On Thu, 2017-09-21 at 08:27 +0200, Andreas Tille wrote: > Hi Steffen, > > On Wed, Sep 20, 2017 at 10:52:55PM +0200, Steffen Möller wrote: > > > ... > > > Error testing example > > > --- tests/example6.out 2017-09-20 13:07:01.000000000 +0000 +++ > > > example6.out 2017-09-20 13:13:53.186064608 +0000 @@ -1 +1,5 @@ - > > > gi|110640213|ref|NC_008253.1| 2852852 8:T>A +- > > > gi|110640213|ref|NC_008253.1| 148810 10:A>G,13:C>G ++ > > > gi|110640213|ref|NC_008253.1| 1093035 2:T>G,15:A>T +- > > > gi|110640213|ref|NC_008253.1| 905664 6:A>G,7:G>T +- > > > gi|110640213|ref|NC_008253.1| 4930433 4:G>T,6:C>G > > > debian/rules:46: recipe for target 'override_dh_auto_test' failed > > > make[1]: *** [override_dh_auto_test] Error 1 > > > make[1]: Leaving directory '/build/bowtie-1.2.1.1+dfsg' > > > debian/rules:14: recipe for target 'build' failed > > > make: *** [build] Error 2 > > > dpkg-buildpackage: error: debian/rules build gave error exit status 2 > > > I: copying local configuration > > > E: Failed autobuilding of package > > > I: user script > > > /var/cache/pbuilder/build/cow.8814/tmp/hooks/C99_failed_build starting > > > root@wr-linux01:/# cd build/bowtie-1.2.1.1+dfsg/ > > > root@wr-linux01:/build/bowtie-1.2.1.1+dfsg# ./bowtie > > > Segmentation fault > > > root@wr-linux01:/build/bowtie-1.2.1.1+dfsg# ./bowtie --version > > > Segmentation fault > > > > > > > > > You need to setup a pbuilder hook to be able to stop the build and > > > end up inside the pbuilder chroot. > > > > Hm. I feel like building that outside the chroot ;) > > > > > root@wr-linux01:/build/bowtie-1.2.1.1+dfsg# apt-get install gdb > > > Reading package lists... Done > > > Building dependency tree > > > Reading state information... Done > > > The following additional packages will be installed: > > > libbabeltrace-ctf1 libbabeltrace1 libdw1 libelf1 libmpdec2 libpopt0 > > > libpython3.5 libpython3.5-minimal libpython3.5-stdlib > > > ... > > > root@wr-linux01:/build/bowtie-1.2.1.1+dfsg# gdb --args bowtie-align-s -- > > > wrapper basic-0 > > > GNU gdb (Debian 7.12-6) 7.12.0.20161007-git > > > ... > > > Type "apropos word" to search for commands related to "word"... > > > Reading symbols from bowtie-align-s...done. > > > (gdb) run > > > Starting program: /build/bowtie-1.2.1.1+dfsg/bowtie-align-s --wrapper > > > basic-0 > > > [Thread debugging using libthread_db enabled] > > > Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1". > > > > > > Program received signal SIGSEGV, Segmentation fault. > > > 0x00007ffff652003e in dlsym () from /lib/x86_64-linux-gnu/libdl.so.2 > > > (gdb) > > > > > > > > > Same happens when testing bowtie-align-l. > > > > > > > > > Does this ring a bell somehow? > > > > Sounds like a missing dynamic library? > > > > ldd bowtie-align-l gives me > > > > linux-vdso.so.1 (0x00007ffcb73f3000) > > libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007faf4d456000) > > libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 > > (0x00007faf4d239000) > > libtbb.so.2 => /usr/lib/x86_64-linux-gnu/libtbb.so.2 > > (0x00007faf4cffb000) > > libtbbmalloc_proxy.so.2 => > > /usr/lib/x86_64-linux-gnu/libtbbmalloc_proxy.so.2 (0x00007faf4cdf7000) > > libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 > > (0x00007faf4ca78000) > > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007faf4c774000) > > libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 > > (0x00007faf4c55d000) > > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007faf4c1c0000) > > /lib64/ld-linux-x86-64.so.2 (0x00007faf4d94c000) > > libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007faf4bfbc000) > > librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007faf4bdb4000) > > libatomic.so.1 => /usr/lib/x86_64-linux-gnu/libatomic.so.1 > > (0x00007faf4bbac000) > > libtbbmalloc.so.2 => /usr/lib/x86_64-linux-gnu/libtbbmalloc.so.2 > > (0x00007faf4b96e000) > > > > anything reported missing by ldd in your pbuilder environment? > > Inside pbuilder chroot: > > root@wr-linux01:/build/bowtie-1.2.1.1+dfsg# ldd bowtie-align- > l > linux-vdso.so.1 (0x00007ffe9511a000) > /usr/lib/cowdancer/libcowdancer.so (0x00007f56d5209000) > libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f56d4feb000) > libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 > (0x00007f56d4dce000) > libtbb.so.2 => /lib/x86_64-linux-gnu/libtbb.so.2 (0x00007f56d4b90000) > libtbbmalloc_proxy.so.2 => /lib/x86_64-linux- > gnu/libtbbmalloc_proxy.so.2 (0x00007f56d498c000) > libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 > (0x00007f56d460b000) > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f56d4307000) > libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 > (0x00007f56d40f0000) > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f56d3d53000) > libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f56d3b4f000) > libncurses.so.5 => /lib/x86_64-linux-gnu/libncurses.so.5 > (0x00007f56d392b000) > libtinfo.so.5 => /lib/x86_64-linux-gnu/libtinfo.so.5 > (0x00007f56d36ff000) > /lib64/ld-linux-x86-64.so.2 (0x0000561b175bb000) > librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f56d34f7000) > libatomic.so.1 => /lib/x86_64-linux-gnu/libatomic.so.1 > (0x00007f56d32ef000) > libtbbmalloc.so.2 => /lib/x86_64-linux-gnu/libtbbmalloc.so.2 > (0x00007f56d30b1000) > > That looks pretty similar and no visible missing. > > Kind regards > > Andreas. >
Hi,
Not part of the project and saw this on mentors.
1. Parallel build.
// Diff starts on line below.
diff --git a/debian/rules b/debian/rules
index 7919361..b536ce7 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,7 +11,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
%:
- dh $@
+ dh $@ --parallel
override_dh_auto_build:
$(MAKE) allall
// Diff ends on line above.
2. At error the unit tests should dump a diff to std error.
The script is very old style and has errors.
// Diff starts on line below.
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
index dfcb0e5..1335a4b 100644
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -5,19 +5,19 @@ if [ "$1" = "test_at_build_time" ] ; then
else
pkg=bowtie
if [ "$ADTTMP" = "" ] ; then
- ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+ ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
fi
- mkdir -p $ADTTMP/tests
- cp -a debian/tests/example* $ADTTMP/tests
- cd $ADTTMP
- cp -a /usr/share/doc/bowtie/examples/indexes $ADTTMP
+ mkdir -p "$ADTTMP"/tests
+ cp -a debian/tests/example* "$ADTTMP"/tests
+ cd "$ADTTMP"
+ cp -a /usr/share/doc/bowtie/examples/indexes "$ADTTMP"
fi
check_result () {
- EDIFF=`diff -u tests/$1.out $1.out`
+ EDIFF=$(diff -u tests/"$1".out "$1".out)
if ! $EDIFF ; then
echo "Error testing example"
- echo $EDIFF
+ echo "$EDIFF"
exit 1
else
echo "$1 OK"
// Diff ends on line above.
A diff is now outputted at example6.
Regards
Phil
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