB]
-Get:6 http://debian.netcologne.de unstable/main Sources [4073kB]
-Get:7 http://incoming.debian.org Release [1604B]
-Get:8 http://incoming.debian.org unstable/main Sources [4071kB]
-Get:9 http://debian.netcologne.de unstable/contrib Sources [38.7kB]
-Get:10 http://debian.netcologne.de unstable/non-free Sources [83.8kB]
-Get:11 http://debian.netcologne.de unstable/main mips Packages [6730kB]
-Get:12 http://debian.netcologne.de unstable/contrib mips Packages [51.5kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [38.7kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [83.8kB]
-Get:15 http://incoming.debian.org unstable/main mips Packages [6731kB]
-Get:16 http://incoming.debian.org unstable/contrib mips Packages [51.5kB]
-Get:17 http://incoming.debian.org Sources [10.0kB]
-Get:18 http://incoming.debian.org Packages [110kB]
-Fetched 22.3MB in 46s (478kB/s)
+Chroot Build Dir: /var/lib/schroot/mount/squeeze-backports-mips-sbuild-76513a66-5133-4980-8d50-d5e46cdaa7e3/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2
+Start Time: 20110320-2225
+Get:1 http://mirror-ubc.debian.org squeeze Release.gpg [1671 B]
+Get:2 http://backports-master.debian.org squeeze-backports Release.gpg [835 B]
+Ign http://mirror-ubc.debian.org/debian/ squeeze/contrib Translation-en
+Ign http://mirror-ubc.debian.org/debian/ squeeze/main Translation-en
+Get:3 http://mirror-ubc.debian.org squeeze-proposed-updates Release.gpg [836 B]
+Ign http://mirror-ubc.debian.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/contrib Translation-en
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/main Translation-en
+Ign http://mirror-ubc.debian.org/debian/ squeeze-proposed-updates/main Translation-en
+Get:4 http://backports-master.debian.org Release.gpg [835 B]
+Ign http://backports-master.debian.org/buildd/squeeze-backports/ Translation-en
+Get:5 http://mirror-ubc.debian.org squeeze Release [79.8 kB]
+Get:6 http://backports-master.debian.org squeeze-backports Release [61.2 kB]
+Get:7 http://backports-master.debian.org Release [1644 B]
+Get:8 http://mirror-ubc.debian.org squeeze-proposed-updates Release [59.0 kB]
+Get:9 http://backports-master.debian.org squeeze-backports/main Sources [9674 B]
+Get:10 http://backports-master.debian.org squeeze-backports/contrib Sources [14 B]
+Get:11 http://backports-master.debian.org squeeze-backports/non-free Sources [14 B]
+Get:12 http://backports-master.debian.org squeeze-backports/main mips Packages [11.4 kB]
+Get:13 http://backports-master.debian.org squeeze-backports/contrib mips Packages [14 B]
+Get:14 http://backports-master.debian.org Sources [747 B]
+Get:15 http://backports-master.debian.org Packages [3328 B]
+Get:16 http://mirror-ubc.debian.org squeeze/main Sources [3721 kB]
+Get:17 http://ftp.debian.org squeeze Release.gpg [1671 B]
+Ign http://ftp.debian.org/debian/ squeeze/contrib Translation-en
+Ign http://ftp.debian.org/debian/ squeeze/main Translation-en
+Get:18 http://ftp.debian.org squeeze-proposed-updates Release.gpg [836 B]
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/main Translation-en
+Get:19 http://ftp.debian.org squeeze Release [79.8 kB]
+Get:20 http://mirror-ubc.debian.org squeeze/contrib Sources [33.9 kB]
+Get:21 http://mirror-ubc.debian.org squeeze/non-free Sources [61.7 kB]
+Get:22 http://mirror-ubc.debian.org squeeze/main mips Packages [6407 kB]
+Get:23 http://ftp.debian.org squeeze-proposed-updates Release [59.0 kB]
+Get:24 http://ftp.debian.org squeeze/main Sources [3721 kB]
+Get:25 http://mirror-ubc.debian.org squeeze/contrib mips Packages [45.1 kB]
+Get:26 http://mirror-ubc.debian.org squeeze-proposed-updates/main Sources [14 B]
+Get:27 http://mirror-ubc.debian.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:28 http://mirror-ubc.debian.org squeeze-proposed-updates/non-free Sources [14 B]
+Get:29 http://mirror-ubc.debian.org squeeze-proposed-updates/main mips Packages [14 B]
+Get:30 http://mirror-ubc.debian.org squeeze-proposed-updates/contrib mips Packages [14 B]
+Get:31 http://ftp.debian.org squeeze/contrib Sources [33.9 kB]
+Get:32 http://ftp.debian.org squeeze/non-free Sources [61.7 kB]
+Get:33 http://ftp.debian.org squeeze/main mips Packages [6407 kB]
+Get:34 http://ftp.debian.org squeeze/contrib mips Packages [45.1 kB]
+Get:35 http://ftp.debian.org squeeze-proposed-updates/main Sources [14 B]
+Get:36 http://ftp.debian.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:37 http://ftp.debian.org squeeze-proposed-updates/non-free Sources [14 B]
+Get:38 http://ftp.debian.org squeeze-proposed-updates/main mips Packages [14 B]
+Get:39 http://ftp.debian.org squeeze-proposed-updates/contrib mips Packages [14 B]
+Fetched 20.9 MB in 48s (435 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -53,151 +106,210 @@ Download source files with APT
Reading package lists...
Building dependency tree...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+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 364kB of source archives.
-Get:1 http://debian.netcologne.de/debian/ unstable/main samtools 0.1.12a-1 (dsc) [1946B]
-Get:2 http://debian.netcologne.de/debian/ unstable/main samtools 0.1.12a-1 (tar) [356kB]
-Get:3 http://debian.netcologne.de/debian/ unstable/main samtools 0.1.12a-1 (diff) [6337B]
-Fetched 364kB in 0s (1758kB/s)
+Need to get 363 kB of source archives.
+Get:1 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (dsc) [1338 B]
+Get:2 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (tar) [356 kB]
+Get:3 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (diff) [6406 B]
+Fetched 363 kB in 0s (3446 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
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install build dependencies (aptitude-based 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 libncurses5 libpcre3 libunistring0 libxml2
- man-db ncurses-bin po-debconf
+ libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5 libsigc++-2.0-0c2a
+ libsqlite3-0 libxapian22
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ tasksel debtags libcwidget-dev xapian-tools
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libgpm2 xml-core libmail-sendmail-perl
+ aptitude-doc-en aptitude-doc apt-xapian-index libparse-debianchangelog-perl
+ libgpm2
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
-The following packages will be upgraded:
- libncurses5 ncurses-bin
-2 upgraded, 19 newly installed, 0 to remove and 54 not upgraded.
-Need to get 12.3MB of archives.
-After this operation, 37.2MB of additional disk space will be used.
-Get:1 http://debian.netcologne.de/debian/ unstable/main ncurses-bin mips 5.7+20100313-4 [317kB]
-Get:2 http://debian.netcologne.de/debian/ unstable/main libncurses5 mips 5.7+20100313-4 [349kB]
-Get:3 http://debian.netcologne.de/debian/ unstable/main bsdmainutils mips 8.0.17 [208kB]
-Get:4 http://debian.netcologne.de/debian/ unstable/main groff-base mips 1.20.1-10 [1190kB]
-Get:5 http://debian.netcologne.de/debian/ unstable/main man-db mips 2.5.7-6 [1251kB]
-Get:6 http://debian.netcologne.de/debian/ unstable/main libmagic1 mips 5.04-5 [239kB]
-Get:7 http://debian.netcologne.de/debian/ unstable/main file mips 5.04-5 [49.7kB]
-Get:8 http://debian.netcologne.de/debian/ unstable/main gettext-base mips 0.18.1.1-3 [153kB]
-Get:9 http://debian.netcologne.de/debian/ unstable/main libpcre3 mips 8.02-1.1 [232kB]
-Get:10 http://debian.netcologne.de/debian/ unstable/main libxml2 mips 2.7.8.dfsg-1 [836kB]
-Get:11 http://debian.netcologne.de/debian/ unstable/main html2text mips 1.3.2a-15 [103kB]
-Get:12 http://debian.netcologne.de/debian/ unstable/main libglib2.0-0 mips 2.24.2-1 [1043kB]
-Get:13 http://debian.netcologne.de/debian/ unstable/main libcroco3 mips 0.6.2-1 [110kB]
-Get:14 http://debian.netcologne.de/debian/ unstable/main libunistring0 mips 0.9.3-3 [415kB]
-Get:15 http://debian.netcologne.de/debian/ unstable/main gettext mips 0.18.1.1-3 [2037kB]
-Get:16 http://debian.netcologne.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8kB]
-Get:17 http://debian.netcologne.de/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223kB]
-Get:18 http://debian.netcologne.de/debian/ unstable/main debhelper all 8.0.0 [454kB]
-Get:19 http://debian.netcologne.de/debian/ unstable/main cdbs all 0.4.89 [1240kB]
-Get:20 http://debian.netcologne.de/debian/ unstable/main libncurses5-dev mips 5.7+20100313-4 [1643kB]
-Get:21 http://debian.netcologne.de/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191kB]
+ aptitude libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5
+ libsigc++-2.0-0c2a libsqlite3-0 libxapian22
+0 upgraded, 8 newly installed, 0 to remove and 3 not upgraded.
+Need to get 6274 kB of archives.
+After this operation, 20.5 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ squeeze/main libboost-iostreams1.42.0 mips 1.42.0-4 [55.3 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ squeeze/main libncursesw5 mips 5.7+20100313-5 [374 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ squeeze/main libsigc++-2.0-0c2a mips 2.2.4.2-1 [39.2 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ squeeze/main libcwidget3 mips 0.5.16-3 [273 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ squeeze/main libxapian22 mips 1.2.3-2 [1098 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ squeeze/main libept1 mips 1.0.4 [137 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ squeeze/main libsqlite3-0 mips 3.7.3-1 [415 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ squeeze/main aptitude mips 0.6.3-3.2 [3882 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 12.3MB in 2s (4710kB/s)
-(Reading database ... 10123 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.7+20100313-3 (using .../ncurses-bin_5.7+20100313-4_mips.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.7+20100313-4) ...
-(Reading database ... 10123 files and directories currently installed.)
-Preparing to replace libncurses5 5.7+20100313-3 (using .../libncurses5_5.7+20100313-4_mips.deb) ...
-Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.7+20100313-4) ...
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 10123 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_mips.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_mips.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_mips.deb) ...
+Fetched 6274 kB in 1s (5211 kB/s)
+Selecting previously deselected package libboost-iostreams1.42.0.
+(Reading database ... 10147 files and directories currently installed.)
+Unpacking libboost-iostreams1.42.0 (from .../libboost-iostreams1.42.0_1.42.0-4_mips.deb) ...
+Selecting previously deselected package libncursesw5.
+Unpacking libncursesw5 (from .../libncursesw5_5.7+20100313-5_mips.deb) ...
+Selecting previously deselected package libsigc++-2.0-0c2a.
+Unpacking libsigc++-2.0-0c2a (from .../libsigc++-2.0-0c2a_2.2.4.2-1_mips.deb) ...
+Selecting previously deselected package libcwidget3.
+Unpacking libcwidget3 (from .../libcwidget3_0.5.16-3_mips.deb) ...
+Selecting previously deselected package libxapian22.
+Unpacking libxapian22 (from .../libxapian22_1.2.3-2_mips.deb) ...
+Selecting previously deselected package libept1.
+Unpacking libept1 (from .../libept1_1.0.4_mips.deb) ...
+Selecting previously deselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.3-1_mips.deb) ...
+Selecting previously deselected package aptitude.
+Unpacking aptitude (from .../aptitude_0.6.3-3.2_mips.deb) ...
+Setting up libboost-iostreams1.42.0 (1.42.0-4) ...
+Setting up libncursesw5 (5.7+20100313-5) ...
+Setting up libsigc++-2.0-0c2a (2.2.4.2-1) ...
+Setting up libcwidget3 (0.5.16-3) ...
+Setting up libxapian22 (1.2.3-2) ...
+Setting up libept1 (1.0.4) ...
+Setting up libsqlite3-0 (3.7.3-1) ...
+Setting up aptitude (0.6.3-3.2) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode.
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/buildd-samtools-mips-dZoSz8/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously deselected package sbuild-build-depends-samtools-dummy.
+(Reading database ... 10355 files and directories currently installed.)
+Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
+dpkg: dependency problems prevent configuration of sbuild-build-depends-samtools-dummy:
+ sbuild-build-depends-samtools-dummy depends on debhelper (>= 8); however:
+ Package debhelper is not installed.
+ sbuild-build-depends-samtools-dummy depends on cdbs; however:
+ Package cdbs is not installed.
+ sbuild-build-depends-samtools-dummy depends on libncurses5-dev; however:
+ Package libncurses5-dev is not installed.
+ sbuild-build-depends-samtools-dummy depends on zlib1g-dev; however:
+ Package zlib1g-dev is not installed.
+dpkg: error processing sbuild-build-depends-samtools-dummy (--install):
+ dependency problems - leaving unconfigured
+Errors were encountered while processing:
+ sbuild-build-depends-samtools-dummy
+aptitude -y --without-recommends -o APT::Install-Recommends=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-samtools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Tier=55000 -o Aptitude::ProblemResolver::Remove-Essential-Tier=maximum install sbuild-build-depends-samtools-dummy
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
+The following NEW packages will be installed:
+ bsdmainutils{a} cdbs{a} debhelper{a} file{a} gettext{a} gettext-base{a}
+ groff-base{a} html2text{a} intltool-debian{a} libcroco3{a}
+ libglib2.0-0{a} libmagic1{a} libncurses5-dev{a} libpcre3{a}
+ libunistring0{a} libxml2{a} man-db{a} po-debconf{a} zlib1g-dev{a}
+The following partially installed packages will be configured:
+ sbuild-build-depends-samtools-dummy
+0 packages upgraded, 19 newly installed, 0 to remove and 3 not upgraded.
+Need to get 11.7 MB of archives. After unpacking 37.2 MB will be used.
+Writing extended state information...
+Get:1 http://mirror-ubc.debian.org/debian/ squeeze/main libmagic1 mips 5.04-5 [239 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ squeeze/main file mips 5.04-5 [49.7 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ squeeze/main html2text mips 1.3.2a-15 [103 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ squeeze/main libpcre3 mips 8.02-1.1 [232 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ squeeze/main libglib2.0-0 mips 2.24.2-1 [1043 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ squeeze/main libxml2 mips 2.7.8.dfsg-2 [837 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ squeeze/main libcroco3 mips 0.6.2-1 [110 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ squeeze/main libunistring0 mips 0.9.3-3 [415 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ squeeze/main gettext-base mips 0.18.1.1-3 [153 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ squeeze/main gettext mips 0.18.1.1-3 [2037 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ squeeze/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ squeeze/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ squeeze/main groff-base mips 1.20.1-10 [1190 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ squeeze/main bsdmainutils mips 8.0.13 [207 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ squeeze/main man-db mips 2.5.7-8 [1251 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ squeeze/main debhelper all 8.0.0 [454 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ squeeze/main cdbs all 0.4.89 [1240 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ squeeze/main libncurses5-dev mips 5.7+20100313-5 [1643 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ squeeze/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 11.7 MB in 2s (5248 kB/s)
Selecting previously deselected package libmagic1.
+(Reading database ... 10355 files and directories currently installed.)
Unpacking libmagic1 (from .../libmagic1_5.04-5_mips.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../archives/file_5.04-5_mips.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mips.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_mips.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_mips.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mips.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.02-1.1_mips.deb) ...
Selecting previously deselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_mips.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_mips.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mips.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-3_mips.deb) ...
+Selecting previously deselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_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_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously deselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.20.1-10_mips.deb) ...
+Selecting previously deselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_mips.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.5.7-8_mips.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_mips.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_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 (8.0.17) ...
-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) ...
-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 libpcre3 (8.02-1.1) ...
Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
+Setting up gettext-base (0.18.1.1-3) ...
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 groff-base (1.20.1-10) ...
+Setting up bsdmainutils (8.0.13) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
+Setting up man-db (2.5.7-8) ...
+debconf: unable to initialize frontend: Dialog
+debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 75.)
+debconf: falling back to frontend: Readline
+debconf: unable to initialize frontend: Readline
+debconf: (This frontend requires a controlling tty.)
+debconf: falling back to frontend: Teletype
+Building database of manual pages ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
-Setting up libncurses5-dev (5.7+20100313-4) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: Linux 2.6.32.2-dsa-mips-swarm mips (mips64)
-Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-23 gcc-4.4_4.4.4-15 g++-4.4_4.4.4-15 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.4-15 libstdc++6_4.4.4-15
-Package versions: apt_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.17 bsdutils_1:2.17.2-3.2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-15 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 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 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-15 gcc_4:4.4.4-2 gcc-4.4_4.4.4-15 gcc-4.4-base_4.4.4-15 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_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.2 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-15 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-15 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.4-15 libstdc++6-4.4-dev_4.4.4-15 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_2:0.1.12-16 libuuid1_2.17.2-3.2 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-24 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.2 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-1 patch_2.6-3 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010l-1 util-linux_2.17.2-3.2 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
+Toolchain package versions: libc6-dev_2.11.2-10 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.32-31 gcc-4.4_4.4.5-8 g++-4.4_4.4.5-8 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-8 libstdc++6_4.4.5-8
+Package versions: apt_0.8.10.3 aptitude_0.6.3-3.2 base-files_6.0 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.0.13 bsdutils_1:2.17.2-9 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-8 dash_0.5.5.1-7.4 debconf_1.5.36.1 debconf-i18n_1.5.36.1 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 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_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-8 gcc_4:4.4.5-1 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 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-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 libboost-iostreams1.42.0_1.42.0-4 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 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcwidget3_0.5.16-3 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.10 libept1_1.0.4 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-8 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-8 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 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 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libsigc++-2.0-0c2a_2.2.4.2-1 libslang2_2.2.2-4 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libstdc++6_4.4.5-8 libstdc++6-4.4-dev_4.4.5-8 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_2:0.1.12-16 libuuid1_2.17.2-9 libxapian22_1.2.3-2 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-31 login_1:4.1.4.2+svn3283-2+squeeze1 lsb-base_3.2-23.2squeeze1 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 mount_2.17.2-9 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2+squeeze1 patch_2.6-2 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 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2.squeeze.1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.23-3 tzdata_2010o-1 util-linux_2.17.2-9 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -208,13 +320,13 @@ 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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Thu Feb 17 08:40:32 2011 UTC using DSA key ID BAFEC7F2
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1~bpo60+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
+dpkg-source: info: unpacking samtools_0.1.12a-1~bpo60+1.debian.tar.gz
Check disc space
────────────────
@@ -229,46 +341,46 @@ 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-buildpackage: source version 0.1.12a-1~bpo60+1
dpkg-source --before-build samtools-0.1.12a
dpkg-buildpackage: host architecture mips
/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-mips-QwKHhy/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
+/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~bpo60+1-mips-XYoEw2/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/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-mips-QwKHhy/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/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-mips-QwKHhy/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/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-mips-QwKHhy/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/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 "."
+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-mips-QwKHhy/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
+/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~bpo60+1-mips-XYoEw2/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/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'
+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
@@ -283,8 +395,8 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-mips-QwKHhy/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/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
@@ -295,10 +407,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-mips-QwKHhy/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/samtools-0.1.12a/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/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
@@ -315,24 +427,24 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-mips-QwKHhy/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/samtools-0.1.12a'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/samtools-0.1.12a/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/samtools-0.1.12a/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/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-mips-QwKHhy/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/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-mips-QwKHhy/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/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
@@ -342,50 +454,50 @@ 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-mips-QwKHhy/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/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-mips-QwKHhy/samtools-0.1.12a'
+make[1]: Nothing to be done for `lib'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/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-mips-QwKHhy/samtools-0.1.12a/examples'
+/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~bpo60+1-mips-XYoEw2/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 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
+../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
+../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
+(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'
+[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
+[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
+<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'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/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 "."
+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
@@ -411,8 +523,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/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
@@ -436,7 +548,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -451,69 +563,66 @@ 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_mips.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1~bpo60+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_0.1.12a-1_mips.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1~bpo60+1_mips.deb'.
+ dpkg-genchanges -B -mmips Build Daemon (corelli) <buildd_mips-corelli at buildd.debian.org> >../samtools_0.1.12a-1~bpo60+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-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101204-0749
+Build finished at 20110320-2308
-samtools_0.1.12a-1_mips.changes:
+samtools_0.1.12a-1~bpo60+1_mips.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Thu, 17 Feb 2011 13:13:09 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mips
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.12a-1~bpo60+1
+Distribution: squeeze-backports
Urgency: low
-Maintainer: Debian Build Daemon <buildd_mips-ball at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: mips Build Daemon (corelli) <buildd_mips-corelli 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 (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.12a-1~bpo60+1) squeeze-backports; 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).
+ * Backported for Squeeze (no changes needed).
Checksums-Sha1:
- 819ca6a39882f43c04698bc7aaaa06631ed10e0b 574528 samtools_0.1.12a-1_mips.deb
- 67683aff48ff5b969fe894fb62879a6a270e2a1d 172934 libbam-dev_0.1.12a-1_mips.deb
+ 32a91265b620fb2b14145c3c719779e909d4504c 579034 samtools_0.1.12a-1~bpo60+1_mips.deb
+ 9ca7e61bb352b19fe1e300b5cee43bd1c05dfba7 172916 libbam-dev_0.1.12a-1~bpo60+1_mips.deb
Checksums-Sha256:
- 0558c06b947bd330216871469e3921cc71144f216eba89a26325ff9e62e8efdb 574528 samtools_0.1.12a-1_mips.deb
- 2fff24c10a6abce81214d6eb3c3973b8a01659ce2a4cbba55edb565f84f96049 172934 libbam-dev_0.1.12a-1_mips.deb
+ a45e557cff5a7f3af0b782f43d13938f152aad14bf9a2f2e8c6bd524c26b7d9e 579034 samtools_0.1.12a-1~bpo60+1_mips.deb
+ 30233e46a20ed9d3484f505000894c9c9d951624ae20107741b6cffc9339e78e 172916 libbam-dev_0.1.12a-1~bpo60+1_mips.deb
Files:
- ad86bf07ab4b83c8e247ce25aa58ce23 574528 science optional samtools_0.1.12a-1_mips.deb
- 713b2da1c6a306a68ca29dd52f92c7b8 172934 libdevel optional libbam-dev_0.1.12a-1_mips.deb
+ e1b83287f4cff9404bd195a0ae85260d 579034 science optional samtools_0.1.12a-1~bpo60+1_mips.deb
+ 6581a533c254f192399e8c9e4f4fc5f5 172916 libdevel optional libbam-dev_0.1.12a-1~bpo60+1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_mips.deb
-───────────────────────────
+samtools_0.1.12a-1~bpo60+1_mips.deb
+───────────────────────────────────
new debian package, version 2.0.
- size 574528 bytes: control archive= 1790 bytes.
- 792 bytes, 16 lines control
+ size 579034 bytes: control archive= 1803 bytes.
+ 800 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.12a-1~bpo60+1
Architecture: mips
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1116
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -525,72 +634,72 @@ samtools_0.1.12a-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 2010-12-04 07:49 ./
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/doc/samtools/
--rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2010-12-04 07:49 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1031 2010-12-03 05:06 ./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 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
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./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 2010-12-04 07:48 ./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 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 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/man/man1/
--rw-r--r-- root/root 7546 2010-12-04 07:49 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2010-12-04 07:49 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./usr/
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./usr/share/samtools/
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 12567 2010-12-02 16:41 ./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 5778 2011-03-20 23:07 ./usr/share/samtools/varfilter.py
-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
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.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 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.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 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 5778 2010-12-04 07:49 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/bin/
--rwxr-xr-x root/root 30712 2010-12-04 07:49 ./usr/bin/razip
--rwxr-xr-x root/root 410760 2010-12-04 07:49 ./usr/bin/samtools
--rwxr-xr-x root/root 108704 2010-12-04 07:49 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/lib/
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/lib/samtools/
--rwxr-xr-x root/root 19928 2010-12-04 07:49 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 9768 2010-12-04 07:49 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7764 2010-12-04 07:49 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 13268 2010-12-04 07:49 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7764 2010-12-04 07:49 ./usr/lib/samtools/maq2sam-short
-lrwxrwxrwx root/root 0 2010-12-04 07:49 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.12a-1_mips.deb
-─────────────────────────────
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-20 23:07 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7546 2011-03-20 23:07 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./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 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./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 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 126609 2011-03-20 22:33 ./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 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 592 2011-02-15 05:37 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-02-15 05:37 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 4927 2011-02-15 05:37 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1966 2011-03-20 23:07 ./usr/share/doc/samtools/README.bcftools
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./usr/lib/samtools/
+-rwxr-xr-x root/root 13268 2011-03-20 23:07 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7764 2011-03-20 23:07 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7764 2011-03-20 23:07 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9768 2011-03-20 23:07 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 19928 2011-03-20 23:07 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./usr/bin/
+-rwxr-xr-x root/root 108704 2011-03-20 23:07 ./usr/bin/bcftools
+-rwxr-xr-x root/root 410760 2011-03-20 23:07 ./usr/bin/samtools
+-rwxr-xr-x root/root 30712 2011-03-20 23:07 ./usr/bin/razip
+lrwxrwxrwx root/root 0 2011-03-20 23:07 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1~bpo60+1_mips.deb
+─────────────────────────────────────
new debian package, version 2.0.
- size 172934 bytes: control archive= 900 bytes.
- 674 bytes, 15 lines control
+ size 172916 bytes: control archive= 910 bytes.
+ 682 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.12a-1~bpo60+1
Architecture: mips
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 448
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 444
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -601,23 +710,764 @@ libbam-dev_0.1.12a-1_mips.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./usr/
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./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 2011-03-20 23:07 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./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 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 4927 2011-02-15 05:37 ./usr/share/doc/libbam-dev/copyright
-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 2010-12-04 07:49 ./usr/include/
+drwxr-xr-x root/root 0 2011-03-20 23:07 ./usr/lib/
+-rw-r--r-- root/root 302830 2011-03-20 23:07 ./usr/lib/libbam.a
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Finished │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Built successfully
+────────────────────────────────────────────────────────────────────────────────
+Purging /var/lib/schroot/mount/squeeze-backports-mips-sbuild-76513a66-5133-4980-8d50-d5e46cdaa7e3/build/buildd-samtools_0.1.12a-1~bpo60+1-mips-XYoEw2
+Not removing build depends: cloned chroot in use
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20110320-2308
+Build needed 00:43:32, 9300k disc space
+
+From buildd at rem.debian.org Wed Mar 16 20:26:16 2011
+Return-path: <buildd at rem.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 rem.debian.org>)
+ id 1PzxIN-0000HL-6x
+ for logs at buildd.debian.org; Wed, 16 Mar 2011 20:26:16 +0000
+Received: from rem.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d06])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=rem.debian.org, EMAIL=hostmaster at rem.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at rem.debian.org>)
+ id 1PzxIJ-0003jK-ES; Wed, 16 Mar 2011 20:26:11 +0000
+Received: from buildd by rem.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at rem.debian.org>)
+ id 1PzxII-0000s9-N8; Wed, 16 Mar 2011 20:26:10 +0000
+Date: Wed, 16 Mar 2011 20:26:10 +0000
+Message-Id: <E1PzxII-0000s9-N8 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_0.1.12a-1~bpo60+1 on mipsel
+ (dist=squeeze-backports)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on rem.debian.org
+
+╔══════════════════════════════════════════════════════════════════════════════╗
+║ samtools 0.1.12a-1~bpo60+1 (mipsel) 16 Mar 2011 20:20 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: samtools
+Version: 0.1.12a-1~bpo60+1
+Architecture: mipsel
+Chroot Build Dir: /var/lib/schroot/mount/squeeze-backports-mipsel-sbuild-77b0bd91-ef4d-4509-a448-0e69ab4a6cf7/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB
+Start Time: 20110316-2020
+Get:1 http://ftp.debian.org squeeze Release.gpg [1671 B]
+Ign http://ftp.debian.org/debian/ squeeze/contrib Translation-en
+Ign http://ftp.debian.org/debian/ squeeze/main Translation-en
+Get:2 http://ftp.debian.org squeeze-proposed-updates Release.gpg [835 B]
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/main Translation-en
+Get:3 http://ftp.debian.org squeeze Release [69.3 kB]
+Get:4 http://ftp.debian.org squeeze-proposed-updates Release [65.4 kB]
+Get:5 http://ftp.debian.org squeeze/main Sources [3720 kB]
+Hit http://mirror.ayous.org squeeze Release.gpg
+Ign http://mirror.ayous.org/debian/ squeeze/contrib Translation-en
+Ign http://mirror.ayous.org/debian/ squeeze/main Translation-en
+Get:6 http://mirror.ayous.org squeeze-proposed-updates Release.gpg [835 B]
+Ign http://mirror.ayous.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://mirror.ayous.org/debian/ squeeze-proposed-updates/main Translation-en
+Hit http://mirror.ayous.org squeeze Release
+Get:7 http://mirror.ayous.org squeeze-proposed-updates Release [65.4 kB]
+Get:8 http://backports-master.debian.org squeeze-backports Release.gpg [835 B]
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/contrib Translation-en
+Hit http://mirror.ayous.org squeeze/main Sources
+Hit http://mirror.ayous.org squeeze/contrib Sources
+Get:9 http://mirror.ayous.org squeeze/non-free Sources [61.7 kB]
+Hit http://mirror.ayous.org squeeze/main mipsel Packages
+Hit http://mirror.ayous.org squeeze/contrib mipsel Packages
+Get:10 http://mirror.ayous.org squeeze-proposed-updates/main Sources [38.0 kB]
+Get:11 http://mirror.ayous.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:12 http://mirror.ayous.org squeeze-proposed-updates/non-free Sources [926 B]
+Get:13 http://mirror.ayous.org squeeze-proposed-updates/main mipsel Packages [105 kB]
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/main Translation-en
+Get:14 http://backports-master.debian.org Release.gpg [835 B]
+Ign http://backports-master.debian.org/buildd/squeeze-backports/ Translation-en
+Get:15 http://mirror.ayous.org squeeze-proposed-updates/contrib mipsel Packages [14 B]
+Get:16 http://backports-master.debian.org squeeze-backports Release [61.2 kB]
+Get:17 http://backports-master.debian.org Release [1644 B]
+Get:18 http://backports-master.debian.org squeeze-backports/main Sources [9340 B]
+Get:19 http://backports-master.debian.org squeeze-backports/contrib Sources [14 B]
+Get:20 http://backports-master.debian.org squeeze-backports/non-free Sources [14 B]
+Get:21 http://backports-master.debian.org squeeze-backports/main mipsel Packages [18.1 kB]
+Get:22 http://backports-master.debian.org squeeze-backports/contrib mipsel Packages [14 B]
+Get:23 http://backports-master.debian.org Sources [14 B]
+Get:24 http://backports-master.debian.org Packages [24.4 kB]
+Get:25 http://ftp.debian.org squeeze/contrib Sources [33.9 kB]
+Get:26 http://ftp.debian.org squeeze/non-free Sources [61.7 kB]
+Get:27 http://ftp.debian.org squeeze/main mipsel Packages [6417 kB]
+Get:28 http://ftp.debian.org squeeze/contrib mipsel Packages [45.4 kB]
+Get:29 http://ftp.debian.org squeeze-proposed-updates/main Sources [38.0 kB]
+Get:30 http://ftp.debian.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:31 http://ftp.debian.org squeeze-proposed-updates/non-free Sources [926 B]
+Get:32 http://ftp.debian.org squeeze-proposed-updates/main mipsel Packages [105 kB]
+Get:33 http://ftp.debian.org squeeze-proposed-updates/contrib mipsel Packages [14 B]
+Fetched 10.9 MB in 21s (501 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...
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/debian-med/samtools.git
+Need to get 363 kB of source archives.
+Get:1 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (dsc) [1338 B]
+Get:2 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (tar) [356 kB]
+Get:3 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (diff) [6406 B]
+Fetched 363 kB in 2s (167 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 (aptitude-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Reading package lists...
+Building dependency tree...
+The following extra packages will be installed:
+ libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5 libsigc++-2.0-0c2a
+ libsqlite3-0 libxapian22
+Suggested packages:
+ tasksel debtags libcwidget-dev xapian-tools
+Recommended packages:
+ aptitude-doc-en aptitude-doc apt-xapian-index libparse-debianchangelog-perl
+ libgpm2
+The following NEW packages will be installed:
+ aptitude libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5
+ libsigc++-2.0-0c2a libsqlite3-0 libxapian22
+0 upgraded, 8 newly installed, 0 to remove and 6 not upgraded.
+Need to get 6230 kB of archives.
+After this operation, 20.5 MB of additional disk space will be used.
+Get:1 http://mirror.ayous.org/debian/ squeeze/main libboost-iostreams1.42.0 mipsel 1.42.0-4 [55.2 kB]
+Get:2 http://mirror.ayous.org/debian/ squeeze/main libncursesw5 mipsel 5.7+20100313-5 [371 kB]
+Get:3 http://mirror.ayous.org/debian/ squeeze/main libsigc++-2.0-0c2a mipsel 2.2.4.2-1 [39.2 kB]
+Get:4 http://mirror.ayous.org/debian/ squeeze/main libcwidget3 mipsel 0.5.16-3 [270 kB]
+Get:5 http://mirror.ayous.org/debian/ squeeze/main libxapian22 mipsel 1.2.3-2 [1089 kB]
+Get:6 http://mirror.ayous.org/debian/ squeeze/main libept1 mipsel 1.0.4 [135 kB]
+Get:7 http://mirror.ayous.org/debian/ squeeze/main libsqlite3-0 mipsel 3.7.3-1 [414 kB]
+Get:8 http://mirror.ayous.org/debian/ squeeze/main aptitude mipsel 0.6.3-3.2 [3856 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 6230 kB in 0s (7539 kB/s)
+Selecting previously deselected package libboost-iostreams1.42.0.
+(Reading database ... 10135 files and directories currently installed.)
+Unpacking libboost-iostreams1.42.0 (from .../libboost-iostreams1.42.0_1.42.0-4_mipsel.deb) ...
+Selecting previously deselected package libncursesw5.
+Unpacking libncursesw5 (from .../libncursesw5_5.7+20100313-5_mipsel.deb) ...
+Selecting previously deselected package libsigc++-2.0-0c2a.
+Unpacking libsigc++-2.0-0c2a (from .../libsigc++-2.0-0c2a_2.2.4.2-1_mipsel.deb) ...
+Selecting previously deselected package libcwidget3.
+Unpacking libcwidget3 (from .../libcwidget3_0.5.16-3_mipsel.deb) ...
+Selecting previously deselected package libxapian22.
+Unpacking libxapian22 (from .../libxapian22_1.2.3-2_mipsel.deb) ...
+Selecting previously deselected package libept1.
+Unpacking libept1 (from .../libept1_1.0.4_mipsel.deb) ...
+Selecting previously deselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.3-1_mipsel.deb) ...
+Selecting previously deselected package aptitude.
+Unpacking aptitude (from .../aptitude_0.6.3-3.2_mipsel.deb) ...
+Setting up libboost-iostreams1.42.0 (1.42.0-4) ...
+Setting up libncursesw5 (5.7+20100313-5) ...
+Setting up libsigc++-2.0-0c2a (2.2.4.2-1) ...
+Setting up libcwidget3 (0.5.16-3) ...
+Setting up libxapian22 (1.2.3-2) ...
+Setting up libept1 (1.0.4) ...
+Setting up libsqlite3-0 (3.7.3-1) ...
+Setting up aptitude (0.6.3-3.2) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode.
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/buildd-samtools-mipsel-Imn2IT/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously deselected package sbuild-build-depends-samtools-dummy.
+(Reading database ... 10343 files and directories currently installed.)
+Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
+dpkg: dependency problems prevent configuration of sbuild-build-depends-samtools-dummy:
+ sbuild-build-depends-samtools-dummy depends on debhelper (>= 8); however:
+ Package debhelper is not installed.
+ sbuild-build-depends-samtools-dummy depends on cdbs; however:
+ Package cdbs is not installed.
+ sbuild-build-depends-samtools-dummy depends on libncurses5-dev; however:
+ Package libncurses5-dev is not installed.
+ sbuild-build-depends-samtools-dummy depends on zlib1g-dev; however:
+ Package zlib1g-dev is not installed.
+dpkg: error processing sbuild-build-depends-samtools-dummy (--install):
+ dependency problems - leaving unconfigured
+Errors were encountered while processing:
+ sbuild-build-depends-samtools-dummy
+aptitude -y --without-recommends -o APT::Install-Recommends=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-samtools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Tier=55000 -o Aptitude::ProblemResolver::Remove-Essential-Tier=maximum install sbuild-build-depends-samtools-dummy
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
+The following NEW packages will be installed:
+ bsdmainutils{a} cdbs{a} debhelper{a} file{a} gettext{a} gettext-base{a}
+ groff-base{a} html2text{a} intltool-debian{a} libcroco3{a}
+ libglib2.0-0{a} libmagic1{a} libncurses5-dev{a} libpcre3{a}
+ libunistring0{a} libxml2{a} man-db{a} po-debconf{a} zlib1g-dev{a}
+The following partially installed packages will be configured:
+ sbuild-build-depends-samtools-dummy
+0 packages upgraded, 19 newly installed, 0 to remove and 6 not upgraded.
+Need to get 11.6 MB of archives. After unpacking 37.2 MB will be used.
+Writing extended state information...
+Get:1 http://mirror.ayous.org/debian/ squeeze/main libmagic1 mipsel 5.04-5 [238 kB]
+Get:2 http://mirror.ayous.org/debian/ squeeze/main file mipsel 5.04-5 [49.5 kB]
+Get:3 http://mirror.ayous.org/debian/ squeeze/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:4 http://mirror.ayous.org/debian/ squeeze/main libpcre3 mipsel 8.02-1.1 [233 kB]
+Get:5 http://mirror.ayous.org/debian/ squeeze/main libglib2.0-0 mipsel 2.24.2-1 [1039 kB]
+Get:6 http://mirror.ayous.org/debian/ squeeze/main libxml2 mipsel 2.7.8.dfsg-2 [833 kB]
+Get:7 http://mirror.ayous.org/debian/ squeeze/main libcroco3 mipsel 0.6.2-1 [110 kB]
+Get:8 http://mirror.ayous.org/debian/ squeeze/main libunistring0 mipsel 0.9.3-3 [411 kB]
+Get:9 http://mirror.ayous.org/debian/ squeeze/main gettext-base mipsel 0.18.1.1-3 [152 kB]
+Get:10 http://mirror.ayous.org/debian/ squeeze/main gettext mipsel 0.18.1.1-3 [2023 kB]
+Get:11 http://mirror.ayous.org/debian/ squeeze/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:12 http://mirror.ayous.org/debian/ squeeze/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:13 http://mirror.ayous.org/debian/ squeeze/main groff-base mipsel 1.20.1-10 [1188 kB]
+Get:14 http://mirror.ayous.org/debian/ squeeze/main bsdmainutils mipsel 8.0.13 [205 kB]
+Get:15 http://mirror.ayous.org/debian/ squeeze/main man-db mipsel 2.5.7-8 [1248 kB]
+Get:16 http://mirror.ayous.org/debian/ squeeze/main debhelper all 8.0.0 [454 kB]
+Get:17 http://mirror.ayous.org/debian/ squeeze/main cdbs all 0.4.89 [1240 kB]
+Get:18 http://mirror.ayous.org/debian/ squeeze/main libncurses5-dev mipsel 5.7+20100313-5 [1639 kB]
+Get:19 http://mirror.ayous.org/debian/ squeeze/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 11.6 MB in 1s (7840 kB/s)
+Selecting previously deselected package libmagic1.
+(Reading database ... 10343 files and directories currently installed.)
+Unpacking libmagic1 (from .../libmagic1_5.04-5_mipsel.deb) ...
+Selecting previously deselected package file.
+Unpacking file (from .../file_5.04-5_mipsel.deb) ...
+Selecting previously deselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.02-1.1_mipsel.deb) ...
+Selecting previously deselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_mipsel.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_mipsel.deb) ...
+Selecting previously deselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mipsel.deb) ...
+Selecting previously deselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-3_mipsel.deb) ...
+Selecting previously deselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mipsel.deb) ...
+Selecting previously deselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-3_mipsel.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 groff-base.
+Unpacking groff-base (from .../groff-base_1.20.1-10_mipsel.deb) ...
+Selecting previously deselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_mipsel.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.5.7-8_mipsel.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+20100313-5_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 libmagic1 (5.04-5) ...
+Setting up file (5.04-5) ...
+Setting up html2text (1.3.2a-15) ...
+Setting up libpcre3 (8.02-1.1) ...
+Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up libcroco3 (0.6.2-1) ...
+Setting up libunistring0 (0.9.3-3) ...
+Setting up gettext-base (0.18.1.1-3) ...
+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 groff-base (1.20.1-10) ...
+Setting up bsdmainutils (8.0.13) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
+Setting up man-db (2.5.7-8) ...
+debconf: unable to initialize frontend: Dialog
+debconf: (TERM is not set, so the dialog frontend is not usable.)
+debconf: falling back to frontend: Readline
+debconf: unable to initialize frontend: Readline
+debconf: (This frontend requires a controlling tty.)
+debconf: falling back to frontend: Teletype
+Building database of manual pages ...
+Setting up debhelper (8.0.0) ...
+Setting up cdbs (0.4.89) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
+Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
+Toolchain package versions: libc6-dev_2.11.2-10 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-8 g++-4.4_4.4.5-8 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-8 libstdc++6_4.4.5-8
+Package versions: apt_0.8.10.3 aptitude_0.6.3-3.2 base-files_6.0 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.0.13 bsdutils_1:2.17.2-9 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-8 dash_0.5.5.1-7.4 debconf_1.5.36.1 debconf-i18n_1.5.36.1 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 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_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-8 gcc_4:4.4.5-1 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 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-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 libboost-iostreams1.42.0_1.42.0-4 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 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcwidget3_0.5.16-3 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.10 libept1_1.0.4 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-8 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-8 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 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 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libsigc++-2.0-0c2a_2.2.4.2-1 libslang2_2.2.2-4 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libstdc++6_4.4.5-8 libstdc++6-4.4-dev_4.4.5-8 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_2:0.1.12-16 libuuid1_2.17.2-9 libxapian22_1.2.3-2 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-30 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-23.2squeeze1 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 mount_2.17.2-9 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6-2 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 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2.squeeze.1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.23-3 tzdata_2010o-1 util-linux_2.17.2-9 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
+─────────────
+
+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 Thu Feb 17 08:40:32 2011 UTC using DSA key ID BAFEC7F2
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1~bpo60+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~bpo60+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~bpo60+1
+ dpkg-source --before-build samtools-0.1.12a
+dpkg-buildpackage: host architecture mipsel
+ /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~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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~bpo60+1-mipsel-tXBHmB/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~bpo60+1-mipsel-tXBHmB/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~bpo60+1-mipsel-tXBHmB/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~bpo60+1-mipsel-tXBHmB/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~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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~bpo60+1-mipsel-tXBHmB/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~bpo60+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_0.1.12a-1~bpo60+1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org> >../samtools_0.1.12a-1~bpo60+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-0.1.12a
+dpkg-buildpackage: binary only upload (no source included)
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20110316-2026
+
+samtools_0.1.12a-1~bpo60+1_mipsel.changes:
+Format: 1.8
+Date: Thu, 17 Feb 2011 13:13:09 +0900
+Source: samtools
+Binary: samtools libbam-dev
+Architecture: mipsel
+Version: 0.1.12a-1~bpo60+1
+Distribution: squeeze-backports
+Urgency: low
+Maintainer: mipsel Build Daemon (rem) <buildd_mipsel-rem 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 (0.1.12a-1~bpo60+1) squeeze-backports; urgency=low
+ .
+ * Backported for Squeeze (no changes needed).
+Checksums-Sha1:
+ fb157f1c2cbbc3c87eb7d18a4ca77e117375ac29 585356 samtools_0.1.12a-1~bpo60+1_mipsel.deb
+ 3a28366d265189407847a4854caab3b0895c6fe1 173480 libbam-dev_0.1.12a-1~bpo60+1_mipsel.deb
+Checksums-Sha256:
+ 02a944fcf0b6acd99546da280ce9cda8e79aacf7f550a9fedc0a4e41b56df588 585356 samtools_0.1.12a-1~bpo60+1_mipsel.deb
+ fb4394147b7d2675fc42b2e8119c4660600353f5816eef8a87883be026f23bd4 173480 libbam-dev_0.1.12a-1~bpo60+1_mipsel.deb
+Files:
+ 2321126a2cff3b76b441207220a5b629 585356 science optional samtools_0.1.12a-1~bpo60+1_mipsel.deb
+ 8051e75b663456e6cf7cf47017d70a3a 173480 libdevel optional libbam-dev_0.1.12a-1~bpo60+1_mipsel.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_0.1.12a-1~bpo60+1_mipsel.deb
+─────────────────────────────────────
+
+ new debian package, version 2.0.
+ size 585356 bytes: control archive= 1806 bytes.
+ 802 bytes, 16 lines control
+ 2517 bytes, 38 lines md5sums
+ Package: samtools
+ Version: 0.1.12a-1~bpo60+1
+ Architecture: mipsel
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1116
+ 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 2011-03-16 20:25 ./
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/lib/samtools/
+-rwxr-xr-x root/root 9768 2011-03-16 20:25 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7764 2011-03-16 20:25 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 19944 2011-03-16 20:25 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 13268 2011-03-16 20:25 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7764 2011-03-16 20:25 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-16 20:25 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7546 2011-03-16 20:25 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2011-03-16 20:25 ./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 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 12567 2010-12-02 16:41 ./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 2011-03-16 20:25 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./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 2011-02-15 05:37 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./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 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 2011-03-16 20:25 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 1966 2011-03-16 20:25 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 4927 2011-02-15 05:37 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 592 2011-02-15 05:37 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/bin/
+-rwxr-xr-x root/root 410760 2011-03-16 20:25 ./usr/bin/samtools
+-rwxr-xr-x root/root 108704 2011-03-16 20:25 ./usr/bin/bcftools
+-rwxr-xr-x root/root 30584 2011-03-16 20:25 ./usr/bin/razip
+lrwxrwxrwx root/root 0 2011-03-16 20:25 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1~bpo60+1_mipsel.deb
+───────────────────────────────────────
+
+ new debian package, version 2.0.
+ size 173480 bytes: control archive= 909 bytes.
+ 684 bytes, 15 lines control
+ 618 bytes, 10 lines md5sums
+ Package: libbam-dev
+ Source: samtools
+ Version: 0.1.12a-1~bpo60+1
+ Architecture: mipsel
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 444
+ 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 2011-03-16 20:25 ./
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./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 2010-12-04 07:49 ./usr/lib/
--rw-r--r-- root/root 303238 2010-12-04 07:49 ./usr/lib/libbam.a
+-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/lib/
+-rw-r--r-- root/root 302950 2011-03-16 20:25 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./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 4927 2011-02-15 05:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -626,10 +1476,9 @@ drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/lib/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mips-sbuild-f75c9a7d-199d-45ad-ba56-a30973cbabf2/build/buildd-samtools_0.1.12a-1-mips-QwKHhy
+Purging /var/lib/schroot/mount/squeeze-backports-mipsel-sbuild-77b0bd91-ef4d-4509-a448-0e69ab4a6cf7/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101204-0749
-Build needed 00:06:58, 9308k disc space
+Finished at 20110316-2026
+Build needed 00:05:31, 9304k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/mipsel.log b/mipsel.log
index 9a312ca..5831e5d 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,53 +1,94 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/mipsel received Fri Dec 3 09:45:45 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=mipsel">mipsel</a> >> Fri Dec 3 09:45:45 2010<pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on monteverdi.ayous.org
+From buildd at rem.debian.org Wed Mar 16 20:26:16 2011
+Return-path: <buildd at rem.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 rem.debian.org>)
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+ for logs at buildd.debian.org; Wed, 16 Mar 2011 20:26:16 +0000
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+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=rem.debian.org, EMAIL=hostmaster at rem.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
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+ id 1PzxII-0000s9-N8; Wed, 16 Mar 2011 20:26:10 +0000
+Date: Wed, 16 Mar 2011 20:26:10 +0000
+Message-Id: <E1PzxII-0000s9-N8 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_0.1.12a-1~bpo60+1 on mipsel
+ (dist=squeeze-backports)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on rem.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (mipsel) 03 Dec 2010 09:24 ║
+║ samtools 0.1.12a-1~bpo60+1 (mipsel) 16 Mar 2011 20:20 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.12a-1~bpo60+1
Architecture: mipsel
-Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-a7788f0e-a45d-4a01-9fc1-0c7f0fe22793/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN
-Start Time: 20101203-0924
-Get:1 http://incoming.debian.org unstable Release.gpg [835 B]
-Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
-Ign http://incoming.debian.org/debian/ unstable/main Translation-en
-Get:2 http://incoming.debian.org Release.gpg [835 B]
-Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:3 http://incoming.debian.org unstable Release [104 kB]
-Get:4 http://mirror.ayous.org unstable Release.gpg [835 B]
-Ign http://mirror.ayous.org/debian/ unstable/contrib Translation-en
-Ign http://mirror.ayous.org/debian/ unstable/main Translation-en
-Get:5 http://mirror.ayous.org unstable Release [104 kB]
-Ign http://mirror.ayous.org unstable/main Sources
-Ign http://mirror.ayous.org unstable/contrib Sources
-Ign http://mirror.ayous.org unstable/non-free Sources
-Ign http://mirror.ayous.org unstable/main mipsel Packages
-Ign http://mirror.ayous.org unstable/contrib mipsel Packages
-Get:6 http://incoming.debian.org Release [1604 B]
-Get:7 http://mirror.ayous.org unstable/main Sources [5242 kB]
-Ign http://incoming.debian.org unstable/main Sources
-Ign http://incoming.debian.org unstable/contrib Sources
-Ign http://incoming.debian.org unstable/non-free Sources
-Ign http://incoming.debian.org unstable/main mipsel Packages
-Ign http://incoming.debian.org unstable/contrib mipsel Packages
-Ign http://incoming.debian.org Sources
-Ign http://incoming.debian.org Packages
-Get:8 http://incoming.debian.org unstable/main Sources [5242 kB]
-Get:9 http://mirror.ayous.org unstable/contrib Sources [46.1 kB]
-Get:10 http://mirror.ayous.org unstable/non-free Sources [101 kB]
-Get:11 http://mirror.ayous.org unstable/main mipsel Packages [8868 kB]
-Get:12 http://incoming.debian.org unstable/contrib Sources [46.1 kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:14 http://incoming.debian.org unstable/main mipsel Packages [8868 kB]
-Get:15 http://mirror.ayous.org unstable/contrib mipsel Packages [62.4 kB]
-Get:16 http://incoming.debian.org unstable/contrib mipsel Packages [62.4 kB]
-Get:17 http://incoming.debian.org Sources [8378 B]
-Get:18 http://incoming.debian.org Packages [262 kB]
-Fetched 29.1 MB in 48s (600 kB/s)
+Chroot Build Dir: /var/lib/schroot/mount/squeeze-backports-mipsel-sbuild-77b0bd91-ef4d-4509-a448-0e69ab4a6cf7/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB
+Start Time: 20110316-2020
+Get:1 http://ftp.debian.org squeeze Release.gpg [1671 B]
+Ign http://ftp.debian.org/debian/ squeeze/contrib Translation-en
+Ign http://ftp.debian.org/debian/ squeeze/main Translation-en
+Get:2 http://ftp.debian.org squeeze-proposed-updates Release.gpg [835 B]
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/main Translation-en
+Get:3 http://ftp.debian.org squeeze Release [69.3 kB]
+Get:4 http://ftp.debian.org squeeze-proposed-updates Release [65.4 kB]
+Get:5 http://ftp.debian.org squeeze/main Sources [3720 kB]
+Hit http://mirror.ayous.org squeeze Release.gpg
+Ign http://mirror.ayous.org/debian/ squeeze/contrib Translation-en
+Ign http://mirror.ayous.org/debian/ squeeze/main Translation-en
+Get:6 http://mirror.ayous.org squeeze-proposed-updates Release.gpg [835 B]
+Ign http://mirror.ayous.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://mirror.ayous.org/debian/ squeeze-proposed-updates/main Translation-en
+Hit http://mirror.ayous.org squeeze Release
+Get:7 http://mirror.ayous.org squeeze-proposed-updates Release [65.4 kB]
+Get:8 http://backports-master.debian.org squeeze-backports Release.gpg [835 B]
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/contrib Translation-en
+Hit http://mirror.ayous.org squeeze/main Sources
+Hit http://mirror.ayous.org squeeze/contrib Sources
+Get:9 http://mirror.ayous.org squeeze/non-free Sources [61.7 kB]
+Hit http://mirror.ayous.org squeeze/main mipsel Packages
+Hit http://mirror.ayous.org squeeze/contrib mipsel Packages
+Get:10 http://mirror.ayous.org squeeze-proposed-updates/main Sources [38.0 kB]
+Get:11 http://mirror.ayous.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:12 http://mirror.ayous.org squeeze-proposed-updates/non-free Sources [926 B]
+Get:13 http://mirror.ayous.org squeeze-proposed-updates/main mipsel Packages [105 kB]
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/main Translation-en
+Get:14 http://backports-master.debian.org Release.gpg [835 B]
+Ign http://backports-master.debian.org/buildd/squeeze-backports/ Translation-en
+Get:15 http://mirror.ayous.org squeeze-proposed-updates/contrib mipsel Packages [14 B]
+Get:16 http://backports-master.debian.org squeeze-backports Release [61.2 kB]
+Get:17 http://backports-master.debian.org Release [1644 B]
+Get:18 http://backports-master.debian.org squeeze-backports/main Sources [9340 B]
+Get:19 http://backports-master.debian.org squeeze-backports/contrib Sources [14 B]
+Get:20 http://backports-master.debian.org squeeze-backports/non-free Sources [14 B]
+Get:21 http://backports-master.debian.org squeeze-backports/main mipsel Packages [18.1 kB]
+Get:22 http://backports-master.debian.org squeeze-backports/contrib mipsel Packages [14 B]
+Get:23 http://backports-master.debian.org Sources [14 B]
+Get:24 http://backports-master.debian.org Packages [24.4 kB]
+Get:25 http://ftp.debian.org squeeze/contrib Sources [33.9 kB]
+Get:26 http://ftp.debian.org squeeze/non-free Sources [61.7 kB]
+Get:27 http://ftp.debian.org squeeze/main mipsel Packages [6417 kB]
+Get:28 http://ftp.debian.org squeeze/contrib mipsel Packages [45.4 kB]
+Get:29 http://ftp.debian.org squeeze-proposed-updates/main Sources [38.0 kB]
+Get:30 http://ftp.debian.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:31 http://ftp.debian.org squeeze-proposed-updates/non-free Sources [926 B]
+Get:32 http://ftp.debian.org squeeze-proposed-updates/main mipsel Packages [105 kB]
+Get:33 http://ftp.debian.org squeeze-proposed-updates/contrib mipsel Packages [14 B]
+Fetched 10.9 MB in 21s (501 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -65,141 +106,208 @@ 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:
+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://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
-Fetched 364 kB in 3s (99.7 kB/s)
+Need to get 363 kB of source archives.
+Get:1 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (dsc) [1338 B]
+Get:2 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (tar) [356 kB]
+Get:3 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (diff) [6406 B]
+Fetched 363 kB in 2s (167 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
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install build dependencies (aptitude-based 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
+ libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5 libsigc++-2.0-0c2a
+ libsqlite3-0 libxapian22
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ tasksel debtags libcwidget-dev xapian-tools
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ aptitude-doc-en aptitude-doc apt-xapian-index libparse-debianchangelog-perl
+ libgpm2
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 44 not upgraded.
-Need to get 11.6 MB of archives.
-After this operation, 37.2 MB of additional disk space will be used.
-Get:1 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.0.17 [208 kB]
-Get:2 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.20.1-10 [1188 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.5.7-6 [1247 kB]
-Get:4 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.04-5 [238 kB]
-Get:5 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.04-5 [49.5 kB]
-Get:6 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152 kB]
-Get:7 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.02-1.1 [233 kB]
-Get:8 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-1 [832 kB]
-Get:9 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
-Get:10 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.24.2-1 [1039 kB]
-Get:11 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
-Get:12 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-3 [411 kB]
-Get:13 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023 kB]
-Get:14 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:15 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:16 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.0.0 [454 kB]
-Get:17 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.89 [1240 kB]
-Get:18 http://mirror.ayous.org/debian/ unstable/main libncurses5-dev mipsel 5.7+20100313-4 [1639 kB]
-Get:19 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
+ aptitude libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5
+ libsigc++-2.0-0c2a libsqlite3-0 libxapian22
+0 upgraded, 8 newly installed, 0 to remove and 6 not upgraded.
+Need to get 6230 kB of archives.
+After this operation, 20.5 MB of additional disk space will be used.
+Get:1 http://mirror.ayous.org/debian/ squeeze/main libboost-iostreams1.42.0 mipsel 1.42.0-4 [55.2 kB]
+Get:2 http://mirror.ayous.org/debian/ squeeze/main libncursesw5 mipsel 5.7+20100313-5 [371 kB]
+Get:3 http://mirror.ayous.org/debian/ squeeze/main libsigc++-2.0-0c2a mipsel 2.2.4.2-1 [39.2 kB]
+Get:4 http://mirror.ayous.org/debian/ squeeze/main libcwidget3 mipsel 0.5.16-3 [270 kB]
+Get:5 http://mirror.ayous.org/debian/ squeeze/main libxapian22 mipsel 1.2.3-2 [1089 kB]
+Get:6 http://mirror.ayous.org/debian/ squeeze/main libept1 mipsel 1.0.4 [135 kB]
+Get:7 http://mirror.ayous.org/debian/ squeeze/main libsqlite3-0 mipsel 3.7.3-1 [414 kB]
+Get:8 http://mirror.ayous.org/debian/ squeeze/main aptitude mipsel 0.6.3-3.2 [3856 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.6 MB in 2s (4941 kB/s)
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 10134 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_mipsel.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_mipsel.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_mipsel.deb) ...
+Fetched 6230 kB in 0s (7539 kB/s)
+Selecting previously deselected package libboost-iostreams1.42.0.
+(Reading database ... 10135 files and directories currently installed.)
+Unpacking libboost-iostreams1.42.0 (from .../libboost-iostreams1.42.0_1.42.0-4_mipsel.deb) ...
+Selecting previously deselected package libncursesw5.
+Unpacking libncursesw5 (from .../libncursesw5_5.7+20100313-5_mipsel.deb) ...
+Selecting previously deselected package libsigc++-2.0-0c2a.
+Unpacking libsigc++-2.0-0c2a (from .../libsigc++-2.0-0c2a_2.2.4.2-1_mipsel.deb) ...
+Selecting previously deselected package libcwidget3.
+Unpacking libcwidget3 (from .../libcwidget3_0.5.16-3_mipsel.deb) ...
+Selecting previously deselected package libxapian22.
+Unpacking libxapian22 (from .../libxapian22_1.2.3-2_mipsel.deb) ...
+Selecting previously deselected package libept1.
+Unpacking libept1 (from .../libept1_1.0.4_mipsel.deb) ...
+Selecting previously deselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.3-1_mipsel.deb) ...
+Selecting previously deselected package aptitude.
+Unpacking aptitude (from .../aptitude_0.6.3-3.2_mipsel.deb) ...
+Setting up libboost-iostreams1.42.0 (1.42.0-4) ...
+Setting up libncursesw5 (5.7+20100313-5) ...
+Setting up libsigc++-2.0-0c2a (2.2.4.2-1) ...
+Setting up libcwidget3 (0.5.16-3) ...
+Setting up libxapian22 (1.2.3-2) ...
+Setting up libept1 (1.0.4) ...
+Setting up libsqlite3-0 (3.7.3-1) ...
+Setting up aptitude (0.6.3-3.2) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode.
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/buildd-samtools-mipsel-Imn2IT/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously deselected package sbuild-build-depends-samtools-dummy.
+(Reading database ... 10343 files and directories currently installed.)
+Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
+dpkg: dependency problems prevent configuration of sbuild-build-depends-samtools-dummy:
+ sbuild-build-depends-samtools-dummy depends on debhelper (>= 8); however:
+ Package debhelper is not installed.
+ sbuild-build-depends-samtools-dummy depends on cdbs; however:
+ Package cdbs is not installed.
+ sbuild-build-depends-samtools-dummy depends on libncurses5-dev; however:
+ Package libncurses5-dev is not installed.
+ sbuild-build-depends-samtools-dummy depends on zlib1g-dev; however:
+ Package zlib1g-dev is not installed.
+dpkg: error processing sbuild-build-depends-samtools-dummy (--install):
+ dependency problems - leaving unconfigured
+Errors were encountered while processing:
+ sbuild-build-depends-samtools-dummy
+aptitude -y --without-recommends -o APT::Install-Recommends=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-samtools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Tier=55000 -o Aptitude::ProblemResolver::Remove-Essential-Tier=maximum install sbuild-build-depends-samtools-dummy
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
+The following NEW packages will be installed:
+ bsdmainutils{a} cdbs{a} debhelper{a} file{a} gettext{a} gettext-base{a}
+ groff-base{a} html2text{a} intltool-debian{a} libcroco3{a}
+ libglib2.0-0{a} libmagic1{a} libncurses5-dev{a} libpcre3{a}
+ libunistring0{a} libxml2{a} man-db{a} po-debconf{a} zlib1g-dev{a}
+The following partially installed packages will be configured:
+ sbuild-build-depends-samtools-dummy
+0 packages upgraded, 19 newly installed, 0 to remove and 6 not upgraded.
+Need to get 11.6 MB of archives. After unpacking 37.2 MB will be used.
+Writing extended state information...
+Get:1 http://mirror.ayous.org/debian/ squeeze/main libmagic1 mipsel 5.04-5 [238 kB]
+Get:2 http://mirror.ayous.org/debian/ squeeze/main file mipsel 5.04-5 [49.5 kB]
+Get:3 http://mirror.ayous.org/debian/ squeeze/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:4 http://mirror.ayous.org/debian/ squeeze/main libpcre3 mipsel 8.02-1.1 [233 kB]
+Get:5 http://mirror.ayous.org/debian/ squeeze/main libglib2.0-0 mipsel 2.24.2-1 [1039 kB]
+Get:6 http://mirror.ayous.org/debian/ squeeze/main libxml2 mipsel 2.7.8.dfsg-2 [833 kB]
+Get:7 http://mirror.ayous.org/debian/ squeeze/main libcroco3 mipsel 0.6.2-1 [110 kB]
+Get:8 http://mirror.ayous.org/debian/ squeeze/main libunistring0 mipsel 0.9.3-3 [411 kB]
+Get:9 http://mirror.ayous.org/debian/ squeeze/main gettext-base mipsel 0.18.1.1-3 [152 kB]
+Get:10 http://mirror.ayous.org/debian/ squeeze/main gettext mipsel 0.18.1.1-3 [2023 kB]
+Get:11 http://mirror.ayous.org/debian/ squeeze/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:12 http://mirror.ayous.org/debian/ squeeze/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:13 http://mirror.ayous.org/debian/ squeeze/main groff-base mipsel 1.20.1-10 [1188 kB]
+Get:14 http://mirror.ayous.org/debian/ squeeze/main bsdmainutils mipsel 8.0.13 [205 kB]
+Get:15 http://mirror.ayous.org/debian/ squeeze/main man-db mipsel 2.5.7-8 [1248 kB]
+Get:16 http://mirror.ayous.org/debian/ squeeze/main debhelper all 8.0.0 [454 kB]
+Get:17 http://mirror.ayous.org/debian/ squeeze/main cdbs all 0.4.89 [1240 kB]
+Get:18 http://mirror.ayous.org/debian/ squeeze/main libncurses5-dev mipsel 5.7+20100313-5 [1639 kB]
+Get:19 http://mirror.ayous.org/debian/ squeeze/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 11.6 MB in 1s (7840 kB/s)
Selecting previously deselected package libmagic1.
+(Reading database ... 10343 files and directories currently installed.)
Unpacking libmagic1 (from .../libmagic1_5.04-5_mipsel.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5_mipsel.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mipsel.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_mipsel.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_mipsel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.02-1.1_mipsel.deb) ...
Selecting previously deselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_mipsel.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_mipsel.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mipsel.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-3_mipsel.deb) ...
+Selecting previously deselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mipsel.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_mipsel.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 groff-base.
+Unpacking groff-base (from .../groff-base_1.20.1-10_mipsel.deb) ...
+Selecting previously deselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_mipsel.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.5.7-8_mipsel.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_mipsel.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_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 (8.0.17) ...
-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) ...
-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 libpcre3 (8.02-1.1) ...
Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
+Setting up gettext-base (0.18.1.1-3) ...
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 groff-base (1.20.1-10) ...
+Setting up bsdmainutils (8.0.13) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
+Setting up man-db (2.5.7-8) ...
+debconf: unable to initialize frontend: Dialog
+debconf: (TERM is not set, so the dialog frontend is not usable.)
+debconf: falling back to frontend: Readline
+debconf: unable to initialize frontend: Readline
+debconf: (This frontend requires a controlling tty.)
+debconf: falling back to frontend: Teletype
+Building database of manual pages ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
-Setting up libncurses5-dev (5.7+20100313-4) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: Linux 2.6.33-rc7 mipsel (mips64)
-Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-23 gcc-4.4_4.4.5-2 g++-4.4_4.4.5-2 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-2 libstdc++6_4.4.5-2
-Package versions: apt_0.8.6 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.17 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-2 dash_0.5.5.1-7 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 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 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.5-1 g++-4.4_4.4.5-2 gcc_4:4.4.5-1 gcc-4.4_4.4.5-2 gcc-4.4-base_4.4.5-2 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_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 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_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-2 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-2 libstdc++6-4.4-dev_4.4.5-2 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_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 make_3.81-8 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 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010m-1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
+Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
+Toolchain package versions: libc6-dev_2.11.2-10 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-8 g++-4.4_4.4.5-8 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-8 libstdc++6_4.4.5-8
+Package versions: apt_0.8.10.3 aptitude_0.6.3-3.2 base-files_6.0 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.0.13 bsdutils_1:2.17.2-9 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-8 dash_0.5.5.1-7.4 debconf_1.5.36.1 debconf-i18n_1.5.36.1 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 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_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-8 gcc_4:4.4.5-1 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 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-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 libboost-iostreams1.42.0_1.42.0-4 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 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcwidget3_0.5.16-3 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.10 libept1_1.0.4 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-8 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-8 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 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 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libsigc++-2.0-0c2a_2.2.4.2-1 libslang2_2.2.2-4 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libstdc++6_4.4.5-8 libstdc++6-4.4-dev_4.4.5-8 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_2:0.1.12-16 libuuid1_2.17.2-9 libxapian22_1.2.3-2 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-30 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-23.2squeeze1 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 mount_2.17.2-9 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6-2 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 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2.squeeze.1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.23-3 tzdata_2010o-1 util-linux_2.17.2-9 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -210,13 +318,13 @@ 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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Thu Feb 17 08:40:32 2011 UTC using DSA key ID BAFEC7F2
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1~bpo60+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
+dpkg-source: info: unpacking samtools_0.1.12a-1~bpo60+1.debian.tar.gz
Check disc space
────────────────
@@ -231,46 +339,46 @@ 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-buildpackage: source version 0.1.12a-1~bpo60+1
dpkg-source --before-build samtools-0.1.12a
dpkg-buildpackage: host architecture mipsel
/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-mipsel-COPfIN/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
+/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~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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-mipsel-COPfIN/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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-mipsel-COPfIN/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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-mipsel-COPfIN/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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 "."
+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-mipsel-COPfIN/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
+/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~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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'
+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
@@ -285,8 +393,8 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-mipsel-COPfIN/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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
@@ -297,10 +405,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-mipsel-COPfIN/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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
@@ -317,24 +425,24 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-mipsel-COPfIN/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/misc'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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-mipsel-COPfIN/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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-mipsel-COPfIN/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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
@@ -344,50 +452,50 @@ 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-mipsel-COPfIN/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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-mipsel-COPfIN/samtools-0.1.12a'
+make[1]: Nothing to be done for `lib'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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-mipsel-COPfIN/samtools-0.1.12a/examples'
+/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~bpo60+1-mipsel-tXBHmB/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 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
+../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
+../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
+(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'
+[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
+[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
+<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'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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 "."
+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
@@ -413,8 +521,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/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
@@ -438,7 +546,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -453,69 +561,66 @@ 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_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1~bpo60+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_0.1.12a-1_mipsel.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1~bpo60+1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org> >../samtools_0.1.12a-1~bpo60+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-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0930
+Build finished at 20110316-2026
-samtools_0.1.12a-1_mipsel.changes:
+samtools_0.1.12a-1~bpo60+1_mipsel.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Thu, 17 Feb 2011 13:13:09 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.12a-1~bpo60+1
+Distribution: squeeze-backports
Urgency: low
-Maintainer: mipsel Build Daemon (monteverdi) <buildd_mipsel-monteverdi at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: mipsel Build Daemon (rem) <buildd_mipsel-rem 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 (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.12a-1~bpo60+1) squeeze-backports; 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).
+ * Backported for Squeeze (no changes needed).
Checksums-Sha1:
- f29fd836ed041a1f2088c9d36c8a46ad110d0d4f 578292 samtools_0.1.12a-1_mipsel.deb
- cd679f7269405f59939c75dfd77d99bf3d62e704 173498 libbam-dev_0.1.12a-1_mipsel.deb
+ fb157f1c2cbbc3c87eb7d18a4ca77e117375ac29 585356 samtools_0.1.12a-1~bpo60+1_mipsel.deb
+ 3a28366d265189407847a4854caab3b0895c6fe1 173480 libbam-dev_0.1.12a-1~bpo60+1_mipsel.deb
Checksums-Sha256:
- a875f6bd7b1d39080160048bf0d7711496303b61d528f637c6798bb7725611bf 578292 samtools_0.1.12a-1_mipsel.deb
- 072b4c5f5635ddb791b86e2be2fa5e5bcb16c4fc03581aa0b181720d5671e5cf 173498 libbam-dev_0.1.12a-1_mipsel.deb
+ 02a944fcf0b6acd99546da280ce9cda8e79aacf7f550a9fedc0a4e41b56df588 585356 samtools_0.1.12a-1~bpo60+1_mipsel.deb
+ fb4394147b7d2675fc42b2e8119c4660600353f5816eef8a87883be026f23bd4 173480 libbam-dev_0.1.12a-1~bpo60+1_mipsel.deb
Files:
- 7de915c17da9a27be7c7aaeeae84489e 578292 science optional samtools_0.1.12a-1_mipsel.deb
- 912706773b87a79e5be0c4df0c4003ec 173498 libdevel optional libbam-dev_0.1.12a-1_mipsel.deb
+ 2321126a2cff3b76b441207220a5b629 585356 science optional samtools_0.1.12a-1~bpo60+1_mipsel.deb
+ 8051e75b663456e6cf7cf47017d70a3a 173480 libdevel optional libbam-dev_0.1.12a-1~bpo60+1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_mipsel.deb
-─────────────────────────────
+samtools_0.1.12a-1~bpo60+1_mipsel.deb
+─────────────────────────────────────
new debian package, version 2.0.
- size 578292 bytes: control archive= 1796 bytes.
- 794 bytes, 16 lines control
+ size 585356 bytes: control archive= 1806 bytes.
+ 802 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.12a-1~bpo60+1
Architecture: mipsel
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1116
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -527,71 +632,71 @@ samtools_0.1.12a-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 2010-12-03 09:30 ./
-drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/samtools/
--rwxr-xr-x root/root 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/lib/samtools/
+-rwxr-xr-x root/root 9768 2011-03-16 20:25 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7764 2011-03-16 20:25 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 19944 2011-03-16 20:25 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 13268 2011-03-16 20:25 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7764 2011-03-16 20:25 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-16 20:25 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7546 2011-03-16 20:25 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2011-03-16 20:25 ./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 5778 2010-12-03 09:30 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.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 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 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 12567 2010-12-02 16:41 ./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 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.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 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
-drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1966 2010-12-03 09:30 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./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 2011-02-15 05:37 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./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 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 126609 2010-12-03 09:30 ./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 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 126609 2011-03-16 20:25 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 1966 2011-03-16 20:25 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 4927 2011-02-15 05:37 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.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 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
--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 09:30 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/man/man1/
--rw-r--r-- root/root 7546 2010-12-03 09:30 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2010-12-03 09:30 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/bin/
--rwxr-xr-x root/root 410760 2010-12-03 09:30 ./usr/bin/samtools
--rwxr-xr-x root/root 30584 2010-12-03 09:30 ./usr/bin/razip
--rwxr-xr-x root/root 108704 2010-12-03 09:30 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/lib/
-drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/lib/samtools/
--rwxr-xr-x root/root 13268 2010-12-03 09:30 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7764 2010-12-03 09:30 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 9768 2010-12-03 09:30 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7764 2010-12-03 09:30 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 19944 2010-12-03 09:30 ./usr/lib/samtools/wgsim
-lrwxrwxrwx root/root 0 2010-12-03 09:30 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.12a-1_mipsel.deb
-───────────────────────────────
+-rw-r--r-- root/root 592 2011-02-15 05:37 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/bin/
+-rwxr-xr-x root/root 410760 2011-03-16 20:25 ./usr/bin/samtools
+-rwxr-xr-x root/root 108704 2011-03-16 20:25 ./usr/bin/bcftools
+-rwxr-xr-x root/root 30584 2011-03-16 20:25 ./usr/bin/razip
+lrwxrwxrwx root/root 0 2011-03-16 20:25 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1~bpo60+1_mipsel.deb
+───────────────────────────────────────
new debian package, version 2.0.
- size 173498 bytes: control archive= 899 bytes.
- 676 bytes, 15 lines control
+ size 173480 bytes: control archive= 909 bytes.
+ 684 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.12a-1~bpo60+1
Architecture: mipsel
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 444
Section: libdevel
Priority: optional
@@ -603,23 +708,23 @@ libbam-dev_0.1.12a-1_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-12-03 09:30 ./
-drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:30 ./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 1128 2010-12-03 05:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.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
-drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/include/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./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 24124 2010-11-17 04:16 ./usr/include/bam.h
-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.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 09:30 ./usr/lib/
--rw-r--r-- root/root 302950 2010-12-03 09:30 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/lib/
+-rw-r--r-- root/root 302950 2011-03-16 20:25 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-16 20:25 ./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 4927 2011-02-15 05:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -628,10 +733,9 @@ drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/lib/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-a7788f0e-a45d-4a01-9fc1-0c7f0fe22793/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN
+Purging /var/lib/schroot/mount/squeeze-backports-mipsel-sbuild-77b0bd91-ef4d-4509-a448-0e69ab4a6cf7/build/buildd-samtools_0.1.12a-1~bpo60+1-mipsel-tXBHmB
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0930
-Build needed 00:06:40, 9296k disc space
+Finished at 20110316-2026
+Build needed 00:05:31, 9304k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/powerpc.log b/powerpc.log
index 0eaa76a..698afcf 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,36 +1,96 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/powerpc received Fri Dec 3 09:22:35 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=powerpc">powerpc</a> >> Fri Dec 3 09:22:35 2010<pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on praetorius.debian.org
+From buildd at praetorius.debian.org Mon Mar 14 15:32:02 2011
+Return-path: <buildd at praetorius.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 praetorius.debian.org>)
+ id 1Pz9kX-0002qo-PV
+ for logs at buildd.debian.org; Mon, 14 Mar 2011 15:32:02 +0000
+Received: from [2001:6b0:e:2a18:204:acff:fede:459f]
+ (helo=praetorius.debian.org)
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=praetorius.debian.org,
+ EMAIL=hostmaster at praetorius.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at praetorius.debian.org>)
+ id 1Pz9kV-0004AJ-WA; Mon, 14 Mar 2011 15:32:00 +0000
+Received: from buildd by praetorius.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at praetorius.debian.org>)
+ id 1Pz9kU-0003NS-3m; Mon, 14 Mar 2011 15:31:58 +0000
+From: buildd on praetorius <buildd at praetorius.debian.org>
+To: wouter+buildd at grep.be,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.12a-1~bpo60+1 on powerpc
+ (dist=squeeze-backports)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1Pz9kU-0003NS-3m at praetorius.debian.org>
+Date: Mon, 14 Mar 2011 15:31:58 +0000
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.5 (14 Nov 2010) on praetorius.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (powerpc) 03 Dec 2010 09:19 ║
+║ samtools 0.1.12a-1~bpo60+1 (powerpc) 14 Mar 2011 15:28 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.12a-1~bpo60+1
Architecture: powerpc
-Chroot Build Dir: /var/lib/schroot/mount/sid-powerpc-sbuild-f6484d4d-a7cc-4101-9c13-f7b72cf926c7/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf
-Start Time: 20101203-0919
-Get:1 http://ftp.se.debian.org unstable Release.gpg [835B]
-Get:2 http://ftp.se.debian.org unstable Release [104kB]
-Get:3 http://incoming.debian.org unstable Release.gpg [835B]
-Get:4 http://incoming.debian.org Release.gpg [835B]
-Get:5 http://ftp.se.debian.org unstable/main Packages [6845kB]
-Get:6 http://incoming.debian.org unstable Release [104kB]
-Get:7 http://ftp.se.debian.org unstable/contrib Packages [50.1kB]
-Get:8 http://ftp.se.debian.org unstable/main Sources [4071kB]
-Get:9 http://ftp.se.debian.org unstable/contrib Sources [38.7kB]
-Get:10 http://ftp.se.debian.org unstable/non-free Sources [83.8kB]
-Get:11 http://incoming.debian.org Release [1604B]
-Get:12 http://incoming.debian.org unstable/main Packages [6845kB]
-Get:13 http://incoming.debian.org unstable/contrib Packages [50.1kB]
-Get:14 http://incoming.debian.org unstable/main Sources [4071kB]
-Get:15 http://incoming.debian.org unstable/contrib Sources [38.7kB]
-Get:16 http://incoming.debian.org unstable/non-free Sources [83.8kB]
-Get:17 http://incoming.debian.org Packages [169kB]
-Get:18 http://incoming.debian.org Sources [8014B]
-Fetched 22.6MB in 23s (980kB/s)
+Chroot Build Dir: /var/lib/schroot/mount/squeeze-backports-powerpc-sbuild-9098bcd5-d126-4764-abab-8f168d4a6ddb/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB
+Start Time: 20110314-1528
+Hit http://ftp.se.debian.org squeeze Release.gpg
+Ign http://ftp.se.debian.org/debian/ squeeze/contrib Translation-en
+Ign http://ftp.se.debian.org/debian/ squeeze/main Translation-en
+Get:1 http://ftp.se.debian.org squeeze-proposed-updates Release.gpg [835 B]
+Ign http://ftp.se.debian.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://ftp.se.debian.org/debian/ squeeze-proposed-updates/main Translation-en
+Hit http://ftp.se.debian.org squeeze Release
+Get:2 http://ftp.se.debian.org squeeze-proposed-updates Release [59.0 kB]
+Hit http://ftp.se.debian.org squeeze/main Sources
+Hit http://ftp.se.debian.org squeeze/contrib Sources
+Get:3 http://ftp.se.debian.org squeeze/non-free Sources [61.7 kB]
+Hit http://ftp.se.debian.org squeeze/main powerpc Packages
+Hit http://ftp.se.debian.org squeeze/contrib powerpc Packages
+Get:4 http://ftp.se.debian.org squeeze-proposed-updates/main Sources [33.3 kB]
+Get:5 http://ftp.se.debian.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:6 http://ftp.se.debian.org squeeze-proposed-updates/non-free Sources [926 B]
+Get:7 http://ftp.se.debian.org squeeze-proposed-updates/main powerpc Packages [96.5 kB]
+Get:8 http://ftp.debian.org squeeze Release.gpg [1671 B]
+Ign http://ftp.debian.org/debian/ squeeze/contrib Translation-en
+Get:9 http://ftp.se.debian.org squeeze-proposed-updates/contrib powerpc Packages [14 B]
+Ign http://ftp.debian.org/debian/ squeeze/main Translation-en
+Get:10 http://ftp.debian.org squeeze-proposed-updates Release.gpg [835 B]
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/main Translation-en
+Get:11 http://ftp.debian.org squeeze Release [69.3 kB]
+Get:12 http://ftp.debian.org squeeze-proposed-updates Release [59.0 kB]
+Get:13 http://backports-master.debian.org squeeze-backports Release.gpg [835 B]
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/contrib Translation-en
+Get:14 http://ftp.debian.org squeeze/main Sources [3720 kB]
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/main Translation-en
+Get:15 http://backports-master.debian.org Release.gpg [835 B]
+Ign http://backports-master.debian.org/buildd/squeeze-backports/ Translation-en
+Get:16 http://backports-master.debian.org squeeze-backports Release [61.2 kB]
+Get:17 http://ftp.debian.org squeeze/contrib Sources [33.9 kB]
+Get:18 http://ftp.debian.org squeeze/non-free Sources [61.7 kB]
+Get:19 http://ftp.debian.org squeeze/main powerpc Packages [6489 kB]
+Get:20 http://backports-master.debian.org Release [1644 B]
+Get:21 http://ftp.debian.org squeeze/contrib powerpc Packages [44.8 kB]
+Get:22 http://ftp.debian.org squeeze-proposed-updates/main Sources [36.2 kB]
+Get:23 http://ftp.debian.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:24 http://ftp.debian.org squeeze-proposed-updates/non-free Sources [926 B]
+Get:25 http://ftp.debian.org squeeze-proposed-updates/main powerpc Packages [102 kB]
+Get:26 http://ftp.debian.org squeeze-proposed-updates/contrib powerpc Packages [14 B]
+Get:27 http://backports-master.debian.org squeeze-backports/main Sources [9340 B]
+Get:28 http://backports-master.debian.org squeeze-backports/contrib Sources [14 B]
+Get:29 http://backports-master.debian.org squeeze-backports/non-free Sources [14 B]
+Get:30 http://backports-master.debian.org squeeze-backports/main powerpc Packages [10.5 kB]
+Get:31 http://backports-master.debian.org squeeze-backports/contrib powerpc Packages [14 B]
+Get:32 http://backports-master.debian.org Sources [605 B]
+Get:33 http://backports-master.debian.org Packages [10.8 kB]
+Fetched 11.0 MB in 9s (1100 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -49,18 +109,20 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-Need to get 364kB of source archives.
-Get:1 http://incoming.debian.org samtools 0.1.12a-1 (dsc) [1946B]
-Get:2 http://incoming.debian.org samtools 0.1.12a-1 (tar) [356kB]
-Get:3 http://incoming.debian.org samtools 0.1.12a-1 (diff) [6337B]
-Fetched 364kB in 1s (352kB/s)
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/debian-med/samtools.git
+Need to get 363 kB of source archives.
+Get:1 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (dsc) [1338 B]
+Get:2 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (tar) [356 kB]
+Get:3 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (diff) [6406 B]
+Fetched 363 kB in 1s (194 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
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -79,61 +141,49 @@ 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 libunistring0 libxml2
- man-db ncurses-bin po-debconf
+ 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
- libgpm2 xml-core libmail-sendmail-perl
+ 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
-The following packages will be upgraded:
- libncurses5 ncurses-bin
-2 upgraded, 19 newly installed, 0 to remove and 64 not upgraded.
-Need to get 12.5MB of archives.
-After this operation, 36.2MB of additional disk space will be used.
-Get:1 http://ftp.se.debian.org unstable/main ncurses-bin 5.7+20100313-4 [319kB]
-Get:2 http://ftp.se.debian.org unstable/main libncurses5 5.7+20100313-4 [360kB]
-Get:3 http://ftp.se.debian.org unstable/main bsdmainutils 8.0.17 [207kB]
-Get:4 http://ftp.se.debian.org unstable/main groff-base 1.20.1-10 [1196kB]
-Get:5 http://ftp.se.debian.org unstable/main man-db 2.5.7-6 [1285kB]
-Get:6 http://ftp.se.debian.org unstable/main libmagic1 5.04-5 [241kB]
-Get:7 http://ftp.se.debian.org unstable/main file 5.04-5 [49.9kB]
-Get:8 http://ftp.se.debian.org unstable/main gettext-base 0.18.1.1-3 [141kB]
-Get:9 http://ftp.se.debian.org unstable/main libpcre3 8.02-1.1 [231kB]
-Get:10 http://ftp.se.debian.org unstable/main libxml2 2.7.8.dfsg-1 [849kB]
-Get:11 http://ftp.se.debian.org unstable/main html2text 1.3.2a-15 [105kB]
-Get:12 http://ftp.se.debian.org unstable/main libglib2.0-0 2.24.2-1 [1111kB]
-Get:13 http://ftp.se.debian.org unstable/main libcroco3 0.6.2-1 [128kB]
-Get:14 http://ftp.se.debian.org unstable/main libunistring0 0.9.3-3 [422kB]
-Get:15 http://ftp.se.debian.org unstable/main gettext 0.18.1.1-3 [2046kB]
-Get:16 http://ftp.se.debian.org unstable/main intltool-debian 0.35.0+20060710.1 [30.8kB]
-Get:17 http://ftp.se.debian.org unstable/main po-debconf 1.0.16+nmu1 [223kB]
-Get:18 http://ftp.se.debian.org unstable/main debhelper 8.0.0 [454kB]
-Get:19 http://ftp.se.debian.org unstable/main cdbs 0.4.89 [1240kB]
-Get:20 http://ftp.se.debian.org unstable/main libncurses5-dev 5.7+20100313-4 [1633kB]
-Get:21 http://ftp.se.debian.org unstable/main zlib1g-dev 1:1.2.3.4.dfsg-3 [190kB]
+0 upgraded, 19 newly installed, 0 to remove and 6 not upgraded.
+Need to get 11.8 MB of archives.
+After this operation, 36.2 MB of additional disk space will be used.
+Get:1 http://ftp.se.debian.org/debian/ squeeze/main bsdmainutils powerpc 8.0.13 [205 kB]
+Get:2 http://ftp.se.debian.org/debian/ squeeze/main groff-base powerpc 1.20.1-10 [1196 kB]
+Get:3 http://ftp.se.debian.org/debian/ squeeze/main man-db powerpc 2.5.7-8 [1286 kB]
+Get:4 http://ftp.se.debian.org/debian/ squeeze/main libmagic1 powerpc 5.04-5 [241 kB]
+Get:5 http://ftp.se.debian.org/debian/ squeeze/main file powerpc 5.04-5 [49.9 kB]
+Get:6 http://ftp.se.debian.org/debian/ squeeze/main gettext-base powerpc 0.18.1.1-3 [141 kB]
+Get:7 http://ftp.se.debian.org/debian/ squeeze/main libpcre3 powerpc 8.02-1.1 [231 kB]
+Get:8 http://ftp.se.debian.org/debian/ squeeze/main libxml2 powerpc 2.7.8.dfsg-2 [849 kB]
+Get:9 http://ftp.se.debian.org/debian/ squeeze/main html2text powerpc 1.3.2a-15 [105 kB]
+Get:10 http://ftp.se.debian.org/debian/ squeeze/main libglib2.0-0 powerpc 2.24.2-1 [1111 kB]
+Get:11 http://ftp.se.debian.org/debian/ squeeze/main libcroco3 powerpc 0.6.2-1 [128 kB]
+Get:12 http://ftp.se.debian.org/debian/ squeeze/main libunistring0 powerpc 0.9.3-3 [422 kB]
+Get:13 http://ftp.se.debian.org/debian/ squeeze/main gettext powerpc 0.18.1.1-3 [2046 kB]
+Get:14 http://ftp.se.debian.org/debian/ squeeze/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:15 http://ftp.se.debian.org/debian/ squeeze/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:16 http://ftp.se.debian.org/debian/ squeeze/main debhelper all 8.0.0 [454 kB]
+Get:17 http://ftp.se.debian.org/debian/ squeeze/main cdbs all 0.4.89 [1240 kB]
+Get:18 http://ftp.se.debian.org/debian/ squeeze/main libncurses5-dev powerpc 5.7+20100313-5 [1633 kB]
+Get:19 http://ftp.se.debian.org/debian/ squeeze/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 12.5MB in 1s (9491kB/s)
-(Reading database ... 9867 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.7+20100313-2 (using .../ncurses-bin_5.7+20100313-4_powerpc.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.7+20100313-4) ...
-(Reading database ... 9867 files and directories currently installed.)
-Preparing to replace libncurses5 5.7+20100313-2 (using .../libncurses5_5.7+20100313-4_powerpc.deb) ...
-Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.7+20100313-4) ...
+Fetched 11.8 MB in 1s (8805 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 9867 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_powerpc.deb) ...
+(Reading database ... 10939 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_powerpc.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.20.1-10_powerpc.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_powerpc.deb) ...
+Unpacking man-db (from .../man-db_2.5.7-8_powerpc.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_powerpc.deb) ...
Selecting previously deselected package file.
@@ -143,7 +193,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_powerpc.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.02-1.1_powerpc.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_powerpc.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_powerpc.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -163,20 +213,20 @@ 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_powerpc.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_powerpc.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_powerpc.deb) ...
-Setting up bsdmainutils (8.0.17) ...
+Setting up bsdmainutils (8.0.13) ...
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) ...
-Setting up man-db (2.5.7-6) ...
+Setting up man-db (2.5.7-8) ...
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 libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
@@ -186,13 +236,13 @@ 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 libncurses5-dev (5.7+20100313-5) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.26-2-powerpc64 powerpc (ppc64)
-Toolchain package versions: libc6-dev_2.11.1-3 dpkg-dev_1.15.7.2 linux-libc-dev_2.6.32-15 gcc-4.4_4.4.4-4 g++-4.4_4.4.4-4 binutils_2.20.1-10 libstdc++6-4.4-dev_4.4.4-4 libstdc++6_4.4.4-4
-Package versions: apt_0.7.25.3 base-files_5.7 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-10 bsdmainutils_8.0.17 bsdutils_1:2.17.2-3 build-essential_11.5 bzip2_1.0.5-4 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-4 dash_0.5.5.1-6 debconf_1.5.32 debconf-i18n_1.5.32 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2009.01.31 debianutils_3.2.3 diffutils_1:3.0-1 dpkg_1.15.7.2 dpkg-dev_1.15.7.2 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++_4:4.4.4-2 g++-4.4_4.4.4-4 gcc_4:4.4.4-2 gcc-4.4_4.4.4-4 gcc-4.4-base_4.4.4-4 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_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-7 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-3 libattr1_1:2.4.44-2 libblkid1_2.17.2-3 libbz2-1.0_1.0.5-4 libc-bin_2.11.1-3 libc-dev-bin_2.11.1-3 libc6_2.11.1-3 libc6-dev_2.11.1-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-1 libdpkg-perl_1.15.7.2 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-4 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-4 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100527-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-3 libpam-runtime_1.1.1-3 libpam0g_1.1.1-3 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.94-1 libsepol1_2.0.41-1 libss2_1.41.12-2 libstdc++6_4.4.4-4 libstdc++6-4.4-dev_4.4.4-4 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_2:0.1.12-15 libuuid1_2.17.2-3 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-15 login_1:4.1.4.2-1 lsb-base_3.2-23.1 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2-1 patch_2.6-2 perl_5.10.1-13 perl-base_5.10.1-13 perl-modules_5.10.1-13 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.2p6-1 sysv-rc_2.88dsf-7 sysvinit_2.88dsf-7 sysvinit-utils_2.88dsf-7 tar_1.23-1 tzdata_2010j-1 util-linux_2.17.2-3 xz-utils_4.999.9beta+20100527-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6-dev_2.11.2-10 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-8 g++-4.4_4.4.5-8 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-8 libstdc++6_4.4.5-8
+Package versions: apt_0.8.10.3 base-files_6.0 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.0.13 bsdutils_1:2.17.2-9 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.3_4.3.5-4 cpp-4.4_4.4.5-8 dash_0.5.5.1-7.4 debconf_1.5.36.1 debconf-i18n_1.5.36.1 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 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_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.3_4.3.5-4 g++-4.4_4.4.5-8 gcc_4:4.4.5-1 gcc-4.3_4.3.5-4 gcc-4.3-base_4.3.5-4 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 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-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 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 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.10 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-8 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-8 liblocale-gettext-perl_1.05-6 liblzma1_4.999.9beta+20091116-1 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 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 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-8 libstdc++6-4.3-dev_4.3.5-4 libstdc++6-4.4-dev_4.4.5-8 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_2:0.1.12-16 libuuid1_2.17.2-9 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-30 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-23.2squeeze1 lzma_4.43-14 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 mount_2.17.2-9 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6-2 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_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2.squeeze.1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.23-3 tzdata_2010o-1 util-linux_2.17.2-9 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -203,13 +253,13 @@ 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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Thu Feb 17 08:40:32 2011 UTC using DSA key ID BAFEC7F2
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1~bpo60+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
+dpkg-source: info: unpacking samtools_0.1.12a-1~bpo60+1.debian.tar.gz
Check disc space
────────────────
@@ -218,51 +268,52 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
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-buildpackage: source version 0.1.12a-1~bpo60+1
+ dpkg-source --before-build samtools-0.1.12a
dpkg-buildpackage: host architecture powerpc
/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-powerpc-g9O8gf/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
+/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~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/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-powerpc-g9O8gf/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/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-powerpc-g9O8gf/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/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-powerpc-g9O8gf/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/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 "."
+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-powerpc-g9O8gf/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
+/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~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/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'
+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
@@ -277,8 +328,8 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-powerpc-g9O8gf/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/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
@@ -289,10 +340,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-powerpc-g9O8gf/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/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
@@ -309,24 +360,24 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-powerpc-g9O8gf/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/misc'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/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-powerpc-g9O8gf/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/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-powerpc-g9O8gf/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/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
@@ -336,50 +387,50 @@ 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-powerpc-g9O8gf/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/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-powerpc-g9O8gf/samtools-0.1.12a'
+make[1]: Nothing to be done for `lib'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/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-powerpc-g9O8gf/samtools-0.1.12a/examples'
+/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~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a/examples'
../samtools faidx ex1.fa
-[sam_header_read2] 2 sequences loaded.
../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
+[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
+../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
+../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
+(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...
+../samtools rmdup ex1f.bam ex1f-rmduppe.bam
[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'
+[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
+[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
+<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'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/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 "."
+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
@@ -405,8 +456,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/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
@@ -430,7 +481,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -445,68 +496,66 @@ 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_powerpc.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1~bpo60+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_0.1.12a-1_powerpc.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1~bpo60+1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org> >../samtools_0.1.12a-1~bpo60+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-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0922
+Build finished at 20110314-1531
-samtools_0.1.12a-1_powerpc.changes:
+samtools_0.1.12a-1~bpo60+1_powerpc.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Thu, 17 Feb 2011 13:13:09 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: powerpc
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.12a-1~bpo60+1
+Distribution: squeeze-backports
Urgency: low
-Maintainer: powerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: powerpc Build Daemon (praetorius) <buildd_powerpc-praetorius 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 (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.12a-1~bpo60+1) squeeze-backports; 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).
+ * Backported for Squeeze (no changes needed).
Checksums-Sha1:
- b8ae505c9c5fa2cdf3754cfbd3432b433940abc1 560870 samtools_0.1.12a-1_powerpc.deb
- fcf051bc2b68143cb4e792f96e74ce4d0f031dd9 162450 libbam-dev_0.1.12a-1_powerpc.deb
+ 1ab8ccb51bf130a853b01b93f841d904a128dd6f 561028 samtools_0.1.12a-1~bpo60+1_powerpc.deb
+ c99f5e2ce20312c1e99e77203b8bea33111f6361 162448 libbam-dev_0.1.12a-1~bpo60+1_powerpc.deb
Checksums-Sha256:
- 26ccc7ee17384c17b348c7e4327b37c51f32a93035a26fd2eb03b84aad8c7314 560870 samtools_0.1.12a-1_powerpc.deb
- 4671231fe66c2f4a647c8b80c269088e9383d1e50bcc07ca6b912fc483d8f4f5 162450 libbam-dev_0.1.12a-1_powerpc.deb
+ 061491ab83256bc6513ce4baf9bba3856c9752ea7a26dc0a0ce84112b8beab0d 561028 samtools_0.1.12a-1~bpo60+1_powerpc.deb
+ 41fd920c24bd2951296a572b3486487bb373830976aefb9181e0f9f78cffe060 162448 libbam-dev_0.1.12a-1~bpo60+1_powerpc.deb
Files:
- 028831887d836951c07eaf52b9b105b2 560870 science optional samtools_0.1.12a-1_powerpc.deb
- ef55d1299cc1be05e27fdf90636ffbe9 162450 libdevel optional libbam-dev_0.1.12a-1_powerpc.deb
+ a7fff29e5a4e23bb4f20323bdc9beb65 561028 science optional samtools_0.1.12a-1~bpo60+1_powerpc.deb
+ 82f2730a18dcab703ed3f9affcfab728 162448 libdevel optional libbam-dev_0.1.12a-1~bpo60+1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_powerpc.deb
-──────────────────────────────
+samtools_0.1.12a-1~bpo60+1_powerpc.deb
+──────────────────────────────────────
new debian package, version 2.0.
- size 560870 bytes: control archive= 1794 bytes.
- 795 bytes, 16 lines control
+ size 561028 bytes: control archive= 1799 bytes.
+ 803 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.12a-1~bpo60+1
Architecture: powerpc
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1020
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -518,44 +567,44 @@ samtools_0.1.12a-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 2010-12-03 09:22 ./
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/bin/
--rwxr-xr-x root/root 93516 2010-12-03 09:22 ./usr/bin/bcftools
--rwxr-xr-x root/root 26828 2010-12-03 09:22 ./usr/bin/razip
--rwxr-xr-x root/root 343648 2010-12-03 09:22 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/lib/
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/lib/samtools/
--rwxr-xr-x root/root 7352 2010-12-03 09:22 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 11116 2010-12-03 09:22 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 19388 2010-12-03 09:22 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7352 2010-12-03 09:22 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 8008 2010-12-03 09:22 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/man/man1/
--rw-r--r-- root/root 7546 2010-12-03 09:22 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2010-12-03 09:22 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./usr/
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./usr/bin/
+-rwxr-xr-x root/root 93516 2011-03-14 15:31 ./usr/bin/bcftools
+-rwxr-xr-x root/root 26828 2011-03-14 15:31 ./usr/bin/razip
+-rwxr-xr-x root/root 343520 2011-03-14 15:31 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./usr/lib/samtools/
+-rwxr-xr-x root/root 7352 2011-03-14 15:31 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 11116 2011-03-14 15:31 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 19388 2011-03-14 15:31 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7352 2011-03-14 15:31 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 8008 2011-03-14 15:31 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./usr/share/man/man1/
+-rw-r--r-- root/root 7546 2011-03-14 15:31 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-03-14 15:31 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1031 2011-02-15 05:37 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 4927 2011-02-15 05:37 ./usr/share/doc/samtools/copyright
-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 09:22 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126609 2010-12-03 09:21 ./usr/share/doc/samtools/examples/ex1.bam.gz
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126609 2011-03-14 15:31 ./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 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 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 1966 2010-12-03 09:22 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1966 2011-03-14 15:31 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.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 09:22 ./usr/share/samtools/
+-rw-r--r-- root/root 592 2011-02-15 05:37 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./usr/share/samtools/
-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 09:22 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-03-14 15:31 ./usr/share/samtools/varfilter.py
-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 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
@@ -568,21 +617,21 @@ drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/samtools/
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
-rwxr-xr-x root/root 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
-lrwxrwxrwx root/root 0 2010-12-03 09:22 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+lrwxrwxrwx root/root 0 2011-03-14 15:31 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.12a-1_powerpc.deb
-────────────────────────────────
+libbam-dev_0.1.12a-1~bpo60+1_powerpc.deb
+────────────────────────────────────────
new debian package, version 2.0.
- size 162450 bytes: control archive= 898 bytes.
- 677 bytes, 15 lines control
+ size 162448 bytes: control archive= 903 bytes.
+ 685 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.12a-1~bpo60+1
Architecture: powerpc
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 404
Section: libdevel
Priority: optional
@@ -594,21 +643,21 @@ libbam-dev_0.1.12a-1_powerpc.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/lib/
--rw-r--r-- root/root 260866 2010-12-03 09:22 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/include/
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./usr/
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./usr/lib/
+-rw-r--r-- root/root 260698 2011-03-14 15:31 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./usr/include/
-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
-rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/libbam-dev/
--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 2011-03-14 15:31 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-14 15:31 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 4927 2011-02-15 05:37 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
@@ -619,10 +668,9 @@ drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/libbam-dev/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-f6484d4d-a7cc-4101-9c13-f7b72cf926c7/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf
+Purging /var/lib/schroot/mount/squeeze-backports-powerpc-sbuild-9098bcd5-d126-4764-abab-8f168d4a6ddb/build/buildd-samtools_0.1.12a-1~bpo60+1-powerpc-hn5IcB
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0922
-Build needed 00:02:57, 8908k disc space
+Finished at 20110314-1531
+Build needed 00:03:42, 8908k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
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 4b20c51..5515fb7 100644
--- a/s390.log
+++ b/s390.log
@@ -1,41 +1,95 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/s390 received Fri Dec 3 09:24:16 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=s390">s390</a> >> Fri Dec 3 09:24:16 2010<pre>
+From buildd at zandonai.debian.org Thu Feb 24 19:17:53 2011
+Return-path: <buildd at zandonai.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
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+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
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+ id 1PsghA-0002Iz-C2; Thu, 24 Feb 2011 19:17:48 +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_0.1.12a-1~bpo60+1 on s390
+ (dist=squeeze-backports)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1PsghA-0002Iz-C2 at zandonai.debian.org>
+Date: Thu, 24 Feb 2011 19:17:48 +0000
+Delivered-To: logs at buildd.debian.org
+
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (s390) 03 Dec 2010 09:22 ║
+║ samtools 0.1.12a-1~bpo60+1 (s390) 24 Feb 2011 19:16 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.12a-1~bpo60+1
Architecture: s390
-Chroot Build Dir: /var/lib/schroot/mount/sid-s390-sbuild-235df352-e04a-4a75-a746-dc247b89ec10/build/buildd-samtools_0.1.12a-1-s390-zpFbOY
-Start Time: 20101203-0922
-Get:1 http://ftp.de.debian.org unstable Release.gpg [835 B]
-Ign http://ftp.de.debian.org/debian/ unstable/contrib Translation-en
-Ign http://ftp.de.debian.org/debian/ unstable/main Translation-en
-Get:2 http://ftp.de.debian.org unstable Release [104 kB]
-Get:3 http://incoming.debian.org unstable Release.gpg [835 B]
-Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
-Ign http://incoming.debian.org/debian/ unstable/main Translation-en
-Get:4 http://ftp.de.debian.org unstable/main Sources [4071 kB]
-Get:5 http://incoming.debian.org Release.gpg [835 B]
-Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:6 http://incoming.debian.org unstable Release [104 kB]
-Get:7 http://incoming.debian.org Release [1604 B]
-Get:8 http://incoming.debian.org unstable/main Sources [4071 kB]
-Get:9 http://ftp.de.debian.org unstable/contrib Sources [38.7 kB]
-Get:10 http://ftp.de.debian.org unstable/non-free Sources [83.8 kB]
-Get:11 http://ftp.de.debian.org unstable/main s390 Packages [6754 kB]
-Get:12 http://ftp.de.debian.org unstable/contrib s390 Packages [48.8 kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [38.7 kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [83.8 kB]
-Get:15 http://incoming.debian.org unstable/main s390 Packages [6754 kB]
-Get:16 http://incoming.debian.org unstable/contrib s390 Packages [48.8 kB]
-Get:17 http://incoming.debian.org Sources [8014 B]
-Get:18 http://incoming.debian.org Packages [169 kB]
-Fetched 22.4 MB in 25s (866 kB/s)
+Chroot Build Dir: /var/lib/schroot/mount/squeeze-backports-s390-sbuild-5462a02f-6a20-4712-a8ff-8093f63578d0/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j
+Start Time: 20110224-1916
+Get:1 http://ftp.de.debian.org squeeze Release.gpg [1671 B]
+Ign http://ftp.de.debian.org/debian/ squeeze/contrib Translation-en
+Ign http://ftp.de.debian.org/debian/ squeeze/main Translation-en
+Get:2 http://ftp.de.debian.org squeeze-proposed-updates Release.gpg [835 B]
+Ign http://ftp.de.debian.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://ftp.de.debian.org/debian/ squeeze-proposed-updates/main Translation-en
+Get:3 http://ftp.de.debian.org squeeze Release [69.3 kB]
+Get:4 http://ftp.debian.org squeeze Release.gpg [1671 B]
+Ign http://ftp.debian.org/debian/ squeeze/contrib Translation-en
+Ign http://ftp.debian.org/debian/ squeeze/main Translation-en
+Get:5 http://ftp.debian.org squeeze-proposed-updates Release.gpg [835 B]
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/main Translation-en
+Get:6 http://ftp.debian.org squeeze Release [69.3 kB]
+Get:7 http://ftp.de.debian.org squeeze-proposed-updates Release [58.4 kB]
+Get:8 http://ftp.debian.org squeeze-proposed-updates Release [58.4 kB]
+Get:9 http://ftp.debian.org squeeze/main Sources [3720 kB]
+Get:10 http://ftp.de.debian.org squeeze/main Sources [3720 kB]
+Get:11 http://backports-master.debian.org squeeze-backports Release.gpg [835 B]
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/contrib Translation-en
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/main Translation-en
+Get:12 http://backports-master.debian.org Release.gpg [835 B]
+Ign http://backports-master.debian.org/buildd/squeeze-backports/ Translation-en
+Get:13 http://backports-master.debian.org squeeze-backports Release [61.2 kB]
+Get:14 http://ftp.de.debian.org squeeze/contrib Sources [33.9 kB]
+Get:15 http://ftp.de.debian.org squeeze/non-free Sources [61.7 kB]
+Get:16 http://ftp.de.debian.org squeeze/main s390 Packages [6417 kB]
+Get:17 http://backports-master.debian.org Release [1644 B]
+Get:18 http://backports-master.debian.org squeeze-backports/main Sources [5961 B]
+Get:19 http://ftp.debian.org squeeze/contrib Sources [33.9 kB]
+Get:20 http://ftp.debian.org squeeze/non-free Sources [61.7 kB]
+Get:21 http://backports-master.debian.org squeeze-backports/contrib Sources [14 B]
+Get:22 http://backports-master.debian.org squeeze-backports/non-free Sources [14 B]
+Get:23 http://backports-master.debian.org squeeze-backports/main s390 Packages [6183 B]
+Get:24 http://backports-master.debian.org squeeze-backports/contrib s390 Packages [14 B]
+Get:25 http://backports-master.debian.org Sources [14 B]
+Get:26 http://backports-master.debian.org Packages [14 B]
+Get:27 http://ftp.debian.org squeeze/main s390 Packages [6417 kB]
+Get:28 http://ftp.de.debian.org squeeze/contrib s390 Packages [44.4 kB]
+Get:29 http://ftp.de.debian.org squeeze-proposed-updates/main Sources [17.8 kB]
+Get:30 http://ftp.de.debian.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:31 http://ftp.de.debian.org squeeze-proposed-updates/non-free Sources [14 B]
+Get:32 http://ftp.de.debian.org squeeze-proposed-updates/main s390 Packages [55.4 kB]
+Get:33 http://ftp.de.debian.org squeeze-proposed-updates/contrib s390 Packages [14 B]
+Get:34 http://ftp.debian.org squeeze/contrib s390 Packages [44.4 kB]
+Get:35 http://ftp.debian.org squeeze-proposed-updates/main Sources [17.8 kB]
+Get:36 http://ftp.debian.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:37 http://ftp.debian.org squeeze-proposed-updates/non-free Sources [14 B]
+Get:38 http://ftp.debian.org squeeze-proposed-updates/main s390 Packages [55.4 kB]
+Get:39 http://ftp.debian.org squeeze-proposed-updates/contrib s390 Packages [14 B]
+Fetched 21.0 MB in 8s (2438 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -54,140 +108,209 @@ 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:
+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://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
-Fetched 364 kB in 1s (264 kB/s)
+Need to get 363 kB of source archives.
+Get:1 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (dsc) [1338 B]
+Get:2 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (tar) [356 kB]
+Get:3 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (diff) [6406 B]
+Fetched 363 kB in 1s (202 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
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install build dependencies (aptitude-based 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
+ libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5 libsigc++-2.0-0c2a
+ libsqlite3-0 libxapian22
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ tasksel debtags libcwidget-dev xapian-tools
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ aptitude-doc-en aptitude-doc apt-xapian-index libparse-debianchangelog-perl
+ libgpm2
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 28 not upgraded.
-Need to get 11.8 MB of archives.
-After this operation, 35.7 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.0.17 [207 kB]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.20.1-10 [1112 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.5.7-6 [1308 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.04-5 [243 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main file s390 5.04-5 [50.0 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-3 [142 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.02-1.1 [239 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-1 [872 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.24.2-1 [1140 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-1 [128 kB]
-Get:12 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-3 [431 kB]
-Get:13 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-3 [2068 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:16 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.0.0 [454 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.89 [1240 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.7+20100313-4 [1634 kB]
-Get:19 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.3.4.dfsg-3 [193 kB]
+ aptitude libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5
+ libsigc++-2.0-0c2a libsqlite3-0 libxapian22
+0 upgraded, 8 newly installed, 0 to remove and 21 not upgraded.
+Need to get 6233 kB of archives.
+After this operation, 17.7 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ squeeze/main libboost-iostreams1.42.0 s390 1.42.0-4 [57.8 kB]
+Get:2 http://ftp.de.debian.org/debian/ squeeze/main libncursesw5 s390 5.7+20100313-5 [396 kB]
+Get:3 http://ftp.de.debian.org/debian/ squeeze/main libsigc++-2.0-0c2a s390 2.2.4.2-1 [39.9 kB]
+Get:4 http://ftp.de.debian.org/debian/ squeeze/main libcwidget3 s390 0.5.16-3 [303 kB]
+Get:5 http://ftp.de.debian.org/debian/ squeeze/main libxapian22 s390 1.2.3-2 [1150 kB]
+Get:6 http://ftp.de.debian.org/debian/ squeeze/main libept1 s390 1.0.4 [148 kB]
+Get:7 http://ftp.de.debian.org/debian/ squeeze/main libsqlite3-0 s390 3.7.3-1 [420 kB]
+Get:8 http://ftp.de.debian.org/debian/ squeeze/main aptitude s390 0.6.3-3.2 [3719 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.8 MB in 5s (2352 kB/s)
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 10060 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_s390.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_s390.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_s390.deb) ...
+Fetched 6233 kB in 1s (3262 kB/s)
+Selecting previously deselected package libboost-iostreams1.42.0.
+(Reading database ... 10065 files and directories currently installed.)
+Unpacking libboost-iostreams1.42.0 (from .../libboost-iostreams1.42.0_1.42.0-4_s390.deb) ...
+Selecting previously deselected package libncursesw5.
+Unpacking libncursesw5 (from .../libncursesw5_5.7+20100313-5_s390.deb) ...
+Selecting previously deselected package libsigc++-2.0-0c2a.
+Unpacking libsigc++-2.0-0c2a (from .../libsigc++-2.0-0c2a_2.2.4.2-1_s390.deb) ...
+Selecting previously deselected package libcwidget3.
+Unpacking libcwidget3 (from .../libcwidget3_0.5.16-3_s390.deb) ...
+Selecting previously deselected package libxapian22.
+Unpacking libxapian22 (from .../libxapian22_1.2.3-2_s390.deb) ...
+Selecting previously deselected package libept1.
+Unpacking libept1 (from .../libept1_1.0.4_s390.deb) ...
+Selecting previously deselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.3-1_s390.deb) ...
+Selecting previously deselected package aptitude.
+Unpacking aptitude (from .../aptitude_0.6.3-3.2_s390.deb) ...
+Setting up libboost-iostreams1.42.0 (1.42.0-4) ...
+Setting up libncursesw5 (5.7+20100313-5) ...
+Setting up libsigc++-2.0-0c2a (2.2.4.2-1) ...
+Setting up libcwidget3 (0.5.16-3) ...
+Setting up libxapian22 (1.2.3-2) ...
+Setting up libept1 (1.0.4) ...
+Setting up libsqlite3-0 (3.7.3-1) ...
+Setting up aptitude (0.6.3-3.2) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode.
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/buildd-samtools-s390-L3vgih/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously deselected package sbuild-build-depends-samtools-dummy.
+(Reading database ... 10273 files and directories currently installed.)
+Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
+dpkg: dependency problems prevent configuration of sbuild-build-depends-samtools-dummy:
+ sbuild-build-depends-samtools-dummy depends on debhelper (>= 8); however:
+ Package debhelper is not installed.
+ sbuild-build-depends-samtools-dummy depends on cdbs; however:
+ Package cdbs is not installed.
+ sbuild-build-depends-samtools-dummy depends on libncurses5-dev; however:
+ Package libncurses5-dev is not installed.
+ sbuild-build-depends-samtools-dummy depends on zlib1g-dev; however:
+ Package zlib1g-dev is not installed.
+dpkg: error processing sbuild-build-depends-samtools-dummy (--install):
+ dependency problems - leaving unconfigured
+Errors were encountered while processing:
+ sbuild-build-depends-samtools-dummy
+aptitude -y --without-recommends -o APT::Install-Recommends=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-samtools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Tier=55000 -o Aptitude::ProblemResolver::Remove-Essential-Tier=maximum install sbuild-build-depends-samtools-dummy
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
+The following NEW packages will be installed:
+ bsdmainutils{a} cdbs{a} debhelper{a} file{a} gettext{a} gettext-base{a}
+ groff-base{a} html2text{a} intltool-debian{a} libcroco3{a}
+ libglib2.0-0{a} libmagic1{a} libncurses5-dev{a} libpcre3{a}
+ libunistring0{a} libxml2{a} man-db{a} po-debconf{a} zlib1g-dev{a}
+The following partially installed packages will be configured:
+ sbuild-build-depends-samtools-dummy
+0 packages upgraded, 19 newly installed, 0 to remove and 21 not upgraded.
+Need to get 11.8 MB of archives. After unpacking 35.7 MB will be used.
+Writing extended state information...
+Get:1 http://ftp.de.debian.org/debian/ squeeze/main libmagic1 s390 5.04-5 [243 kB]
+Get:2 http://ftp.de.debian.org/debian/ squeeze/main file s390 5.04-5 [50.0 kB]
+Get:3 http://ftp.de.debian.org/debian/ squeeze/main html2text s390 1.3.2a-15 [101 kB]
+Get:4 http://ftp.de.debian.org/debian/ squeeze/main libpcre3 s390 8.02-1.1 [239 kB]
+Get:5 http://ftp.de.debian.org/debian/ squeeze/main libglib2.0-0 s390 2.24.2-1 [1140 kB]
+Get:6 http://ftp.de.debian.org/debian/ squeeze/main libxml2 s390 2.7.8.dfsg-2 [873 kB]
+Get:7 http://ftp.de.debian.org/debian/ squeeze/main libcroco3 s390 0.6.2-1 [128 kB]
+Get:8 http://ftp.de.debian.org/debian/ squeeze/main libunistring0 s390 0.9.3-3 [431 kB]
+Get:9 http://ftp.de.debian.org/debian/ squeeze/main gettext-base s390 0.18.1.1-3 [142 kB]
+Get:10 http://ftp.de.debian.org/debian/ squeeze/main gettext s390 0.18.1.1-3 [2068 kB]
+Get:11 http://ftp.de.debian.org/debian/ squeeze/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:12 http://ftp.de.debian.org/debian/ squeeze/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:13 http://ftp.de.debian.org/debian/ squeeze/main groff-base s390 1.20.1-10 [1112 kB]
+Get:14 http://ftp.de.debian.org/debian/ squeeze/main bsdmainutils s390 8.0.13 [206 kB]
+Get:15 http://ftp.de.debian.org/debian/ squeeze/main man-db s390 2.5.7-8 [1303 kB]
+Get:16 http://ftp.de.debian.org/debian/ squeeze/main debhelper all 8.0.0 [454 kB]
+Get:17 http://ftp.de.debian.org/debian/ squeeze/main cdbs all 0.4.89 [1240 kB]
+Get:18 http://ftp.de.debian.org/debian/ squeeze/main libncurses5-dev s390 5.7+20100313-5 [1634 kB]
+Get:19 http://ftp.de.debian.org/debian/ squeeze/main zlib1g-dev s390 1:1.2.3.4.dfsg-3 [193 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 11.8 MB in 3s (3427 kB/s)
Selecting previously deselected package libmagic1.
+(Reading database ... 10273 files and directories currently installed.)
Unpacking libmagic1 (from .../libmagic1_5.04-5_s390.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../archives/file_5.04-5_s390.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_s390.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_s390.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_s390.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_s390.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.02-1.1_s390.deb) ...
Selecting previously deselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_s390.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_s390.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_s390.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-3_s390.deb) ...
+Selecting previously deselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_s390.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_s390.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 groff-base.
+Unpacking groff-base (from .../groff-base_1.20.1-10_s390.deb) ...
+Selecting previously deselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_s390.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.5.7-8_s390.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_s390.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_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 (8.0.17) ...
-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) ...
-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 libpcre3 (8.02-1.1) ...
Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
+Setting up gettext-base (0.18.1.1-3) ...
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 groff-base (1.20.1-10) ...
+Setting up bsdmainutils (8.0.13) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
+Setting up man-db (2.5.7-8) ...
+debconf: unable to initialize frontend: Dialog
+debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 75.)
+debconf: falling back to frontend: Readline
+debconf: unable to initialize frontend: Readline
+debconf: (This frontend requires a controlling tty.)
+debconf: falling back to frontend: Teletype
+Building database of manual pages ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
-Setting up libncurses5-dev (5.7+20100313-4) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Removing negative dependencies:
-Checking correctness of source dependencies...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
Kernel: Linux 2.6.32-bpo.5-s390x s390 (s390x)
-Toolchain package versions: libc6-dev_2.11.2-7 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-27 gcc-4.4_4.4.5-7 g++-4.4_4.4.5-7 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-7 libstdc++6_4.4.5-7
-Package versions: apt_0.8.8 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.17 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-7 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 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 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-7 gcc_4:4.4.5-1 gcc-4.4_4.4.5-7 gcc-4.4-base_4.4.5-7 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_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 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 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-7 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-7 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 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 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-7 libstdc++6-4.4-dev_4.4.5-7 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_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-27 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 make_3.81-8 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 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 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.5 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 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 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6-dev_2.11.2-7 dpkg-dev_1.15.8.7 linux-libc-dev_2.6.32-29 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: apt_0.8.10 aptitude_0.6.3-3.2 base-files_6.0 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-5 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-8 dash_0.5.5.1-7.4 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 diffutils_1:3.0-1 dpkg_1.15.8.7 dpkg-dev_1.15.8.7 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-8 gcc_4:4.4.5-1 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 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-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_2.17.2-5 libboost-iostreams1.42.0_1.42.0-4 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 libcwidget3_0.5.16-3 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.7 libept1_1.0.4 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-8 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-8 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 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 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libsigc++-2.0-0c2a_2.2.4.2-1 libslang2_2.2.2-4 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libstdc++6_4.4.5-8 libstdc++6-4.4-dev_4.4.5-8 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_2:0.1.12-16 libuuid1_2.17.2-5 libxapian22_1.2.3-2 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-29 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15 mount_2.17.2-5 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6-2 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 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.23-3 tzdata_2010o-1 util-linux_2.17.2-5 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -198,13 +321,13 @@ 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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Thu Feb 17 08:40:32 2011 UTC using DSA key ID BAFEC7F2
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1~bpo60+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
+dpkg-source: info: unpacking samtools_0.1.12a-1~bpo60+1.debian.tar.gz
Check disc space
────────────────
@@ -219,35 +342,35 @@ 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-buildpackage: source version 0.1.12a-1~bpo60+1
dpkg-source --before-build samtools-0.1.12a
dpkg-buildpackage: host architecture s390
/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-s390-zpFbOY/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
+/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~bpo60+1-s390-lTFK7j/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/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-s390-zpFbOY/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/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-s390-zpFbOY/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/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-s390-zpFbOY/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/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 "."
+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-s390-zpFbOY/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
+/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~bpo60+1-s390-lTFK7j/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/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
@@ -267,8 +390,8 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-s390-zpFbOY/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/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
@@ -279,10 +402,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-s390-zpFbOY/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/samtools-0.1.12a/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/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
@@ -299,24 +422,24 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-s390-zpFbOY/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/misc'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/samtools-0.1.12a'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/samtools-0.1.12a/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/samtools-0.1.12a/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/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-s390-zpFbOY/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/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-s390-zpFbOY/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/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
@@ -326,50 +449,50 @@ 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-s390-zpFbOY/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/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-s390-zpFbOY/samtools-0.1.12a'
+make[1]: Nothing to be done for `lib'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/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-s390-zpFbOY/samtools-0.1.12a/examples'
+/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~bpo60+1-s390-lTFK7j/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 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
+../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
+../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
+(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'
+[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
+[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
+<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'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/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 "."
+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
@@ -395,8 +518,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/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
@@ -420,7 +543,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -435,69 +558,66 @@ 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_s390.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1~bpo60+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_0.1.12a-1_s390.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1~bpo60+1_s390.deb'.
+ dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.12a-1~bpo60+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-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0924
+Build finished at 20110224-1917
-samtools_0.1.12a-1_s390.changes:
+samtools_0.1.12a-1~bpo60+1_s390.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Thu, 17 Feb 2011 13:13:09 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: s390
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.12a-1~bpo60+1
+Distribution: squeeze-backports
Urgency: low
-Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai 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 (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.12a-1~bpo60+1) squeeze-backports; 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).
+ * Backported for Squeeze (no changes needed).
Checksums-Sha1:
- 63f318ed9acaa790b238ac22e0ac2d313b09754e 568074 samtools_0.1.12a-1_s390.deb
- 15ccbda0b9f67f67811be5cbcaa6bcbb71bd4611 163484 libbam-dev_0.1.12a-1_s390.deb
+ 3ee58db3603448d5c40f0a97166f458ce0582730 568270 samtools_0.1.12a-1~bpo60+1_s390.deb
+ 93135b8a65947f0821c837e7f5ca185e8b627f25 163502 libbam-dev_0.1.12a-1~bpo60+1_s390.deb
Checksums-Sha256:
- 1f8c1fb50700acfdcddf4ae12261b0484d0226ae70a98b3432c0c65d5f36815c 568074 samtools_0.1.12a-1_s390.deb
- fe61bcca670f8c22ad0e3531def8caa07711a97d088a47eb4239af12f204aa46 163484 libbam-dev_0.1.12a-1_s390.deb
+ d9c3bd3d08f22d9208a4f4cfe16add41691db6b1b9d35bdc4ffe34f3016923e3 568270 samtools_0.1.12a-1~bpo60+1_s390.deb
+ 7ff34f8744c3f0f98ff20ba61dc0034072a8cb1858ca46f0f31071d01048fdce 163502 libbam-dev_0.1.12a-1~bpo60+1_s390.deb
Files:
- 1e960b993581b710a92f6a85a2ea1cf4 568074 science optional samtools_0.1.12a-1_s390.deb
- ccf263db0121acdae17ea2f30ff59265 163484 libdevel optional libbam-dev_0.1.12a-1_s390.deb
+ 7384881228e6660bd9a3d72dba7a76f6 568270 science optional samtools_0.1.12a-1~bpo60+1_s390.deb
+ bb720835cabe72b262bc5f2c8af4322d 163502 libdevel optional libbam-dev_0.1.12a-1~bpo60+1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_s390.deb
-───────────────────────────
+samtools_0.1.12a-1~bpo60+1_s390.deb
+───────────────────────────────────
new debian package, version 2.0.
- size 568074 bytes: control archive= 1785 bytes.
- 792 bytes, 16 lines control
+ size 568270 bytes: control archive= 1794 bytes.
+ 800 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.12a-1~bpo60+1
Architecture: s390
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1032
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -509,25 +629,25 @@ samtools_0.1.12a-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 2010-12-03 09:24 ./
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/bin/
--rwxr-xr-x root/root 92244 2010-12-03 09:24 ./usr/bin/bcftools
--rwxr-xr-x root/root 354472 2010-12-03 09:24 ./usr/bin/samtools
--rwxr-xr-x root/root 27364 2010-12-03 09:24 ./usr/bin/razip
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/lib/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/lib/samtools/
--rwxr-xr-x root/root 11324 2010-12-03 09:24 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7188 2010-12-03 09:24 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 7188 2010-12-03 09:24 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7932 2010-12-03 09:24 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 18572 2010-12-03 09:24 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/man/man1/
--rw-r--r-- root/root 7546 2010-12-03 09:24 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2010-12-03 09:24 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./usr/
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./usr/bin/
+-rwxr-xr-x root/root 92244 2011-02-24 19:17 ./usr/bin/bcftools
+-rwxr-xr-x root/root 354472 2011-02-24 19:17 ./usr/bin/samtools
+-rwxr-xr-x root/root 27364 2011-02-24 19:17 ./usr/bin/razip
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./usr/lib/
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./usr/lib/samtools/
+-rwxr-xr-x root/root 11324 2011-02-24 19:17 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7188 2011-02-24 19:17 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 7188 2011-02-24 19:17 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7932 2011-02-24 19:17 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 18572 2011-02-24 19:17 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./usr/share/man/man1/
+-rw-r--r-- root/root 7546 2011-02-24 19:17 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-02-24 19:17 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./usr/share/samtools/
-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./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
@@ -538,42 +658,42 @@ drwxr-xr-x root/root 0 2010-12-03 09:24 ./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 2010-12-03 09:24 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-02-24 19:17 ./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 2010-12-03 09:24 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./usr/share/doc/samtools/
-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 1031 2011-02-15 05:37 ./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 2010-12-03 05:06 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1966 2010-12-03 09:24 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 592 2011-02-15 05:37 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1966 2011-02-24 19:17 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
--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
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 1179 2011-02-17 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 4927 2011-02-15 05:37 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./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 2010-12-03 09:23 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-02-24 19:17 ./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
-lrwxrwxrwx root/root 0 2010-12-03 09:24 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+lrwxrwxrwx root/root 0 2011-02-24 19:17 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.12a-1_s390.deb
-─────────────────────────────
+libbam-dev_0.1.12a-1~bpo60+1_s390.deb
+─────────────────────────────────────
new debian package, version 2.0.
- size 163484 bytes: control archive= 894 bytes.
- 674 bytes, 15 lines control
+ size 163502 bytes: control archive= 898 bytes.
+ 682 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.12a-1~bpo60+1
Architecture: s390
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 400
Section: libdevel
Priority: optional
@@ -585,23 +705,23 @@ libbam-dev_0.1.12a-1_s390.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/include/
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./usr/
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./usr/include/
-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
-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
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/lib/
--rw-r--r-- root/root 256726 2010-12-03 09:24 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./usr/lib/
+-rw-r--r-- root/root 256726 2011-02-24 19:17 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./usr/share/
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-02-24 19:17 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 6692 2010-12-02 21:16 ./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 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
--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 1179 2011-02-17 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 4927 2011-02-15 05:37 ./usr/share/doc/libbam-dev/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -610,10 +730,9 @@ drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/libbam-dev/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-s390-sbuild-235df352-e04a-4a75-a746-dc247b89ec10/build/buildd-samtools_0.1.12a-1-s390-zpFbOY
+Purging /var/lib/schroot/mount/squeeze-backports-s390-sbuild-5462a02f-6a20-4712-a8ff-8093f63578d0/build/buildd-samtools_0.1.12a-1~bpo60+1-s390-lTFK7j
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0924
-Build needed 00:01:38, 9204k disc space
+Finished at 20110224-1917
+Build needed 00:01:24, 9204k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
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 e265982..f198813 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,36 +1,96 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/sparc received Fri Dec 3 09:29:08 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=sparc">sparc</a> >> Fri Dec 3 09:29:08 2010<pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on spontini.debian.org
+From buildd at schroeder.debian.org Fri Feb 18 17:47:02 2011
+Return-path: <buildd at schroeder.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 schroeder.debian.org>)
+ id 1PqUQ2-0007I7-DO
+ for logs at buildd.debian.org; Fri, 18 Feb 2011 17:47:02 +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 kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at schroeder.debian.org>)
+ id 1PqUQ0-0005h1-EY
+ for logs at buildd.debian.org; Fri, 18 Feb 2011 17:47:00 +0000
+Received: from buildd by schroeder.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at schroeder.debian.org>)
+ id 1PqUPz-0008Ca-Ak; Fri, 18 Feb 2011 17:46:59 +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_0.1.12a-1~bpo60+1 on sparc
+ (dist=squeeze-backports)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1PqUPz-0008Ca-Ak at schroeder.debian.org>
+Date: Fri, 18 Feb 2011 17:46:59 +0000
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on schroeder.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (sparc) 03 Dec 2010 09:22 ║
+║ samtools 0.1.12a-1~bpo60+1 (sparc) 18 Feb 2011 17:43 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.12a-1~bpo60+1
Architecture: sparc
-Chroot Build Dir: /var/lib/schroot/mount/sid-sparc-sbuild-5f94f0dc-8583-4e98-bc68-e5cff85fb5ae/build/buildd-samtools_0.1.12a-1-sparc-UAUacU
-Start Time: 20101203-0922
-Get:1 http://mirrors.ece.ubc.ca unstable Release.gpg [835B]
-Get:2 http://mirrors.ece.ubc.ca unstable Release [104kB]
-Get:3 http://incoming.debian.org unstable Release.gpg [835B]
-Get:4 http://incoming.debian.org Release.gpg [835B]
-Get:5 http://incoming.debian.org unstable Release [104kB]
-Get:6 http://mirrors.ece.ubc.ca unstable/main Packages [6789kB]
-Get:7 http://incoming.debian.org Release [1604B]
-Get:8 http://incoming.debian.org unstable/main Packages [6789kB]
-Get:9 http://mirrors.ece.ubc.ca unstable/contrib Packages [51.2kB]
-Get:10 http://mirrors.ece.ubc.ca unstable/main Sources [4071kB]
-Get:11 http://mirrors.ece.ubc.ca unstable/contrib Sources [38.7kB]
-Get:12 http://mirrors.ece.ubc.ca unstable/non-free Sources [83.8kB]
-Get:13 http://incoming.debian.org unstable/contrib Packages [51.2kB]
-Get:14 http://incoming.debian.org unstable/main Sources [4071kB]
-Get:15 http://incoming.debian.org unstable/contrib Sources [38.7kB]
-Get:16 http://incoming.debian.org unstable/non-free Sources [83.8kB]
-Get:17 http://incoming.debian.org Packages [169kB]
-Get:18 http://incoming.debian.org Sources [8014B]
-Fetched 22.5MB in 53s (416kB/s)
+Chroot Build Dir: /var/lib/schroot/mount/squeeze-backports-sparc-sbuild-b44c52b4-d702-4057-b3e6-b9cb317cb01b/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB
+Start Time: 20110218-1743
+Hit http://ftp.carnet.hr squeeze Release.gpg
+Get:1 http://ftp.debian.org squeeze Release.gpg [1671 B]
+Ign http://ftp.debian.org/debian/ squeeze/contrib Translation-en
+Ign http://ftp.debian.org/debian/ squeeze/main Translation-en
+Get:2 http://ftp.debian.org squeeze-proposed-updates Release.gpg [835 B]
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/contrib Translation-en
+Ign http://ftp.debian.org/debian/ squeeze-proposed-updates/main Translation-en
+Get:3 http://ftp.debian.org squeeze Release [69.3 kB]
+Ign http://ftp.carnet.hr/debian/ squeeze/contrib Translation-en
+Get:4 http://backports-master.debian.org squeeze-backports Release.gpg [835 B]
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/contrib Translation-en
+Get:5 http://ftp.debian.org squeeze-proposed-updates Release [58.4 kB]
+Ign http://backports-master.debian.org/debian-backports/ squeeze-backports/main Translation-en
+Get:6 http://backports-master.debian.org Release.gpg [835 B]
+Ign http://backports-master.debian.org/buildd/squeeze-backports/ Translation-en
+Get:7 http://backports-master.debian.org squeeze-backports Release [61.2 kB]
+Get:8 http://ftp.debian.org squeeze/main Sources [3720 kB]
+Ign http://ftp.carnet.hr/debian/ squeeze/main Translation-en
+Get:9 http://ftp.carnet.hr squeeze-proposed-updates Release.gpg [835 B]
+Get:10 http://backports-master.debian.org Release [1644 B]
+Get:11 http://ftp.debian.org squeeze/contrib Sources [33.9 kB]
+Get:12 http://ftp.debian.org squeeze/non-free Sources [61.7 kB]
+Get:13 http://ftp.debian.org squeeze/main sparc Packages [6448 kB]
+Ign http://ftp.carnet.hr/debian/ squeeze-proposed-updates/contrib Translation-en
+Get:14 http://backports-master.debian.org squeeze-backports/main Sources [4232 B]
+Get:15 http://backports-master.debian.org squeeze-backports/contrib Sources [14 B]
+Get:16 http://backports-master.debian.org squeeze-backports/non-free Sources [14 B]
+Get:17 http://backports-master.debian.org squeeze-backports/main sparc Packages [12.1 kB]
+Ign http://ftp.carnet.hr/debian/ squeeze-proposed-updates/main Translation-en
+Get:18 http://backports-master.debian.org squeeze-backports/contrib sparc Packages [14 B]
+Get:19 http://backports-master.debian.org Sources [1846 B]
+Get:20 http://backports-master.debian.org Packages [3793 B]
+Hit http://ftp.carnet.hr squeeze Release
+Get:21 http://ftp.debian.org squeeze/contrib sparc Packages [44.8 kB]
+Get:22 http://ftp.debian.org squeeze-proposed-updates/main Sources [12.5 kB]
+Get:23 http://ftp.debian.org squeeze-proposed-updates/contrib Sources [14 B]
+Get:24 http://ftp.debian.org squeeze-proposed-updates/non-free Sources [14 B]
+Get:25 http://ftp.debian.org squeeze-proposed-updates/main sparc Packages [44.2 kB]
+Get:26 http://ftp.debian.org squeeze-proposed-updates/contrib sparc Packages [14 B]
+Get:27 http://ftp.carnet.hr squeeze-proposed-updates Release [58.4 kB]
+Hit http://ftp.carnet.hr squeeze/main Sources
+Hit http://ftp.carnet.hr squeeze/contrib Sources
+Get:28 http://ftp.carnet.hr squeeze/non-free Sources [61.7 kB]
+Hit http://ftp.carnet.hr squeeze/main sparc Packages
+Hit http://ftp.carnet.hr squeeze/contrib sparc Packages
+Get:29 http://ftp.carnet.hr squeeze-proposed-updates/main Sources [12.5 kB]
+Get:30 http://ftp.carnet.hr squeeze-proposed-updates/contrib Sources [14 B]
+Get:31 http://ftp.carnet.hr squeeze-proposed-updates/non-free Sources [14 B]
+Get:32 http://ftp.carnet.hr squeeze-proposed-updates/main sparc Packages [44.2 kB]
+Get:33 http://ftp.carnet.hr squeeze-proposed-updates/contrib sparc Packages [14 B]
+Fetched 10.8 MB in 13s (775 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -49,150 +109,209 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-Need to get 364kB of source archives.
-Get:1 http://incoming.debian.org samtools 0.1.12a-1 (dsc) [1946B]
-Get:2 http://incoming.debian.org samtools 0.1.12a-1 (tar) [356kB]
-Get:3 http://incoming.debian.org samtools 0.1.12a-1 (diff) [6337B]
-Fetched 364kB in 1s (352kB/s)
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/debian-med/samtools.git
+Need to get 363 kB of source archives.
+Get:1 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (dsc) [1338 B]
+Get:2 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (tar) [356 kB]
+Get:3 http://backports-master.debian.org/debian-backports/ squeeze-backports/main samtools 0.1.12a-1~bpo60+1 (diff) [6406 B]
+Fetched 363 kB in 1s (183 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
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install build dependencies (aptitude-based 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 libncurses5 libpcre3 libunistring0 libxml2
- man-db ncurses-bin po-debconf
+ libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5 libsigc++-2.0-0c2a
+ libsqlite3-0 libxapian22
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ tasksel debtags libcwidget-dev xapian-tools
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libgpm2 xml-core libmail-sendmail-perl
+ aptitude-doc-en aptitude-doc apt-xapian-index libparse-debianchangelog-perl
+ libgpm2
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
-The following packages will be upgraded:
- libncurses5 ncurses-bin
-2 upgraded, 19 newly installed, 0 to remove and 73 not upgraded.
-Need to get 12.3MB of archives.
-After this operation, 35.6MB of additional disk space will be used.
-Get:1 http://mirrors.ece.ubc.ca unstable/main ncurses-bin 5.7+20100313-4 [322kB]
-Get:2 http://mirrors.ece.ubc.ca unstable/main libncurses5 5.7+20100313-4 [349kB]
-Get:3 http://mirrors.ece.ubc.ca unstable/main bsdmainutils 8.0.17 [203kB]
-Get:4 http://mirrors.ece.ubc.ca unstable/main groff-base 1.20.1-10 [1146kB]
-Get:5 http://mirrors.ece.ubc.ca unstable/main man-db 2.5.7-6 [1283kB]
-Get:6 http://mirrors.ece.ubc.ca unstable/main libmagic1 5.04-5 [239kB]
-Get:7 http://mirrors.ece.ubc.ca unstable/main file 5.04-5 [49.5kB]
-Get:8 http://mirrors.ece.ubc.ca unstable/main gettext-base 0.18.1.1-3 [140kB]
-Get:9 http://mirrors.ece.ubc.ca unstable/main libpcre3 8.02-1.1 [237kB]
-Get:10 http://mirrors.ece.ubc.ca unstable/main libxml2 2.7.8.dfsg-1 [840kB]
-Get:11 http://mirrors.ece.ubc.ca unstable/main html2text 1.3.2a-15 [100kB]
-Get:12 http://mirrors.ece.ubc.ca unstable/main libglib2.0-0 2.24.2-1 [1074kB]
-Get:13 http://mirrors.ece.ubc.ca unstable/main libcroco3 0.6.2-1 [119kB]
-Get:14 http://mirrors.ece.ubc.ca unstable/main libunistring0 0.9.3-3 [424kB]
-Get:15 http://mirrors.ece.ubc.ca unstable/main gettext 0.18.1.1-3 [2006kB]
-Get:16 http://mirrors.ece.ubc.ca unstable/main intltool-debian 0.35.0+20060710.1 [30.8kB]
-Get:17 http://mirrors.ece.ubc.ca unstable/main po-debconf 1.0.16+nmu1 [223kB]
-Get:18 http://mirrors.ece.ubc.ca unstable/main debhelper 8.0.0 [454kB]
-Get:19 http://mirrors.ece.ubc.ca unstable/main cdbs 0.4.89 [1240kB]
-Get:20 http://mirrors.ece.ubc.ca unstable/main libncurses5-dev 5.7+20100313-4 [1610kB]
-Get:21 http://mirrors.ece.ubc.ca unstable/main zlib1g-dev 1:1.2.3.4.dfsg-3 [189kB]
+ aptitude libboost-iostreams1.42.0 libcwidget3 libept1 libncursesw5
+ libsigc++-2.0-0c2a libsqlite3-0 libxapian22
+0 upgraded, 8 newly installed, 0 to remove and 2 not upgraded.
+Need to get 6207 kB of archives.
+After this operation, 17.8 MB of additional disk space will be used.
+Get:1 http://ftp.carnet.hr/debian/ squeeze/main libboost-iostreams1.42.0 sparc 1.42.0-4 [58.6 kB]
+Get:2 http://ftp.carnet.hr/debian/ squeeze/main libncursesw5 sparc 5.7+20100313-5 [373 kB]
+Get:3 http://ftp.carnet.hr/debian/ squeeze/main libsigc++-2.0-0c2a sparc 2.2.4.2-1 [39.2 kB]
+Get:4 http://ftp.carnet.hr/debian/ squeeze/main libcwidget3 sparc 0.5.16-3 [313 kB]
+Get:5 http://ftp.carnet.hr/debian/ squeeze/main libxapian22 sparc 1.2.3-2 [1108 kB]
+Get:6 http://ftp.carnet.hr/debian/ squeeze/main libept1 sparc 1.0.4 [141 kB]
+Get:7 http://ftp.carnet.hr/debian/ squeeze/main libsqlite3-0 sparc 3.7.3-1 [383 kB]
+Get:8 http://ftp.carnet.hr/debian/ squeeze/main aptitude sparc 0.6.3-3.2 [3790 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 12.3MB in 3s (4052kB/s)
-(Reading database ... 10166 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.7+20100313-2 (using .../ncurses-bin_5.7+20100313-4_sparc.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.7+20100313-4) ...
-(Reading database ... 10166 files and directories currently installed.)
-Preparing to replace libncurses5 5.7+20100313-2 (using .../libncurses5_5.7+20100313-4_sparc.deb) ...
-Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.7+20100313-4) ...
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 10166 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_sparc.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_sparc.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_sparc.deb) ...
+Fetched 6207 kB in 3s (1894 kB/s)
+Selecting previously deselected package libboost-iostreams1.42.0.
+(Reading database ... 10428 files and directories currently installed.)
+Unpacking libboost-iostreams1.42.0 (from .../libboost-iostreams1.42.0_1.42.0-4_sparc.deb) ...
+Selecting previously deselected package libncursesw5.
+Unpacking libncursesw5 (from .../libncursesw5_5.7+20100313-5_sparc.deb) ...
+Selecting previously deselected package libsigc++-2.0-0c2a.
+Unpacking libsigc++-2.0-0c2a (from .../libsigc++-2.0-0c2a_2.2.4.2-1_sparc.deb) ...
+Selecting previously deselected package libcwidget3.
+Unpacking libcwidget3 (from .../libcwidget3_0.5.16-3_sparc.deb) ...
+Selecting previously deselected package libxapian22.
+Unpacking libxapian22 (from .../libxapian22_1.2.3-2_sparc.deb) ...
+Selecting previously deselected package libept1.
+Unpacking libept1 (from .../libept1_1.0.4_sparc.deb) ...
+Selecting previously deselected package libsqlite3-0.
+Unpacking libsqlite3-0 (from .../libsqlite3-0_3.7.3-1_sparc.deb) ...
+Selecting previously deselected package aptitude.
+Unpacking aptitude (from .../aptitude_0.6.3-3.2_sparc.deb) ...
+Setting up libboost-iostreams1.42.0 (1.42.0-4) ...
+Setting up libncursesw5 (5.7+20100313-5) ...
+Setting up libsigc++-2.0-0c2a (2.2.4.2-1) ...
+Setting up libcwidget3 (0.5.16-3) ...
+Setting up libxapian22 (1.2.3-2) ...
+Setting up libept1 (1.0.4) ...
+Setting up libsqlite3-0 (3.7.3-1) ...
+Setting up aptitude (0.6.3-3.2) ...
+update-alternatives: using /usr/bin/aptitude-curses to provide /usr/bin/aptitude (aptitude) in auto mode.
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/buildd-samtools-sparc-Md0XIE/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously deselected package sbuild-build-depends-samtools-dummy.
+(Reading database ... 10636 files and directories currently installed.)
+Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
+dpkg: dependency problems prevent configuration of sbuild-build-depends-samtools-dummy:
+ sbuild-build-depends-samtools-dummy depends on debhelper (>= 8); however:
+ Package debhelper is not installed.
+ sbuild-build-depends-samtools-dummy depends on cdbs; however:
+ Package cdbs is not installed.
+ sbuild-build-depends-samtools-dummy depends on libncurses5-dev; however:
+ Package libncurses5-dev is not installed.
+ sbuild-build-depends-samtools-dummy depends on zlib1g-dev; however:
+ Package zlib1g-dev is not installed.
+dpkg: error processing sbuild-build-depends-samtools-dummy (--install):
+ dependency problems - leaving unconfigured
+Errors were encountered while processing:
+ sbuild-build-depends-samtools-dummy
+aptitude -y --without-recommends -o APT::Install-Recommends=false -o Aptitude::ProblemResolver::StepScore=100 -o Aptitude::ProblemResolver::Hints::KeepDummy=reject sbuild-build-depends-samtools-dummy :UNINST -o Aptitude::ProblemResolver::Keep-All-Tier=55000 -o Aptitude::ProblemResolver::Remove-Essential-Tier=maximum install sbuild-build-depends-samtools-dummy
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Initializing package states...
+Writing extended state information...
+The following NEW packages will be installed:
+ bsdmainutils{a} cdbs{a} debhelper{a} file{a} gettext{a} gettext-base{a}
+ groff-base{a} html2text{a} intltool-debian{a} libcroco3{a}
+ libglib2.0-0{a} libmagic1{a} libncurses5-dev{a} libpcre3{a}
+ libunistring0{a} libxml2{a} man-db{a} po-debconf{a} zlib1g-dev{a}
+The following partially installed packages will be configured:
+ sbuild-build-depends-samtools-dummy
+0 packages upgraded, 19 newly installed, 0 to remove and 2 not upgraded.
+Need to get 11.6 MB of archives. After unpacking 35.6 MB will be used.
+Writing extended state information...
+Get:1 http://ftp.carnet.hr/debian/ squeeze/main libmagic1 sparc 5.04-5 [239 kB]
+Get:2 http://ftp.carnet.hr/debian/ squeeze/main file sparc 5.04-5 [49.5 kB]
+Get:3 http://ftp.carnet.hr/debian/ squeeze/main html2text sparc 1.3.2a-15 [100 kB]
+Get:4 http://ftp.carnet.hr/debian/ squeeze/main libpcre3 sparc 8.02-1.1 [237 kB]
+Get:5 http://ftp.carnet.hr/debian/ squeeze/main libglib2.0-0 sparc 2.24.2-1 [1074 kB]
+Get:6 http://ftp.carnet.hr/debian/ squeeze/main libxml2 sparc 2.7.8.dfsg-2 [840 kB]
+Get:7 http://ftp.carnet.hr/debian/ squeeze/main libcroco3 sparc 0.6.2-1 [119 kB]
+Get:8 http://ftp.carnet.hr/debian/ squeeze/main libunistring0 sparc 0.9.3-3 [424 kB]
+Get:9 http://ftp.carnet.hr/debian/ squeeze/main gettext-base sparc 0.18.1.1-3 [140 kB]
+Get:10 http://ftp.carnet.hr/debian/ squeeze/main gettext sparc 0.18.1.1-3 [2006 kB]
+Get:11 http://ftp.carnet.hr/debian/ squeeze/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:12 http://ftp.carnet.hr/debian/ squeeze/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:13 http://ftp.carnet.hr/debian/ squeeze/main groff-base sparc 1.20.1-10 [1146 kB]
+Get:14 http://ftp.carnet.hr/debian/ squeeze/main bsdmainutils sparc 8.0.13 [203 kB]
+Get:15 http://ftp.carnet.hr/debian/ squeeze/main man-db sparc 2.5.7-8 [1283 kB]
+Get:16 http://ftp.carnet.hr/debian/ squeeze/main debhelper all 8.0.0 [454 kB]
+Get:17 http://ftp.carnet.hr/debian/ squeeze/main cdbs all 0.4.89 [1240 kB]
+Get:18 http://ftp.carnet.hr/debian/ squeeze/main libncurses5-dev sparc 5.7+20100313-5 [1611 kB]
+Get:19 http://ftp.carnet.hr/debian/ squeeze/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 11.6 MB in 7s (1517 kB/s)
Selecting previously deselected package libmagic1.
+(Reading database ... 10636 files and directories currently installed.)
Unpacking libmagic1 (from .../libmagic1_5.04-5_sparc.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../archives/file_5.04-5_sparc.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_sparc.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_sparc.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_sparc.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_sparc.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.02-1.1_sparc.deb) ...
Selecting previously deselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_sparc.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_sparc.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_sparc.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-3_sparc.deb) ...
+Selecting previously deselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_sparc.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_sparc.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 groff-base.
+Unpacking groff-base (from .../groff-base_1.20.1-10_sparc.deb) ...
+Selecting previously deselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_sparc.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.5.7-8_sparc.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_sparc.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_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 (8.0.17) ...
-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) ...
-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 libpcre3 (8.02-1.1) ...
Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
+Setting up gettext-base (0.18.1.1-3) ...
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 groff-base (1.20.1-10) ...
+Setting up bsdmainutils (8.0.13) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
+Setting up man-db (2.5.7-8) ...
+debconf: unable to initialize frontend: Dialog
+debconf: (TERM is not set, so the dialog frontend is not usable.)
+debconf: falling back to frontend: Readline
+debconf: unable to initialize frontend: Readline
+debconf: (This frontend requires a controlling tty.)
+debconf: falling back to frontend: Teletype
+Building database of manual pages ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
-Setting up libncurses5-dev (5.7+20100313-4) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Removing negative dependencies:
-Checking correctness of source dependencies...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+Reading extended state information...
+Initializing package states...
+Writing extended state information...
Kernel: Linux 2.6.32-bpo.5-sparc64-smp sparc (sparc64)
-Toolchain package versions: libc6-dev_2.11.2-2 dpkg-dev_1.15.7.2 linux-libc-dev_2.6.32-17 gcc-4.4_4.4.4-6 g++-4.4_4.4.4-6 binutils_2.20.1-12 libstdc++6-4.4-dev_4.4.4-6 libstdc++6_4.4.4-6
-Package versions: apt_0.7.25.3 base-files_5.8 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-12 bsdmainutils_8.0.17 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-4 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-6 dash_0.5.5.1-7 debconf_1.5.33 debconf-i18n_1.5.33 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2009.01.31 debianutils_3.3 diffutils_1:3.0-1 dpkg_1.15.7.2 dpkg-dev_1.15.7.2 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++_4:4.4.4-2 g++-4.4_4.4.4-6 gcc_4:4.4.4-2 gcc-4.4_4.4.4-6 gcc-4.4-base_4.4.4-6 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_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-11 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-3 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.1 libbz2-1.0_1.0.5-4 libc-bin_2.11.2-2 libc-dev-bin_2.11.2-2 libc6_2.11.2-2 libc6-dev_2.11.2-2 libc6-dev-sparc64_2.11.2-2 libc6-sparc64_2.11.2-2 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.26-3 libdpkg-perl_1.15.7.2 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-6 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100527-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-3 libpam-runtime_1.1.1-3 libpam0g_1.1.1-3 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.94-1 libsepol1_2.0.41-1 libss2_1.41.12-2 libstdc++6_4.4.4-6 libstdc++6-4.4-dev_4.4.4-6 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_2:0.1.12-15 libuuid1_2.17.2-3.1 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-17 login_1:4.1.4.2-1 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2-1 patch_2.6-2 perl_5.10.1-13 perl-base_5.10.1-13 perl-modules_5.10.1-13 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.2p7-1 sysv-rc_2.88dsf-11 sysvinit_2.88dsf-11 sysvinit-utils_2.88dsf-11 tar_1.23-2 tzdata_2010j-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100527-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6-dev_2.11.2-10 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-8 g++-4.4_4.4.5-8 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-8 libstdc++6_4.4.5-8
+Package versions: apt_0.8.10.3 aptitude_0.6.3-3.2 base-files_6.0 base-passwd_3.5.22+b1 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.0.13 bsdutils_1:2.17.2-9 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-8 dash_0.5.5.1-7.4 debconf_1.5.36.1 debconf-i18n_1.5.36.1 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 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_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b2 g++_4:4.4.5-1 g++-4.4_4.4.5-8 gcc_4:4.4.5-1 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 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-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 libboost-iostreams1.42.0_1.42.0-4 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 libc6-dev-sparc64_2.11.2-10 libc6-sparc64_2.11.2-10 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcwidget3_0.5.16-3 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.10 libept1_1.0.4 libgc1c2_1:6.8-1.2+b1 libgcc1_1:4.4.5-8 libgdbm3_1.8.3-9+b1 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-8 liblocale-gettext-perl_1.05-6+b1 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 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 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libsigc++-2.0-0c2a_2.2.4.2-1 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libstdc++6_4.4.5-8 libstdc++6-4.4-dev_4.4.5-8 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_2:0.1.12-16 libuuid1_2.17.2-9 libxapian22_1.2.3-2 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-30 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-23.2squeeze1 make_3.81-8 man-db_2.5.7-8 mawk_1.3.3-15+b1 mount_2.17.2-9 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 netbase_4.45 passwd_1:4.1.4.2+svn3283-2 patch_2.6-2 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 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2.squeeze.1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.23-3 tzdata_2010o-1 util-linux_2.17.2-9 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -203,13 +322,13 @@ 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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Thu Feb 17 08:40:32 2011 UTC using DSA key ID BAFEC7F2
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1~bpo60+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
+dpkg-source: info: unpacking samtools_0.1.12a-1~bpo60+1.debian.tar.gz
Check disc space
────────────────
@@ -218,51 +337,52 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
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-buildpackage: source version 0.1.12a-1~bpo60+1
+ dpkg-source --before-build samtools-0.1.12a
dpkg-buildpackage: host architecture sparc
/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-sparc-UAUacU/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
+/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~bpo60+1-sparc-teFFfB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/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-sparc-UAUacU/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/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-sparc-UAUacU/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/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-sparc-UAUacU/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/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 "."
+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-sparc-UAUacU/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
+/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~bpo60+1-sparc-teFFfB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/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'
+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
@@ -277,8 +397,8 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-sparc-UAUacU/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/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
@@ -289,10 +409,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-sparc-UAUacU/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/samtools-0.1.12a/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/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
@@ -309,24 +429,24 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
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-sparc-UAUacU/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/misc'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/samtools-0.1.12a'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/samtools-0.1.12a/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/samtools-0.1.12a/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/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-sparc-UAUacU/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/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-sparc-UAUacU/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/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
@@ -336,30 +456,29 @@ 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-sparc-UAUacU/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/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-sparc-UAUacU/samtools-0.1.12a'
+make[1]: Nothing to be done for `lib'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/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-sparc-UAUacU/samtools-0.1.12a/examples'
+/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~bpo60+1-sparc-teFFfB/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-sparc-UAUacU/samtools-0.1.12a/examples'
+make[1]: *** Deleting file `ex1.bam'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB/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 20101203-0928
+Build finished at 20110218-1746
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-5f94f0dc-8583-4e98-bc68-e5cff85fb5ae/build/buildd-samtools_0.1.12a-1-sparc-UAUacU
+Purging /var/lib/schroot/mount/squeeze-backports-sparc-sbuild-b44c52b4-d702-4057-b3e6-b9cb317cb01b/build/buildd-samtools_0.1.12a-1~bpo60+1-sparc-teFFfB
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0928
-Build needed 00:06:40, 5208k disc space
+Finished at 20110218-1746
+Build needed 00:03:33, 5208k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
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 -->
-
-<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>
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-<br>
-</body>
--
Processing of sequence alignments in SAM and BAM formats.
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