[build-status: 70526] Log for successful build of sigma-align_1.1.1-1 (dist=unstable)
Build Daemon 1
buildd at linux-m32r.org
Mon Apr 23 23:29:15 JST 2007
Automatic build of sigma-align_1.1.1-1 on mappi005 by sbuild/m32r 0.53
Build started at 20070423-2309
******************************************************************************
Checking available source versions...
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Get:1 http://debian.linux-m32r.org 06_devonian/main sigma-align 1.1.1-1 (dsc) [882B]
Get:2 http://debian.linux-m32r.org 06_devonian/main sigma-align 1.1.1-1 (tar) [124kB]
Get:3 http://debian.linux-m32r.org 06_devonian/main sigma-align 1.1.1-1 (diff) [5210B]
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Download complete and in download only mode
** Using build dependencies supplied by package:
Build-Depends: debhelper (>= 5), xsltproc, docbook-xsl, docbook-xml, libglib2.0-dev
Checking for already installed source dependencies...
debhelper: already installed (5.0.48 >= 5 is satisfied)
xsltproc: already installed (1.1.20-1)
docbook-xsl: already installed (1.72.0.dfsg.1-1)
docbook-xml: already installed (4.5-2)
libglib2.0-dev: already installed (2.12.11-3)
Checking for source dependency conflicts...
Checking correctness of source dependencies...
Kernel: Linux 2.6.20 m32r (m32r)
Toolchain package versions: libc6-dev_2.3.6.ds1-13 linux-kernel-headers_2.6.18-7 gcc-4.1_4.1.1-21 g++-4.1_4.1.1-21 binutils_2.17-3 libstdc++6-4.1-dev_4.1.1-21 libstdc++6_4.1.1-21
------------------------------------------------------------------------------
dpkg-source: extracting sigma-align in sigma-align-1.1.1
dpkg-source: unpacking sigma-align_1.1.1.orig.tar.gz
dpkg-source: applying /debian/buildd/build/sigma-align_1.1.1-1.diff.gz
dpkg-buildpackage: source package is sigma-align
dpkg-buildpackage: source version is 1.1.1-1
dpkg-buildpackage: source changed by Charles Plessy <charles-debian-nospam at plessy.org>
dpkg-buildpackage: host architecture m32r
dpkg-buildpackage: source version without epoch 1.1.1-1
/usr/bin/fakeroot debian/rules clean
./configure --prefix=/build/buildd/sigma-align-1.1.1/debian/sigma-align/usr
checking for a BSD-compatible install... /usr/bin/ginstall -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for a BSD-compatible install... /usr/bin/ginstall -c
checking for main in -lm... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for DEPS... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
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checking for stdlib.h... (cached) yes
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checking sys/time.h usability... yes
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checking glib.h usability... yes
checking glib.h presence... yes
checking for glib.h... yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether time.h and sys/time.h may both be included... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for gettimeofday... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
touch configure-stamp
dh_testdir
dh_testroot
/usr/bin/make distclean
make[1]: Entering directory `/build/buildd/sigma-align-1.1.1'
Making distclean in src
make[2]: Entering directory `/build/buildd/sigma-align-1.1.1/src'
test -z "sigma" || rm -f sigma
rm -f *.o
rm -f *.tab.c
test -z "" || rm -f
rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
rm -rf ./.deps
rm -f Makefile
make[2]: Leaving directory `/build/buildd/sigma-align-1.1.1/src'
Making distclean in .
make[2]: Entering directory `/build/buildd/sigma-align-1.1.1'
test -z "" || rm -f
rm -f config.h stamp-h1
rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
make[2]: Leaving directory `/build/buildd/sigma-align-1.1.1'
rm -f config.status config.cache config.log configure.lineno configure.status.lineno
rm -f Makefile
make[1]: Leaving directory `/build/buildd/sigma-align-1.1.1'
dh_clean configure-stamp manpage-stamp
debian/rules build
./configure --prefix=/build/buildd/sigma-align-1.1.1/debian/sigma-align/usr
checking for a BSD-compatible install... /usr/bin/ginstall -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for a BSD-compatible install... /usr/bin/ginstall -c
checking for main in -lm... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for DEPS... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking glib.h usability... yes
checking glib.h presence... yes
checking for glib.h... yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether time.h and sys/time.h may both be included... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for gettimeofday... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
touch configure-stamp
/usr/bin/make
make[1]: Entering directory `/build/buildd/sigma-align-1.1.1'
/usr/bin/make all-recursive
make[2]: Entering directory `/build/buildd/sigma-align-1.1.1'
Making all in src
make[3]: Entering directory `/build/buildd/sigma-align-1.1.1/src'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DDEBUG -O2 -g -Wall -Werror -g -O2 -MT main.o -MD -MP -MF ".deps/main.Tpo" -c -o main.o main.c; \
then mv -f ".deps/main.Tpo" ".deps/main.Po"; else rm -f ".deps/main.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DDEBUG -O2 -g -Wall -Werror -g -O2 -MT parseopts.o -MD -MP -MF ".deps/parseopts.Tpo" -c -o parseopts.o parseopts.c; \
then mv -f ".deps/parseopts.Tpo" ".deps/parseopts.Po"; else rm -f ".deps/parseopts.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DDEBUG -O2 -g -Wall -Werror -g -O2 -MT readfasta.o -MD -MP -MF ".deps/readfasta.Tpo" -c -o readfasta.o readfasta.c; \
then mv -f ".deps/readfasta.Tpo" ".deps/readfasta.Po"; else rm -f ".deps/readfasta.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DDEBUG -O2 -g -Wall -Werror -g -O2 -MT getbgprobs.o -MD -MP -MF ".deps/getbgprobs.Tpo" -c -o getbgprobs.o getbgprobs.c; \
then mv -f ".deps/getbgprobs.Tpo" ".deps/getbgprobs.Po"; else rm -f ".deps/getbgprobs.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DDEBUG -O2 -g -Wall -Werror -g -O2 -MT setbgprobs.o -MD -MP -MF ".deps/setbgprobs.Tpo" -c -o setbgprobs.o setbgprobs.c; \
then mv -f ".deps/setbgprobs.Tpo" ".deps/setbgprobs.Po"; else rm -f ".deps/setbgprobs.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DDEBUG -O2 -g -Wall -Werror -g -O2 -MT initseqfrags.o -MD -MP -MF ".deps/initseqfrags.Tpo" -c -o initseqfrags.o initseqfrags.c; \
then mv -f ".deps/initseqfrags.Tpo" ".deps/initseqfrags.Po"; else rm -f ".deps/initseqfrags.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DDEBUG -O2 -g -Wall -Werror -g -O2 -MT commonroutines.o -MD -MP -MF ".deps/commonroutines.Tpo" -c -o commonroutines.o commonroutines.c; \
then mv -f ".deps/commonroutines.Tpo" ".deps/commonroutines.Po"; else rm -f ".deps/commonroutines.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DDEBUG -O2 -g -Wall -Werror -g -O2 -MT setbgw.o -MD -MP -MF ".deps/setbgw.Tpo" -c -o setbgw.o setbgw.c; \
then mv -f ".deps/setbgw.Tpo" ".deps/setbgw.Po"; else rm -f ".deps/setbgw.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DDEBUG -O2 -g -Wall -Werror -g -O2 -MT printhelp.o -MD -MP -MF ".deps/printhelp.Tpo" -c -o printhelp.o printhelp.c; \
then mv -f ".deps/printhelp.Tpo" ".deps/printhelp.Po"; else rm -f ".deps/printhelp.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DDEBUG -O2 -g -Wall -Werror -g -O2 -MT blockseq.o -MD -MP -MF ".deps/blockseq.Tpo" -c -o blockseq.o blockseq.c; \
then mv -f ".deps/blockseq.Tpo" ".deps/blockseq.Po"; else rm -f ".deps/blockseq.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DDEBUG -O2 -g -Wall -Werror -g -O2 -MT assemble_frags_to_seqs.o -MD -MP -MF ".deps/assemble_frags_to_seqs.Tpo" -c -o assemble_frags_to_seqs.o assemble_frags_to_seqs.c; \
then mv -f ".deps/assemble_frags_to_seqs.Tpo" ".deps/assemble_frags_to_seqs.Po"; else rm -f ".deps/assemble_frags_to_seqs.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DDEBUG -O2 -g -Wall -Werror -g -O2 -MT print_routines.o -MD -MP -MF ".deps/print_routines.Tpo" -c -o print_routines.o print_routines.c; \
then mv -f ".deps/print_routines.Tpo" ".deps/print_routines.Po"; else rm -f ".deps/print_routines.Tpo"; exit 1; fi
gcc -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DDEBUG -O2 -g -Wall -Werror -g -O2 -o sigma main.o parseopts.o readfasta.o getbgprobs.o setbgprobs.o initseqfrags.o commonroutines.o setbgw.o printhelp.o blockseq.o assemble_frags_to_seqs.o print_routines.o -lglib-2.0 -lm
make[3]: Leaving directory `/build/buildd/sigma-align-1.1.1/src'
make[3]: Entering directory `/build/buildd/sigma-align-1.1.1'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/build/buildd/sigma-align-1.1.1'
make[2]: Leaving directory `/build/buildd/sigma-align-1.1.1'
make[1]: Leaving directory `/build/buildd/sigma-align-1.1.1'
xsltproc -''-nonet \
-''-param man.charmap.use.subset "0" \
-''-param make.year.ranges "1" \
-''-param make.single.year.ranges "1" \
sigma.1.xml
Note: meta version: No productnumber sigma
Note: meta version: No refmiscinfo at class=version sigma
Note: meta version: Using releaseinfo sigma
Note: Writing sigma.1
touch manpage-stamp
/usr/bin/fakeroot debian/rules binary-arch
/usr/bin/make
make[1]: Entering directory `/build/buildd/sigma-align-1.1.1'
/usr/bin/make all-recursive
make[2]: Entering directory `/build/buildd/sigma-align-1.1.1'
Making all in src
make[3]: Entering directory `/build/buildd/sigma-align-1.1.1/src'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/build/buildd/sigma-align-1.1.1/src'
make[3]: Entering directory `/build/buildd/sigma-align-1.1.1'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/build/buildd/sigma-align-1.1.1'
make[2]: Leaving directory `/build/buildd/sigma-align-1.1.1'
make[1]: Leaving directory `/build/buildd/sigma-align-1.1.1'
dh_testdir
dh_testroot
dh_clean -k
dh_installdirs /usr/bin
/usr/bin/make install
make[1]: Entering directory `/build/buildd/sigma-align-1.1.1'
Making install in src
make[2]: Entering directory `/build/buildd/sigma-align-1.1.1/src'
make[3]: Entering directory `/build/buildd/sigma-align-1.1.1/src'
test -z "/build/buildd/sigma-align-1.1.1/debian/sigma-align/usr/bin" || mkdir -p -- "/build/buildd/sigma-align-1.1.1/debian/sigma-align/usr/bin"
/usr/bin/ginstall -c 'sigma' '/build/buildd/sigma-align-1.1.1/debian/sigma-align/usr/bin/sigma'
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/build/buildd/sigma-align-1.1.1/src'
make[2]: Leaving directory `/build/buildd/sigma-align-1.1.1/src'
make[2]: Entering directory `/build/buildd/sigma-align-1.1.1'
make[3]: Entering directory `/build/buildd/sigma-align-1.1.1'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/build/buildd/sigma-align-1.1.1/debian/sigma-align/usr/share/man/man1" || mkdir -p -- "/build/buildd/sigma-align-1.1.1/debian/sigma-align/usr/share/man/man1"
/usr/bin/ginstall -c -m 644 './sigma.1' '/build/buildd/sigma-align-1.1.1/debian/sigma-align/usr/share/man/man1/sigma.1'
make[3]: Leaving directory `/build/buildd/sigma-align-1.1.1'
make[2]: Leaving directory `/build/buildd/sigma-align-1.1.1'
make[1]: Leaving directory `/build/buildd/sigma-align-1.1.1'
dh_testdir
dh_testroot
dh_installchangelogs ChangeLog
dh_installdocs README NOTES
dh_installexamples Background
dh_installman sigma.1
dh_link
dh_strip
dh_compress
dh_fixperms
dh_installdeb
dh_shlibdeps
dh_gencontrol
dpkg-gencontrol: warning: unknown substitution variable ${misc:Depends}
dh_md5sums
dh_builddeb
dpkg-deb: building package `sigma-align' in `../sigma-align_1.1.1-1_m32r.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-buildpackage: binary only upload (no source included)
******************************************************************************
Build finished at 20070423-2328
sigma-align_1.1.1-1_m32r.changes:
Format: 1.7
Date: Sun, 8 Apr 2007 15:26:34 +0900
Source: sigma-align
Binary: sigma-align
Architecture: m32r
Version: 1.1.1-1
Distribution: unstable
Urgency: low
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Charles Plessy <charles-debian-nospam at plessy.org>
Description:
sigma-align - Simple greedy multiple alignment of non-coding DNA sequences
Changes:
sigma-align (1.1.1-1) unstable; urgency=low
.
* New upstream release.
- 1.1 : complete rewrite in C.
- 1.1.1 : fixes a building problem on powerpc.
* Manpage adopted and updated by the upstream author of Sigma.
* Add Subversion repository URL to debian/control.
Files:
aef532a08ce10ebfbfa40e6edabbb53f 25726 science optional sigma-align_1.1.1-1_m32r.deb
/debian/buildd/build/chroot-unstable/build/buildd/sigma-align_1.1.1-1_m32r.deb:
new debian package, version 2.0.
size 25726 bytes: control archive= 1142 bytes.
1152 bytes, 22 lines control
644 bytes, 9 lines md5sums
Package: sigma-align
Version: 1.1.1-1
Section: science
Priority: optional
Architecture: m32r
Depends: libc6 (>= 2.3.5-1), libglib2.0-0 (>= 2.12.9)
Installed-Size: 108
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Description: Simple greedy multiple alignment of non-coding DNA sequences
Sigma ("Simple greedy multiple alignment") is an alignment program with a new
algorithm and scoring scheme designed specifically for non-coding DNA
sequence. It uses a strategy of seeking the best possible gapless local
alignments, at each step making the best possible alignment consistent with
existing alignments, and scores the significance of the alignment based on the
lengths of the aligned fragments and a background model which may be supplied
or estimated from an auxiliary file of intergenic DNA. With real data, while
"correctness" can't be directly quantified for the alignment, running the
PhyloGibbs motif finder on pre-aligned sequence suggests that Sigma's
alignments are superior. It has been published in BMC Bioinformatics. 2006 Mar
16;7:143.
.
Homepage: http://www.imsc.res.in/~rsidd/sigma/
/debian/buildd/build/chroot-unstable/build/buildd/sigma-align_1.1.1-1_m32r.deb:
drwxr-xr-x root/root 0 2007-04-23 23:26 ./
drwxr-xr-x root/root 0 2007-04-23 23:25 ./usr/
drwxr-xr-x root/root 0 2007-04-23 23:26 ./usr/bin/
-rwxr-xr-x root/root 32652 2007-04-23 23:26 ./usr/bin/sigma
drwxr-xr-x root/root 0 2007-04-23 23:25 ./usr/share/
drwxr-xr-x root/root 0 2007-04-23 23:25 ./usr/share/doc/
drwxr-xr-x root/root 0 2007-04-23 23:26 ./usr/share/doc/sigma-align/
drwxr-xr-x root/root 0 2007-04-23 23:26 ./usr/share/doc/sigma-align/examples/
drwxr-xr-x root/root 0 2007-04-08 12:46 ./usr/share/doc/sigma-align/examples/Background/
-rw-r--r-- root/root 437 2007-04-02 21:16 ./usr/share/doc/sigma-align/examples/Background/yeast_bg
-rw-r--r-- root/root 950 2007-04-02 21:30 ./usr/share/doc/sigma-align/examples/Background/README
-rw-r--r-- root/root 1152 2007-04-23 23:12 ./usr/share/doc/sigma-align/copyright
-rw-r--r-- root/root 1771 2007-04-05 02:28 ./usr/share/doc/sigma-align/NOTES
-rw-r--r-- root/root 246 2007-04-07 18:19 ./usr/share/doc/sigma-align/changelog.gz
-rw-r--r-- root/root 3035 2007-04-07 18:32 ./usr/share/doc/sigma-align/README
-rw-r--r-- root/root 345 2007-04-23 23:12 ./usr/share/doc/sigma-align/changelog.Debian.gz
drwxr-xr-x root/root 0 2007-04-23 23:25 ./usr/share/man/
drwxr-xr-x root/root 0 2007-04-23 23:26 ./usr/share/man/man1/
-rw-r--r-- root/root 2555 2007-04-23 23:25 ./usr/share/man/man1/sigma.1.gz
******************************************************************************
Built successfully
Purging /debian/buildd/build/chroot-unstable/build/buildd/sigma-align-1.1.1
------------------------------------------------------------------------------
Reading package lists...
Building dependency tree...
E: Package ptex-bin has no installation candidate
Package ptex-bin is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
apt-get failed.
Failed to reinstall removed packages!
******************************************************************************
Finished at 20070423-2329
Build needed 00:17:15, 1308k disk space
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