Re: Bowtie segfaults in pbuilder chroot at build time (Was: Issue with new version of Bowtie)
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
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