Hi Nelson,
It needs g++ to build. If you don't have it installed, it doesn't
build. Thus, there should be a build dependency on it like there
already is for texlive-latex-base, texlive-latex-recommended,
texlive-fonts-recommended. A console log is attached demonstrating a
build that fails, then an install of the g++ package, followed by a
build that succeeds.
Thanks for taking the time to package up mummer, the package is very
useful to us here at SGN.
Rob
Nelson A. de Oliveira wrote:
Hi Robert!
On 9/27/07, Robert Buels <[EMAIL PROTECTED]> wrote:
Justification: fails to build from source
Needs build dependencies on 'g++' or something similar.
I've successfully built mummer here on my machine, using an updated
unstable chroot.
What is exactly the error that you are seeing, please?
Best regards,
Nelson
--
Robert Buels
SGN Bioinformatics Analyst
252A Emerson Hall, Cornell University
Ithaca, NY 14853
Tel: 503-889-8539
[EMAIL PROTECTED]
http://www.sgn.cornell.edu
[EMAIL PROTECTED]:~/c/packages/mummer-3.19$ dpkg-buildpackage -rfakeroot
dpkg-buildpackage: source package is mummer
dpkg-buildpackage: source version is 3.19-1
dpkg-buildpackage: source changed by Andreas Tille <[EMAIL PROTECTED]>
dpkg-buildpackage: host architecture i386
dpkg-buildpackage: source version without epoch 3.19-1
fakeroot debian/rules clean
sed \
-e "s/@cdbs@/, cdbs (>= 0.4.23-1.1), patchutils (>= 0.2.25),
debhelper (>= 5)/g" \
-e "s/^Build-Depends\(\|-Indep\): ,/Build-Depends\1:/g" \
\
-e "s/^Cpu: .*/Architecture: /g" \
-e "/^System: /d" \
\
-e "s/\[cpu: \([^]]*\)\]/\[\`type-handling \\\\\`echo \1 | tr '
' ','\\\\\` any\`\]/g" \
-e "s/\[system: \([^]]*\)\]/\[\`type-handling any \\\\\`echo \1
| tr ' ' ','\\\\\`\`\]/g" \
\
-e "s/\"/\\\\\"/g" \
-e "s/^/echo \"/g" \
-e "s/\\$/\\\\$/g" \
-e "s/$/\"/g" \
< debian/control.in | /bin/sh > debian/control
dpkg-checkbuilddeps -B
test -x debian/rules
test "`id -u`" = 0
/usr/bin/make -f debian/rules reverse-config
make[1]: Entering directory `/home/.rob_clear/packages/mummer-3.19'
make[1]: Nothing to be done for `reverse-config'.
make[1]: Leaving directory `/home/.rob_clear/packages/mummer-3.19'
patches: debian/patches/01sm_docs.diff debian/patches/01sm_scripts.diff
debian/patches/01sm_src.diff debian/patches/02at_Makefile.diff
debian/patches/02at_docs_web.diff
Trying reversed patch debian/patches/02at_docs_web.diff at level
1...0...success.
Trying reversed patch debian/patches/02at_Makefile.diff at level
1...0...success.
Trying reversed patch debian/patches/01sm_src.diff at level 1...0...success.
Trying reversed patch debian/patches/01sm_scripts.diff at level 1...0...success.
Trying reversed patch debian/patches/01sm_docs.diff at level 1...0...success.
if [ "reverse-patches" = "debian/stamp-patched" ] ; then touch
debian/stamp-patched ; \
elif [ "reverse-patches" = "reverse-patches" ] ; then rm -f
debian/stamp-patch* ; \
fi
if [ "reverse-patches" != "reverse-patches" ] ; then \
/usr/bin/make -f debian/rules update-config ; \
fi
for dir in debian/patches ; do \
rm -f $dir/*.log ; \
done
dh_clean
make INSTALL_AUX_BIN_DIR=/usr/lib/mummer/aux_bin INSTALL_BIN_DIR=/usr/bin
INSTALL_SCRIPT_DIR=/usr/share/mummer/scripts -C .; make doc -k clean
/bin/sh: line 0: type: g++: not found
make[1]: Entering directory `/home/.rob_clear/packages/mummer-3.19'
cd /home/.rob_clear/packages/mummer-3.19/src/kurtz; make mummer
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/src/kurtz'
cd libbasedir; make libbase.a
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/libbasedir'
make[3]: `libbase.a' is up to date.
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/libbasedir'
cd streesrc; make libstree.a
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/streesrc'
make[3]: `libstree.a' is up to date.
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/streesrc'
cd mm3src; make mummer
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/mm3src'
/usr/bin/gcc maxmat3.o maxmatopt.o maxmatinp.o findmumcand.o findmaxmat.o
procmaxmat.o ../streesrc/libstree.a ../libbasedir/libbase.a\
-o /home/.rob_clear/packages/mummer-3.19/mummer; chmod 755
/home/.rob_clear/packages/mummer-3.19/mummer
gcc: ../libbasedir/libbase.a-o: No such file or directory
gcc: /home/.rob_clear/packages/mummer-3.19/mummer: No such file or directory
chmod: cannot access `/home/.rob_clear/packages/mummer-3.19/mummer': No such
file or directory
make[3]: *** [mummer] Error 1
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/mm3src'
make[2]: *** [mummer] Error 2
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/src/kurtz'
make[1]: *** [kurtz] Error 2
make[1]: Leaving directory `/home/.rob_clear/packages/mummer-3.19'
/bin/sh: line 0: type: g++: not found
make[1]: Entering directory `/home/.rob_clear/packages/mummer-3.19'
make[1]: *** No rule to make target `doc'.
rm -f *~ core*
cd /home/.rob_clear/packages/mummer-3.19/src/kurtz; make clean
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/src/kurtz'
rm -f *~
cd libbasedir; make clean
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/libbasedir'
rm -f *.splint
rm -f *.[oa] *.dbg.o *.inc *.aux *.dvi *.log *~
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/libbasedir'
cd streesrc; make clean
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/streesrc'
rm -f *.splint
rm -f *.[aox] *~
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/streesrc'
cd mm3src; make clean
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/mm3src'
rm -f *.splint
rm -f *.[ox] shit[123] *~
cd /home/.rob_clear/packages/mummer-3.19; rm -f maxmat3.x maxmat3.dbg.x mummer
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/mm3src'
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/src/kurtz'
cd /home/.rob_clear/packages/mummer-3.19/src/tigr; make clean
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/src/tigr'
rm -f *.o *~
cd /home/.rob_clear/packages/mummer-3.19; rm -f annotate combineMUMs
delta-filter gaps mgaps postnuc postpro prenuc prepro repeat-match show-aligns
show-coords show-tiling show-snps
cd /home/.rob_clear/packages/mummer-3.19/aux_bin; rm -f annotate combineMUMs
delta-filter gaps mgaps postnuc postpro prenuc prepro repeat-match show-aligns
show-coords show-tiling show-snps
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/src/tigr'
cd /home/.rob_clear/packages/mummer-3.19/scripts; make clean
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/scripts'
rm -f *~
cd /home/.rob_clear/packages/mummer-3.19; rm -f exact-tandems mapview
mummerplot nucmer promer run-mummer1 run-mummer3 nucmer2xfig
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/scripts'
cd /home/.rob_clear/packages/mummer-3.19/docs; make clean
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/docs'
rm -f *.dvi *.aux *.log *.out *~ maxmat3man.pdf
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/docs'
make[1]: Leaving directory `/home/.rob_clear/packages/mummer-3.19'
make: [makefile-clean] Error 2 (ignored)
rm -f debian/stamp-makefile-build
rm -f src/tigr/aux_bin
rm -rf bin
# Add here commands to clean up after the build process.
/usr/bin/make distclean
/bin/sh: line 0: type: g++: not found
make[1]: Entering directory `/home/.rob_clear/packages/mummer-3.19'
make[1]: *** No rule to make target `distclean'. Stop.
make[1]: Leaving directory `/home/.rob_clear/packages/mummer-3.19'
make: [clean] Error 2 (ignored)
dpkg-source -b mummer-3.19
dpkg-source: building mummer using existing mummer_3.19.orig.tar.gz
dpkg-source: building mummer in mummer_3.19-1.diff.gz
dpkg-source: building mummer in mummer_3.19-1.dsc
debian/rules build
sed \
-e "s/@cdbs@/, cdbs (>= 0.4.23-1.1), patchutils (>= 0.2.25),
debhelper (>= 5)/g" \
-e "s/^Build-Depends\(\|-Indep\): ,/Build-Depends\1:/g" \
\
-e "s/^Cpu: .*/Architecture: /g" \
-e "/^System: /d" \
\
-e "s/\[cpu: \([^]]*\)\]/\[\`type-handling \\\\\`echo \1 | tr '
' ','\\\\\` any\`\]/g" \
-e "s/\[system: \([^]]*\)\]/\[\`type-handling any \\\\\`echo \1
| tr ' ' ','\\\\\`\`\]/g" \
\
-e "s/\"/\\\\\"/g" \
-e "s/^/echo \"/g" \
-e "s/\\$/\\\\$/g" \
-e "s/$/\"/g" \
< debian/control.in | /bin/sh > debian/control
dpkg-checkbuilddeps -B
test -x debian/rules
mkdir -p "."
/usr/bin/make -f debian/rules reverse-config
make[1]: Entering directory `/home/.rob_clear/packages/mummer-3.19'
make[1]: Nothing to be done for `reverse-config'.
make[1]: Leaving directory `/home/.rob_clear/packages/mummer-3.19'
patches: debian/patches/01sm_docs.diff debian/patches/01sm_scripts.diff
debian/patches/01sm_src.diff debian/patches/02at_Makefile.diff
debian/patches/02at_docs_web.diff
Trying patch debian/patches/01sm_docs.diff at level 1...0...success.
Trying patch debian/patches/01sm_scripts.diff at level 1...0...success.
Trying patch debian/patches/01sm_src.diff at level 1...0...success.
Trying patch debian/patches/02at_Makefile.diff at level 1...0...success.
Trying patch debian/patches/02at_docs_web.diff at level 1...0...success.
if [ "debian/stamp-patched" = "debian/stamp-patched" ] ; then touch
debian/stamp-patched ; \
elif [ "debian/stamp-patched" = "reverse-patches" ] ; then rm -f
debian/stamp-patch* ; \
fi
if [ "debian/stamp-patched" != "reverse-patches" ] ; then \
/usr/bin/make -f debian/rules update-config ; \
fi
make[1]: Entering directory `/home/.rob_clear/packages/mummer-3.19'
make[1]: Nothing to be done for `update-config'.
make[1]: Leaving directory `/home/.rob_clear/packages/mummer-3.19'
make INSTALL_AUX_BIN_DIR=/usr/lib/mummer/aux_bin INSTALL_BIN_DIR=/usr/bin
INSTALL_SCRIPT_DIR=/usr/share/mummer/scripts -C .; make doc
/bin/sh: line 0: type: g++: not found
make[1]: Entering directory `/home/.rob_clear/packages/mummer-3.19'
mkdir -p /home/.rob_clear/packages/mummer-3.19/bin
cd /home/.rob_clear/packages/mummer-3.19/src/kurtz; make mummer
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/src/kurtz'
make -C libbasedir libbase.a
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/libbasedir'
/usr/bin/gcc -Wall -O3 -c -o cleanMUMcand.o cleanMUMcand.c
/usr/bin/gcc -Wall -O3 -c -o clock.o clock.c
/usr/bin/gcc -Wall -O3 -c -o mapfile.o mapfile.c
/usr/bin/gcc -Wall -O3 -c -o multiseq.o multiseq.c
/usr/bin/gcc -Wall -O3 -c -o procopt.o procopt.c
/usr/bin/gcc -Wall -O3 -c -o safescpy.o safescpy.c
/usr/bin/gcc -Wall -O3 -c -o seterror.o seterror.c
/usr/bin/gcc -Wall -O3 -c -o space.o space.c
ar sruv libbase.a cleanMUMcand.o clock.o mapfile.o multiseq.o procopt.o
safescpy.o seterror.o space.o
ar: creating libbase.a
a - cleanMUMcand.o
a - clock.o
a - mapfile.o
a - multiseq.o
a - procopt.o
a - safescpy.o
a - seterror.o
a - space.o
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/libbasedir'
make -C streesrc libstree.a
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/streesrc'
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o construct.o
construct.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o access.o access.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o scanpref.o scanpref.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o linkloc.o linkloc.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o depthtab.o depthtab.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o ex2leav.o ex2leav.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o dfs.o dfs.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o overmax.o overmax.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o oversucc.o oversucc.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o addleafcount.o
addleafcount.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o iterator.o iterator.c
ar sruv libstree.a construct.o access.o scanpref.o linkloc.o depthtab.o
ex2leav.o dfs.o overmax.o oversucc.o addleafcount.o iterator.o
ar: creating libstree.a
a - construct.o
a - access.o
a - scanpref.o
a - linkloc.o
a - depthtab.o
a - ex2leav.o
a - dfs.o
a - overmax.o
a - oversucc.o
a - addleafcount.o
a - iterator.o
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/streesrc'
make BIN_DIR="../../../bin" -C mm3src mummer
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/mm3src'
/usr/bin/gcc -I../libbasedir -I../streesrc -Wall -O3 -c -o maxmat3.o maxmat3.c
/usr/bin/gcc -I../libbasedir -I../streesrc -Wall -O3 -c -o maxmatopt.o
maxmatopt.c
/usr/bin/gcc -I../libbasedir -I../streesrc -Wall -O3 -c -o maxmatinp.o
maxmatinp.c
/usr/bin/gcc -I../libbasedir -I../streesrc -Wall -O3 -c -o findmumcand.o
findmumcand.c
/usr/bin/gcc -I../libbasedir -I../streesrc -Wall -O3 -c -o findmaxmat.o
findmaxmat.c
/usr/bin/gcc -I../libbasedir -I../streesrc -Wall -O3 -c -o procmaxmat.o
procmaxmat.c
/usr/bin/gcc maxmat3.o maxmatopt.o maxmatinp.o findmumcand.o findmaxmat.o
procmaxmat.o ../streesrc/libstree.a ../libbasedir/libbase.a \
-o ../../../bin/mummer && chmod 755 ../../../bin/mummer
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/mm3src'
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/src/kurtz'
cd /home/.rob_clear/packages/mummer-3.19/src/tigr; make all
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/src/tigr'
Wall -O3 tigrinc.cc -c -o tigrinc.o
make[2]: Wall: Command not found
make[2]: [tigrinc.o] Error 127 (ignored)
Wall -O3 annotate.cc tigrinc.o -o
/home/.rob_clear/packages/mummer-3.19/bin/annotate && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/annotate
/bin/sh: Wall: command not found
make[2]: [annotate] Error 127 (ignored)
Wall -O3 combineMUMs.cc tigrinc.o -o
/home/.rob_clear/packages/mummer-3.19/bin/combineMUMs && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/combineMUMs
/bin/sh: Wall: command not found
make[2]: [combineMUMs] Error 127 (ignored)
Wall -O3 delta.cc -c -o delta.o
make[2]: Wall: Command not found
make[2]: [delta.o] Error 127 (ignored)
Wall -O3 delta-filter.cc tigrinc.o delta.o -o
/home/.rob_clear/packages/mummer-3.19/bin/delta-filter && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/delta-filter
/bin/sh: Wall: command not found
make[2]: [delta-filter] Error 127 (ignored)
Wall -O3 gaps.cc tigrinc.o -o /home/.rob_clear/packages/mummer-3.19/bin/gaps &&
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/gaps
/bin/sh: Wall: command not found
make[2]: [gaps] Error 127 (ignored)
Wall -O3 mgaps.cc tigrinc.o -o /home/.rob_clear/packages/mummer-3.19/bin/mgaps
&& chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/mgaps
/bin/sh: Wall: command not found
make[2]: [mgaps] Error 127 (ignored)
Wall -O3 sw_align.cc -c -o sw_align.o
make[2]: Wall: Command not found
make[2]: [sw_align.o] Error 127 (ignored)
Wall -O3 postnuc.cc tigrinc.o sw_align.o -o
/home/.rob_clear/packages/mummer-3.19/aux_bin/postnuc && chmod 755
/home/.rob_clear/packages/mummer-3.19/aux_bin/postnuc
/bin/sh: Wall: command not found
make[2]: [postnuc] Error 127 (ignored)
Wall -O3 translate.cc -c -o translate.o
make[2]: Wall: Command not found
make[2]: [translate.o] Error 127 (ignored)
Wall -O3 postpro.cc tigrinc.o sw_align.o translate.o -o
/home/.rob_clear/packages/mummer-3.19/aux_bin/postpro && chmod 755
/home/.rob_clear/packages/mummer-3.19/aux_bin/postpro
/bin/sh: Wall: command not found
make[2]: [postpro] Error 127 (ignored)
Wall -O3 prenuc.cc tigrinc.o -o
/home/.rob_clear/packages/mummer-3.19/aux_bin/prenuc && chmod 755
/home/.rob_clear/packages/mummer-3.19/aux_bin/prenuc
/bin/sh: Wall: command not found
make[2]: [prenuc] Error 127 (ignored)
Wall -O3 prepro.cc tigrinc.o translate.o -o
/home/.rob_clear/packages/mummer-3.19/aux_bin/prepro && chmod 755
/home/.rob_clear/packages/mummer-3.19/aux_bin/prepro
/bin/sh: Wall: command not found
make[2]: [prepro] Error 127 (ignored)
Wall -O3 repeat-match.cc tigrinc.o -o
/home/.rob_clear/packages/mummer-3.19/bin/repeat-match && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/repeat-match
/bin/sh: Wall: command not found
make[2]: [repeat-match] Error 127 (ignored)
Wall -O3 show-aligns.cc tigrinc.o translate.o delta.o -o
/home/.rob_clear/packages/mummer-3.19/bin/show-aligns && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/show-aligns
/bin/sh: Wall: command not found
make[2]: [show-aligns] Error 127 (ignored)
Wall -O3 show-coords.cc tigrinc.o delta.o -o
/home/.rob_clear/packages/mummer-3.19/bin/show-coords && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/show-coords
/bin/sh: Wall: command not found
make[2]: [show-coords] Error 127 (ignored)
Wall -O3 show-tiling.cc tigrinc.o delta.o -o
/home/.rob_clear/packages/mummer-3.19/bin/show-tiling && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/show-tiling
/bin/sh: Wall: command not found
make[2]: [show-tiling] Error 127 (ignored)
Wall -O3 show-snps.cc tigrinc.o translate.o delta.o -o
/home/.rob_clear/packages/mummer-3.19/bin/show-snps && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/show-snps
/bin/sh: Wall: command not found
make[2]: [show-snps] Error 127 (ignored)
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/src/tigr'
cd /home/.rob_clear/packages/mummer-3.19/scripts; make all
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/scripts'
/bin/sed -e 's?__BIN_DIR?/usr/bin?g' \
-e 's?__SCRIPT_DIR?/usr/share/mummer/scripts?g' \
exact-tandems.sh >
/home/.rob_clear/packages/mummer-3.19/bin/exact-tandems
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/exact-tandems
/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \
-e 's?__SCRIPT_DIR?/usr/share/mummer/scripts?g' \
mapview.pl > /home/.rob_clear/packages/mummer-3.19/bin/mapview
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/mapview
/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \
-e 's?__SCRIPT_DIR?/usr/share/mummer/scripts?g' \
-e 's?__BIN_DIR?/usr/bin?g' \
mummerplot.pl >
/home/.rob_clear/packages/mummer-3.19/bin/mummerplot
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/mummerplot
/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \
-e 's?__SCRIPT_DIR?/usr/share/mummer/scripts?g' \
-e 's?__AUX_BIN_DIR?/usr/lib/mummer/aux_bin?g' \
-e 's?__BIN_DIR?/usr/bin?g' \
nucmer.pl > /home/.rob_clear/packages/mummer-3.19/bin/nucmer
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/nucmer
/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \
-e 's?__SCRIPT_DIR?/usr/share/mummer/scripts?g' \
-e 's?__AUX_BIN_DIR?/usr/lib/mummer/aux_bin?g' \
-e 's?__BIN_DIR?/usr/bin?g' \
promer.pl > /home/.rob_clear/packages/mummer-3.19/bin/promer
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/promer
/bin/sed -e 's?__BIN_DIR?/usr/bin?g' \
run-mummer1.sh >
/home/.rob_clear/packages/mummer-3.19/bin/run-mummer1
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/run-mummer1
/bin/sed -e 's?__BIN_DIR?/usr/bin?g' \
run-mummer3.sh >
/home/.rob_clear/packages/mummer-3.19/bin/run-mummer3
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/run-mummer3
/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \
nucmer2xfig.pl >
/home/.rob_clear/packages/mummer-3.19/bin/nucmer2xfig
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/nucmer2xfig
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/scripts'
make[1]: Leaving directory `/home/.rob_clear/packages/mummer-3.19'
/bin/sh: line 0: type: g++: not found
make[1]: Entering directory `/home/.rob_clear/packages/mummer-3.19'
cd /home/.rob_clear/packages/mummer-3.19/docs; make
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/docs'
pdflatex maxmat3man
This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6)
%&-line parsing enabled.
entering extended mode
(./maxmat3man.tex
LaTeX2e <2005/12/01>
Babel <v3.8h> and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, loaded.
(/usr/share/texmf-texlive/tex/latex/base/article.cls
Document Class: article 2005/09/16 v1.4f Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/size12.clo))
(/usr/share/texmf-texlive/tex/latex/ltxmisc/a4wide.sty
(/usr/share/texmf-texlive/tex/latex/ntgclass/a4.sty))
(/usr/share/texmf-texlive/tex/latex/base/alltt.sty)
(/usr/share/texmf-texlive/tex/latex/tools/xspace.sty)
(/usr/share/texmf-texlive/tex/latex/psnfss/times.sty) (./skaff.sty)
(./optionman.sty)
No file maxmat3man.aux.
(/usr/share/texmf-texlive/tex/latex/psnfss/ot1ptm.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/omsptm.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/ot1pcr.fd)
LaTeX Warning: Reference `SecBasicNotions' on page 1 undefined on input line 34
.
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
LaTeX Warning: Reference `SecBasicNotions' on page 2 undefined on input line 10
2.
[2] [3] [4] [5] [6] (./maxmat3man.aux)
LaTeX Warning: There were undefined references.
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
){/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc}</usr/share/texmf-texli
ve/fonts/type1/bluesky/cm/cmmi12.pfb></usr/share/texmf-texlive/fonts/type1/blue
sky/cm/cmmi8.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr12.pfb></u
sr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr8.pfb></usr/share/texmf-texliv
e/fonts/type1/bluesky/cm/cmsy10.pfb></usr/share/texmf-texlive/fonts/type1/blues
ky/cm/cmsy7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti12.pfb></u
sr/share/texmf-texlive/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texmf-tex
live/fonts/type1/urw/times/utmb8a.pfb></usr/share/texmf-texlive/fonts/type1/urw
/times/utmr8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmri8a.pfb>
Output written on maxmat3man.pdf (6 pages, 104265 bytes).
Transcript written on maxmat3man.log.
pdflatex maxmat3man
This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6)
%&-line parsing enabled.
entering extended mode
(./maxmat3man.tex
LaTeX2e <2005/12/01>
Babel <v3.8h> and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, loaded.
(/usr/share/texmf-texlive/tex/latex/base/article.cls
Document Class: article 2005/09/16 v1.4f Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/size12.clo))
(/usr/share/texmf-texlive/tex/latex/ltxmisc/a4wide.sty
(/usr/share/texmf-texlive/tex/latex/ntgclass/a4.sty))
(/usr/share/texmf-texlive/tex/latex/base/alltt.sty)
(/usr/share/texmf-texlive/tex/latex/tools/xspace.sty)
(/usr/share/texmf-texlive/tex/latex/psnfss/times.sty) (./skaff.sty)
(./optionman.sty) (./maxmat3man.aux)
(/usr/share/texmf-texlive/tex/latex/psnfss/ot1ptm.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/omsptm.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fonts/m
ap/pdftex/updmap/pdftex.map}] [2] [3] [4] [5] [6] (./maxmat3man.aux) ){/usr/sha
re/texmf-texlive/fonts/enc/dvips/base/8r.enc}</usr/share/texmf-texlive/fonts/ty
pe1/bluesky/cm/cmmi12.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi
8.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr12.pfb></usr/share/te
xmf-texlive/fonts/type1/bluesky/cm/cmr8.pfb></usr/share/texmf-texlive/fonts/typ
e1/bluesky/cm/cmsy10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy7
.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti12.pfb></usr/share/te
xmf-texlive/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texmf-texlive/fonts/
type1/urw/times/utmb8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmr
8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmri8a.pfb>
Output written on maxmat3man.pdf (6 pages, 103587 bytes).
Transcript written on maxmat3man.log.
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/docs'
make[1]: Leaving directory `/home/.rob_clear/packages/mummer-3.19'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary
sed \
-e "s/@cdbs@/, cdbs (>= 0.4.23-1.1), patchutils (>= 0.2.25),
debhelper (>= 5)/g" \
-e "s/^Build-Depends\(\|-Indep\): ,/Build-Depends\1:/g" \
\
-e "s/^Cpu: .*/Architecture: /g" \
-e "/^System: /d" \
\
-e "s/\[cpu: \([^]]*\)\]/\[\`type-handling \\\\\`echo \1 | tr '
' ','\\\\\` any\`\]/g" \
-e "s/\[system: \([^]]*\)\]/\[\`type-handling any \\\\\`echo \1
| tr ' ' ','\\\\\`\`\]/g" \
\
-e "s/\"/\\\\\"/g" \
-e "s/^/echo \"/g" \
-e "s/\\$/\\\\$/g" \
-e "s/$/\"/g" \
< debian/control.in | /bin/sh > debian/control
dpkg-checkbuilddeps -B
test -x debian/rules
test "`id -u`" = 0
dh_clean -k
dh_installdirs -A
mkdir -p "."
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install
target
dh_installdirs -pmummer-doc
dh_installdocs -pmummer-doc ./README
dh_installexamples -pmummer-doc
dh_installman -pmummer-doc
dh_installinfo -pmummer-doc
dh_installmenu -pmummer-doc
dh_installcron -pmummer-doc
dh_installinit -pmummer-doc
dh_installdebconf -pmummer-doc
dh_installemacsen -pmummer-doc
dh_installcatalogs -pmummer-doc
dh_installpam -pmummer-doc
dh_installlogrotate -pmummer-doc
dh_installlogcheck -pmummer-doc
dh_installmime -pmummer-doc
dh_installchangelogs -pmummer-doc ./ChangeLog
dh_installudev -pmummer-doc
dh_install -pmummer-doc
dh_link -pmummer-doc
dh_strip -pmummer-doc
dh_compress -pmummer-doc -X .pdf
dh_fixperms -pmummer-doc
dh_makeshlibs -pmummer-doc
dh_installdeb -pmummer-doc
dh_perl -pmummer-doc
dh_shlibdeps -pmummer-doc
dh_gencontrol -pmummer-doc
dh_md5sums -pmummer-doc
dh_builddeb -pmummer-doc
dpkg-deb: building package `mummer-doc' in `../mummer-doc_3.19-1_all.deb'.
dh_installdirs -pmummer
# install desktop file
# dh_desktop
# prevent name space pollution because libgd-tools contains /usr/bin/annotate
mv bin/annotate bin/mummer-annotate
mv: cannot stat `bin/annotate': No such file or directory
make: *** [install/mummer] Error 1
[EMAIL PROTECTED]:~/c/packages/mummer-3.19$ sudo apt-get install g++
Reading package lists... Done
Building dependency tree... Done
The following extra packages will be installed:
g++-4.2 libstdc++6-4.2-dev
Suggested packages:
g++-multilib g++-4.2-multilib gcc-4.2-doc libstdc++6-4.2-doc
The following NEW packages will be installed:
g++ g++-4.2 libstdc++6-4.2-dev
0 upgraded, 3 newly installed, 0 to remove and 1421 not upgraded.
Need to get 0B/3964kB of archives.
After unpacking 14.9MB of additional disk space will be used.
Do you want to continue [Y/n]?
Selecting previously deselected package libstdc++6-4.2-dev.
(Reading database ... 206585 files and directories currently installed.)
Unpacking libstdc++6-4.2-dev (from .../libstdc++6-4.2-dev_4.2.1-5_i386.deb) ...
Selecting previously deselected package g++-4.2.
Unpacking g++-4.2 (from .../g++-4.2_4.2.1-5_i386.deb) ...
Selecting previously deselected package g++.
Unpacking g++ (from .../g++_4%3a4.2.1-6_i386.deb) ...
Setting up g++-4.2 (4.2.1-5) ...
Setting up libstdc++6-4.2-dev (4.2.1-5) ...
Setting up g++ (4.2.1-6) ...
[EMAIL PROTECTED]:~/c/packages/mummer-3.19$ dpkg-buildpackage -rfakeroot
dpkg-buildpackage: source package is mummer
dpkg-buildpackage: source version is 3.19-1
dpkg-buildpackage: source changed by Andreas Tille <[EMAIL PROTECTED]>
dpkg-buildpackage: host architecture i386
dpkg-buildpackage: source version without epoch 3.19-1
fakeroot debian/rules clean
sed \
-e "s/@cdbs@/, cdbs (>= 0.4.23-1.1), patchutils (>= 0.2.25),
debhelper (>= 5)/g" \
-e "s/^Build-Depends\(\|-Indep\): ,/Build-Depends\1:/g" \
\
-e "s/^Cpu: .*/Architecture: /g" \
-e "/^System: /d" \
\
-e "s/\[cpu: \([^]]*\)\]/\[\`type-handling \\\\\`echo \1 | tr '
' ','\\\\\` any\`\]/g" \
-e "s/\[system: \([^]]*\)\]/\[\`type-handling any \\\\\`echo \1
| tr ' ' ','\\\\\`\`\]/g" \
\
-e "s/\"/\\\\\"/g" \
-e "s/^/echo \"/g" \
-e "s/\\$/\\\\$/g" \
-e "s/$/\"/g" \
< debian/control.in | /bin/sh > debian/control
dpkg-checkbuilddeps -B
test -x debian/rules
test "`id -u`" = 0
/usr/bin/make -f debian/rules reverse-config
make[1]: Entering directory `/home/.rob_clear/packages/mummer-3.19'
make[1]: Nothing to be done for `reverse-config'.
make[1]: Leaving directory `/home/.rob_clear/packages/mummer-3.19'
patches: debian/patches/01sm_docs.diff debian/patches/01sm_scripts.diff
debian/patches/01sm_src.diff debian/patches/02at_Makefile.diff
debian/patches/02at_docs_web.diff
Trying reversed patch debian/patches/02at_docs_web.diff at level
1...0...success.
Trying reversed patch debian/patches/02at_Makefile.diff at level
1...0...success.
Trying reversed patch debian/patches/01sm_src.diff at level 1...0...success.
Trying reversed patch debian/patches/01sm_scripts.diff at level 1...0...success.
Trying reversed patch debian/patches/01sm_docs.diff at level 1...0...success.
if [ "reverse-patches" = "debian/stamp-patched" ] ; then touch
debian/stamp-patched ; \
elif [ "reverse-patches" = "reverse-patches" ] ; then rm -f
debian/stamp-patch* ; \
fi
if [ "reverse-patches" != "reverse-patches" ] ; then \
/usr/bin/make -f debian/rules update-config ; \
fi
for dir in debian/patches ; do \
rm -f $dir/*.log ; \
done
dh_clean
make INSTALL_AUX_BIN_DIR=/usr/lib/mummer/aux_bin INSTALL_BIN_DIR=/usr/bin
INSTALL_SCRIPT_DIR=/usr/share/mummer/scripts -C .; make doc -k clean
make[1]: Entering directory `/home/.rob_clear/packages/mummer-3.19'
cd /home/.rob_clear/packages/mummer-3.19/src/kurtz; make mummer
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/src/kurtz'
cd libbasedir; make libbase.a
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/libbasedir'
make[3]: `libbase.a' is up to date.
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/libbasedir'
cd streesrc; make libstree.a
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/streesrc'
make[3]: `libstree.a' is up to date.
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/streesrc'
cd mm3src; make mummer
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/mm3src'
/usr/bin/gcc maxmat3.o maxmatopt.o maxmatinp.o findmumcand.o findmaxmat.o
procmaxmat.o ../streesrc/libstree.a ../libbasedir/libbase.a\
-o /home/.rob_clear/packages/mummer-3.19/mummer; chmod 755
/home/.rob_clear/packages/mummer-3.19/mummer
gcc: ../libbasedir/libbase.a-o: No such file or directory
gcc: /home/.rob_clear/packages/mummer-3.19/mummer: No such file or directory
chmod: cannot access `/home/.rob_clear/packages/mummer-3.19/mummer': No such
file or directory
make[3]: *** [mummer] Error 1
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/mm3src'
make[2]: *** [mummer] Error 2
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/src/kurtz'
make[1]: *** [kurtz] Error 2
make[1]: Leaving directory `/home/.rob_clear/packages/mummer-3.19'
make[1]: Entering directory `/home/.rob_clear/packages/mummer-3.19'
make[1]: *** No rule to make target `doc'.
rm -f *~ core*
cd /home/.rob_clear/packages/mummer-3.19/src/kurtz; make clean
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/src/kurtz'
rm -f *~
cd libbasedir; make clean
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/libbasedir'
rm -f *.splint
rm -f *.[oa] *.dbg.o *.inc *.aux *.dvi *.log *~
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/libbasedir'
cd streesrc; make clean
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/streesrc'
rm -f *.splint
rm -f *.[aox] *~
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/streesrc'
cd mm3src; make clean
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/mm3src'
rm -f *.splint
rm -f *.[ox] shit[123] *~
cd /home/.rob_clear/packages/mummer-3.19; rm -f maxmat3.x maxmat3.dbg.x mummer
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/mm3src'
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/src/kurtz'
cd /home/.rob_clear/packages/mummer-3.19/src/tigr; make clean
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/src/tigr'
rm -f *.o *~
cd /home/.rob_clear/packages/mummer-3.19; rm -f annotate combineMUMs
delta-filter gaps mgaps postnuc postpro prenuc prepro repeat-match show-aligns
show-coords show-tiling show-snps
cd /home/.rob_clear/packages/mummer-3.19/aux_bin; rm -f annotate combineMUMs
delta-filter gaps mgaps postnuc postpro prenuc prepro repeat-match show-aligns
show-coords show-tiling show-snps
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/src/tigr'
cd /home/.rob_clear/packages/mummer-3.19/scripts; make clean
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/scripts'
rm -f *~
cd /home/.rob_clear/packages/mummer-3.19; rm -f exact-tandems mapview
mummerplot nucmer promer run-mummer1 run-mummer3 nucmer2xfig
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/scripts'
cd /home/.rob_clear/packages/mummer-3.19/docs; make clean
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/docs'
rm -f *.dvi *.aux *.log *.out *~ maxmat3man.pdf
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/docs'
make[1]: Leaving directory `/home/.rob_clear/packages/mummer-3.19'
make: [makefile-clean] Error 2 (ignored)
rm -f debian/stamp-makefile-build
rm -f src/tigr/aux_bin
rm -rf bin
# Add here commands to clean up after the build process.
/usr/bin/make distclean
make[1]: Entering directory `/home/.rob_clear/packages/mummer-3.19'
make[1]: *** No rule to make target `distclean'. Stop.
make[1]: Leaving directory `/home/.rob_clear/packages/mummer-3.19'
make: [clean] Error 2 (ignored)
dpkg-source -b mummer-3.19
dpkg-source: building mummer using existing mummer_3.19.orig.tar.gz
dpkg-source: building mummer in mummer_3.19-1.diff.gz
dpkg-source: building mummer in mummer_3.19-1.dsc
debian/rules build
sed \
-e "s/@cdbs@/, cdbs (>= 0.4.23-1.1), patchutils (>= 0.2.25),
debhelper (>= 5)/g" \
-e "s/^Build-Depends\(\|-Indep\): ,/Build-Depends\1:/g" \
\
-e "s/^Cpu: .*/Architecture: /g" \
-e "/^System: /d" \
\
-e "s/\[cpu: \([^]]*\)\]/\[\`type-handling \\\\\`echo \1 | tr '
' ','\\\\\` any\`\]/g" \
-e "s/\[system: \([^]]*\)\]/\[\`type-handling any \\\\\`echo \1
| tr ' ' ','\\\\\`\`\]/g" \
\
-e "s/\"/\\\\\"/g" \
-e "s/^/echo \"/g" \
-e "s/\\$/\\\\$/g" \
-e "s/$/\"/g" \
< debian/control.in | /bin/sh > debian/control
dpkg-checkbuilddeps -B
test -x debian/rules
mkdir -p "."
/usr/bin/make -f debian/rules reverse-config
make[1]: Entering directory `/home/.rob_clear/packages/mummer-3.19'
make[1]: Nothing to be done for `reverse-config'.
make[1]: Leaving directory `/home/.rob_clear/packages/mummer-3.19'
patches: debian/patches/01sm_docs.diff debian/patches/01sm_scripts.diff
debian/patches/01sm_src.diff debian/patches/02at_Makefile.diff
debian/patches/02at_docs_web.diff
Trying patch debian/patches/01sm_docs.diff at level 1...0...success.
Trying patch debian/patches/01sm_scripts.diff at level 1...0...success.
Trying patch debian/patches/01sm_src.diff at level 1...0...success.
Trying patch debian/patches/02at_Makefile.diff at level 1...0...success.
Trying patch debian/patches/02at_docs_web.diff at level 1...0...success.
if [ "debian/stamp-patched" = "debian/stamp-patched" ] ; then touch
debian/stamp-patched ; \
elif [ "debian/stamp-patched" = "reverse-patches" ] ; then rm -f
debian/stamp-patch* ; \
fi
if [ "debian/stamp-patched" != "reverse-patches" ] ; then \
/usr/bin/make -f debian/rules update-config ; \
fi
make[1]: Entering directory `/home/.rob_clear/packages/mummer-3.19'
make[1]: Nothing to be done for `update-config'.
make[1]: Leaving directory `/home/.rob_clear/packages/mummer-3.19'
make INSTALL_AUX_BIN_DIR=/usr/lib/mummer/aux_bin INSTALL_BIN_DIR=/usr/bin
INSTALL_SCRIPT_DIR=/usr/share/mummer/scripts -C .; make doc
make[1]: Entering directory `/home/.rob_clear/packages/mummer-3.19'
mkdir -p /home/.rob_clear/packages/mummer-3.19/bin
cd /home/.rob_clear/packages/mummer-3.19/src/kurtz; make mummer
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/src/kurtz'
make -C libbasedir libbase.a
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/libbasedir'
/usr/bin/gcc -Wall -O3 -c -o cleanMUMcand.o cleanMUMcand.c
/usr/bin/gcc -Wall -O3 -c -o clock.o clock.c
/usr/bin/gcc -Wall -O3 -c -o mapfile.o mapfile.c
/usr/bin/gcc -Wall -O3 -c -o multiseq.o multiseq.c
/usr/bin/gcc -Wall -O3 -c -o procopt.o procopt.c
/usr/bin/gcc -Wall -O3 -c -o safescpy.o safescpy.c
/usr/bin/gcc -Wall -O3 -c -o seterror.o seterror.c
/usr/bin/gcc -Wall -O3 -c -o space.o space.c
ar sruv libbase.a cleanMUMcand.o clock.o mapfile.o multiseq.o procopt.o
safescpy.o seterror.o space.o
ar: creating libbase.a
a - cleanMUMcand.o
a - clock.o
a - mapfile.o
a - multiseq.o
a - procopt.o
a - safescpy.o
a - seterror.o
a - space.o
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/libbasedir'
make -C streesrc libstree.a
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/streesrc'
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o construct.o
construct.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o access.o access.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o scanpref.o scanpref.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o linkloc.o linkloc.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o depthtab.o depthtab.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o ex2leav.o ex2leav.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o dfs.o dfs.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o overmax.o overmax.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o oversucc.o oversucc.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o addleafcount.o
addleafcount.c
/usr/bin/gcc -I../libbasedir -DSTREEHUGE -Wall -O3 -c -o iterator.o iterator.c
ar sruv libstree.a construct.o access.o scanpref.o linkloc.o depthtab.o
ex2leav.o dfs.o overmax.o oversucc.o addleafcount.o iterator.o
ar: creating libstree.a
a - construct.o
a - access.o
a - scanpref.o
a - linkloc.o
a - depthtab.o
a - ex2leav.o
a - dfs.o
a - overmax.o
a - oversucc.o
a - addleafcount.o
a - iterator.o
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/streesrc'
make BIN_DIR="../../../bin" -C mm3src mummer
make[3]: Entering directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/mm3src'
/usr/bin/gcc -I../libbasedir -I../streesrc -Wall -O3 -c -o maxmat3.o maxmat3.c
/usr/bin/gcc -I../libbasedir -I../streesrc -Wall -O3 -c -o maxmatopt.o
maxmatopt.c
/usr/bin/gcc -I../libbasedir -I../streesrc -Wall -O3 -c -o maxmatinp.o
maxmatinp.c
/usr/bin/gcc -I../libbasedir -I../streesrc -Wall -O3 -c -o findmumcand.o
findmumcand.c
/usr/bin/gcc -I../libbasedir -I../streesrc -Wall -O3 -c -o findmaxmat.o
findmaxmat.c
/usr/bin/gcc -I../libbasedir -I../streesrc -Wall -O3 -c -o procmaxmat.o
procmaxmat.c
/usr/bin/gcc maxmat3.o maxmatopt.o maxmatinp.o findmumcand.o findmaxmat.o
procmaxmat.o ../streesrc/libstree.a ../libbasedir/libbase.a \
-o ../../../bin/mummer && chmod 755 ../../../bin/mummer
make[3]: Leaving directory
`/home/.rob_clear/packages/mummer-3.19/src/kurtz/mm3src'
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/src/kurtz'
cd /home/.rob_clear/packages/mummer-3.19/src/tigr; make all
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/src/tigr'
/usr/bin/g++ -Wall -O3 tigrinc.cc -c -o tigrinc.o
/usr/bin/g++ -Wall -O3 annotate.cc tigrinc.o -o
/home/.rob_clear/packages/mummer-3.19/bin/annotate && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/annotate
/usr/bin/g++ -Wall -O3 combineMUMs.cc tigrinc.o -o
/home/.rob_clear/packages/mummer-3.19/bin/combineMUMs && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/combineMUMs
combineMUMs.cc:109: warning: deprecated conversion from string constant to
'char*'
combineMUMs.cc:135: warning: deprecated conversion from string constant to
'char*'
combineMUMs.cc:145: warning: deprecated conversion from string constant to
'char*'
/usr/bin/g++ -Wall -O3 delta.cc -c -o delta.o
/usr/bin/g++ -Wall -O3 delta-filter.cc tigrinc.o delta.o -o
/home/.rob_clear/packages/mummer-3.19/bin/delta-filter && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/delta-filter
/usr/bin/g++ -Wall -O3 gaps.cc tigrinc.o -o
/home/.rob_clear/packages/mummer-3.19/bin/gaps && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/gaps
/usr/bin/g++ -Wall -O3 mgaps.cc tigrinc.o -o
/home/.rob_clear/packages/mummer-3.19/bin/mgaps && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/mgaps
mgaps.cc: In function 'int Process_Cluster(Match_t*, int, char*)':
mgaps.cc:533: warning: deprecated conversion from string constant to 'char*'
mgaps.cc: In function 'void Process_Matches(Match_t*, int, char*)':
mgaps.cc:620: warning: deprecated conversion from string constant to 'char*'
/usr/bin/g++ -Wall -O3 sw_align.cc -c -o sw_align.o
/usr/bin/g++ -Wall -O3 postnuc.cc tigrinc.o sw_align.o -o
/home/.rob_clear/packages/mummer-3.19/aux_bin/postnuc && chmod 755
/home/.rob_clear/packages/mummer-3.19/aux_bin/postnuc
/usr/bin/g++ -Wall -O3 translate.cc -c -o translate.o
/usr/bin/g++ -Wall -O3 postpro.cc tigrinc.o sw_align.o translate.o -o
/home/.rob_clear/packages/mummer-3.19/aux_bin/postpro && chmod 755
/home/.rob_clear/packages/mummer-3.19/aux_bin/postpro
/usr/bin/g++ -Wall -O3 prenuc.cc tigrinc.o -o
/home/.rob_clear/packages/mummer-3.19/aux_bin/prenuc && chmod 755
/home/.rob_clear/packages/mummer-3.19/aux_bin/prenuc
/usr/bin/g++ -Wall -O3 prepro.cc tigrinc.o translate.o -o
/home/.rob_clear/packages/mummer-3.19/aux_bin/prepro && chmod 755
/home/.rob_clear/packages/mummer-3.19/aux_bin/prepro
/usr/bin/g++ -Wall -O3 repeat-match.cc tigrinc.o -o
/home/.rob_clear/packages/mummer-3.19/bin/repeat-match && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/repeat-match
/usr/bin/g++ -Wall -O3 show-aligns.cc tigrinc.o translate.o delta.o -o
/home/.rob_clear/packages/mummer-3.19/bin/show-aligns && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/show-aligns
/usr/bin/g++ -Wall -O3 show-coords.cc tigrinc.o delta.o -o
/home/.rob_clear/packages/mummer-3.19/bin/show-coords && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/show-coords
show-coords.cc: In function 'void printBtab(std::vector<AlignStats,
std::allocator<AlignStats> >)':
show-coords.cc:799: warning: deprecated conversion from string constant to
'char*'
show-coords.cc:801: warning: deprecated conversion from string constant to
'char*'
show-coords.cc:803: warning: deprecated conversion from string constant to
'char*'
/usr/bin/g++ -Wall -O3 show-tiling.cc tigrinc.o delta.o -o
/home/.rob_clear/packages/mummer-3.19/bin/show-tiling && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/show-tiling
/usr/bin/g++ -Wall -O3 show-snps.cc tigrinc.o translate.o delta.o -o
/home/.rob_clear/packages/mummer-3.19/bin/show-snps && chmod 755
/home/.rob_clear/packages/mummer-3.19/bin/show-snps
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/src/tigr'
cd /home/.rob_clear/packages/mummer-3.19/scripts; make all
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/scripts'
/bin/sed -e 's?__BIN_DIR?/usr/bin?g' \
-e 's?__SCRIPT_DIR?/usr/share/mummer/scripts?g' \
exact-tandems.sh >
/home/.rob_clear/packages/mummer-3.19/bin/exact-tandems
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/exact-tandems
/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \
-e 's?__SCRIPT_DIR?/usr/share/mummer/scripts?g' \
mapview.pl > /home/.rob_clear/packages/mummer-3.19/bin/mapview
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/mapview
/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \
-e 's?__SCRIPT_DIR?/usr/share/mummer/scripts?g' \
-e 's?__BIN_DIR?/usr/bin?g' \
mummerplot.pl >
/home/.rob_clear/packages/mummer-3.19/bin/mummerplot
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/mummerplot
/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \
-e 's?__SCRIPT_DIR?/usr/share/mummer/scripts?g' \
-e 's?__AUX_BIN_DIR?/usr/lib/mummer/aux_bin?g' \
-e 's?__BIN_DIR?/usr/bin?g' \
nucmer.pl > /home/.rob_clear/packages/mummer-3.19/bin/nucmer
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/nucmer
/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \
-e 's?__SCRIPT_DIR?/usr/share/mummer/scripts?g' \
-e 's?__AUX_BIN_DIR?/usr/lib/mummer/aux_bin?g' \
-e 's?__BIN_DIR?/usr/bin?g' \
promer.pl > /home/.rob_clear/packages/mummer-3.19/bin/promer
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/promer
/bin/sed -e 's?__BIN_DIR?/usr/bin?g' \
run-mummer1.sh >
/home/.rob_clear/packages/mummer-3.19/bin/run-mummer1
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/run-mummer1
/bin/sed -e 's?__BIN_DIR?/usr/bin?g' \
run-mummer3.sh >
/home/.rob_clear/packages/mummer-3.19/bin/run-mummer3
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/run-mummer3
/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \
nucmer2xfig.pl >
/home/.rob_clear/packages/mummer-3.19/bin/nucmer2xfig
chmod 755 /home/.rob_clear/packages/mummer-3.19/bin/nucmer2xfig
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/scripts'
make[1]: Leaving directory `/home/.rob_clear/packages/mummer-3.19'
make[1]: Entering directory `/home/.rob_clear/packages/mummer-3.19'
cd /home/.rob_clear/packages/mummer-3.19/docs; make
make[2]: Entering directory `/home/.rob_clear/packages/mummer-3.19/docs'
pdflatex maxmat3man
This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6)
%&-line parsing enabled.
entering extended mode
(./maxmat3man.tex
LaTeX2e <2005/12/01>
Babel <v3.8h> and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, loaded.
(/usr/share/texmf-texlive/tex/latex/base/article.cls
Document Class: article 2005/09/16 v1.4f Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/size12.clo))
(/usr/share/texmf-texlive/tex/latex/ltxmisc/a4wide.sty
(/usr/share/texmf-texlive/tex/latex/ntgclass/a4.sty))
(/usr/share/texmf-texlive/tex/latex/base/alltt.sty)
(/usr/share/texmf-texlive/tex/latex/tools/xspace.sty)
(/usr/share/texmf-texlive/tex/latex/psnfss/times.sty) (./skaff.sty)
(./optionman.sty)
No file maxmat3man.aux.
(/usr/share/texmf-texlive/tex/latex/psnfss/ot1ptm.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/omsptm.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/ot1pcr.fd)
LaTeX Warning: Reference `SecBasicNotions' on page 1 undefined on input line 34
.
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
LaTeX Warning: Reference `SecBasicNotions' on page 2 undefined on input line 10
2.
[2] [3] [4] [5] [6] (./maxmat3man.aux)
LaTeX Warning: There were undefined references.
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
){/usr/share/texmf-texlive/fonts/enc/dvips/base/8r.enc}</usr/share/texmf-texli
ve/fonts/type1/bluesky/cm/cmmi12.pfb></usr/share/texmf-texlive/fonts/type1/blue
sky/cm/cmmi8.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr12.pfb></u
sr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr8.pfb></usr/share/texmf-texliv
e/fonts/type1/bluesky/cm/cmsy10.pfb></usr/share/texmf-texlive/fonts/type1/blues
ky/cm/cmsy7.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti12.pfb></u
sr/share/texmf-texlive/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texmf-tex
live/fonts/type1/urw/times/utmb8a.pfb></usr/share/texmf-texlive/fonts/type1/urw
/times/utmr8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmri8a.pfb>
Output written on maxmat3man.pdf (6 pages, 104265 bytes).
Transcript written on maxmat3man.log.
pdflatex maxmat3man
This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6)
%&-line parsing enabled.
entering extended mode
(./maxmat3man.tex
LaTeX2e <2005/12/01>
Babel <v3.8h> and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, loaded.
(/usr/share/texmf-texlive/tex/latex/base/article.cls
Document Class: article 2005/09/16 v1.4f Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/size12.clo))
(/usr/share/texmf-texlive/tex/latex/ltxmisc/a4wide.sty
(/usr/share/texmf-texlive/tex/latex/ntgclass/a4.sty))
(/usr/share/texmf-texlive/tex/latex/base/alltt.sty)
(/usr/share/texmf-texlive/tex/latex/tools/xspace.sty)
(/usr/share/texmf-texlive/tex/latex/psnfss/times.sty) (./skaff.sty)
(./optionman.sty) (./maxmat3man.aux)
(/usr/share/texmf-texlive/tex/latex/psnfss/ot1ptm.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/omsptm.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fonts/m
ap/pdftex/updmap/pdftex.map}] [2] [3] [4] [5] [6] (./maxmat3man.aux) ){/usr/sha
re/texmf-texlive/fonts/enc/dvips/base/8r.enc}</usr/share/texmf-texlive/fonts/ty
pe1/bluesky/cm/cmmi12.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmmi
8.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmr12.pfb></usr/share/te
xmf-texlive/fonts/type1/bluesky/cm/cmr8.pfb></usr/share/texmf-texlive/fonts/typ
e1/bluesky/cm/cmsy10.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmsy7
.pfb></usr/share/texmf-texlive/fonts/type1/bluesky/cm/cmti12.pfb></usr/share/te
xmf-texlive/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texmf-texlive/fonts/
type1/urw/times/utmb8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmr
8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmri8a.pfb>
Output written on maxmat3man.pdf (6 pages, 103587 bytes).
Transcript written on maxmat3man.log.
make[2]: Leaving directory `/home/.rob_clear/packages/mummer-3.19/docs'
make[1]: Leaving directory `/home/.rob_clear/packages/mummer-3.19'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary
sed \
-e "s/@cdbs@/, cdbs (>= 0.4.23-1.1), patchutils (>= 0.2.25),
debhelper (>= 5)/g" \
-e "s/^Build-Depends\(\|-Indep\): ,/Build-Depends\1:/g" \
\
-e "s/^Cpu: .*/Architecture: /g" \
-e "/^System: /d" \
\
-e "s/\[cpu: \([^]]*\)\]/\[\`type-handling \\\\\`echo \1 | tr '
' ','\\\\\` any\`\]/g" \
-e "s/\[system: \([^]]*\)\]/\[\`type-handling any \\\\\`echo \1
| tr ' ' ','\\\\\`\`\]/g" \
\
-e "s/\"/\\\\\"/g" \
-e "s/^/echo \"/g" \
-e "s/\\$/\\\\$/g" \
-e "s/$/\"/g" \
< debian/control.in | /bin/sh > debian/control
dpkg-checkbuilddeps -B
test -x debian/rules
test "`id -u`" = 0
dh_clean -k
dh_installdirs -A
mkdir -p "."
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install
target
dh_installdirs -pmummer-doc
dh_installdocs -pmummer-doc ./README
dh_installexamples -pmummer-doc
dh_installman -pmummer-doc
dh_installinfo -pmummer-doc
dh_installmenu -pmummer-doc
dh_installcron -pmummer-doc
dh_installinit -pmummer-doc
dh_installdebconf -pmummer-doc
dh_installemacsen -pmummer-doc
dh_installcatalogs -pmummer-doc
dh_installpam -pmummer-doc
dh_installlogrotate -pmummer-doc
dh_installlogcheck -pmummer-doc
dh_installmime -pmummer-doc
dh_installchangelogs -pmummer-doc ./ChangeLog
dh_installudev -pmummer-doc
dh_install -pmummer-doc
dh_link -pmummer-doc
dh_strip -pmummer-doc
dh_compress -pmummer-doc -X .pdf
dh_fixperms -pmummer-doc
dh_makeshlibs -pmummer-doc
dh_installdeb -pmummer-doc
dh_perl -pmummer-doc
dh_shlibdeps -pmummer-doc
dh_gencontrol -pmummer-doc
dh_md5sums -pmummer-doc
dh_builddeb -pmummer-doc
dpkg-deb: building package `mummer-doc' in `../mummer-doc_3.19-1_all.deb'.
dh_installdirs -pmummer
# install desktop file
# dh_desktop
# prevent name space pollution because libgd-tools contains /usr/bin/annotate
mv bin/annotate bin/mummer-annotate
dh_installdocs -pmummer ./README
dh_installexamples -pmummer
dh_installman -pmummer
dh_installinfo -pmummer
dh_installmenu -pmummer
dh_installcron -pmummer
dh_installinit -pmummer
dh_installdebconf -pmummer
dh_installemacsen -pmummer
dh_installcatalogs -pmummer
dh_installpam -pmummer
dh_installlogrotate -pmummer
dh_installlogcheck -pmummer
dh_installmime -pmummer
dh_installchangelogs -pmummer ./ChangeLog
dh_installudev -pmummer
dh_install -pmummer
dh_link -pmummer
dh_strip -pmummer
dh_compress -pmummer -X .pdf
dh_fixperms -pmummer
dh_makeshlibs -pmummer
dh_installdeb -pmummer
dh_perl -pmummer
dh_shlibdeps -pmummer
dh_gencontrol -pmummer
dpkg-gencontrol: warning: unknown substitution variable ${misc:Depends}
dh_md5sums -pmummer
dh_builddeb -pmummer
dpkg-deb: building package `mummer' in `../mummer_3.19-1_i386.deb'.
signfile mummer_3.19-1.dsc
gpg: skipped "Andreas Tille <[EMAIL PROTECTED]>": secret key not available
gpg: [stdin]: clearsign failed: secret key not available
dpkg-genchanges
dpkg-genchanges: including full source code in upload
dpkg-buildpackage: full upload (original source is included)
(WARNING: Failed to sign .dsc and .changes file)
[EMAIL PROTECTED]:~/c/packages/mummer-3.19$
