Hi Andreas, On 21.09.17 08:27, 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.
You have cowdancer - but you are right. Hm. Just because it works for me without pbuilder - I know the build process takes a while but would you mind much to confirm the crash when executed in your regular environment? Steffen
