Re: Bowtie segfaults in pbuilder chroot at build time (Was: Issue with new version of Bowtie)
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.
--
http://fam-tille.de
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