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

[Andreas Tille <andreas@an3as.eu>]

[switching back to list discussion also involving debian-mentors.
 Please see the gdb output below I get when installing gdb inside the
 pbuilder chroot.]

Hi Steffen,

On Wed, Sep 20, 2017 at 02:26:20PM +0200, Steffen Möller wrote:
> >> /build/bowtie-1.2.1.1+dfsg# ./bowtie -a -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
> >> Segmentation fault
> >>
> >>
> >> I intended to open an issue on Github but when doing so I wanted to leave
> >> a proof that we are using the latest upstream version:
> >>
> >>
> >> /build/bowtie-1.2.1.1+dfsg# ./bowtie -v
> >> Segmentation fault
> >>
> >>
> >> Hups, I think something is wrong at our side and the build has a problem.
> >>
> >> Has anybody some spare cylces to track this down?
> > Any volunteer?
> 
> 
> Not really, except that on my virtual machine "bowtie -v" shows the
> expected (long) usage information.

I guess you try to test the *existing* bowtie package.  Please note
that I was talking about the new version in Git which I try to build
and the segfault happens in the pbuilder chroot (I just learned that
you are rarely using pbuilder - see subsequent fast5 uploads :-P ).
So please try to build latest Git (git.debian.org seems to be offline
currently).  I get:

...
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.

> So, I cannot immediately reproduce
> the behaviour you observe. What does "bowtie --version" do for you? 

See above - but we are most probably talking about different things.

> Should we add "bowtie -v" as an autotest, just testing that it does not
> crash but that it exits with a bad code ( == 1) ?

I assume this test will not be necessary since it is not really
`bowtie -v` which breaks but *any* call of bowtie segfaults inside
the pbuilder environment.

> Another question to me is why we do not have a bowtie-dbgsym package.
> Where is it?

No idea but hey, I installed gdb into the pbuilder environment and did:

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?

Kind regards

      Andreas.

-- 
http://fam-tille.de