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

[Steffen Möller <steffen_moeller@gmx.de>]

Hi Andreas,

On 25.09.17 11:41, Andreas Tille wrote:
> Hi Phil,
>
> On Thu, Sep 21, 2017 at 11:47:40PM +0100, Phil Wyett wrote:
>> At this current time on a pbuilder sid created using:
>>
>> sudo pbuilder create --distribution sid --debootstrapopts --variant=buildd
>>
>> I cannot reproduce seg faults at all. I have tracked back through the med list
>> and done all commands tested, one example:
>>
>> root@ks-yoda:/tmp/buildd/bowtie-1.2.1.1+dfsg# ./bowtie --version
>> bowtie-align version 1.2.1.1
>> 64-bit
>> Built on Debian-reproducible
>> Mon, 04 Sep 2017 14:13:56 +0200
>> Compiler: gcc version 7.2.0
>> Options: -O3  -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2
>> -g -O2 -fdebug-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-
>> security  -g -O2 -fdebug-prefix-map=.=. -fstack-protector-strong -Wformat
>> -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now
>> Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
>> root@ks-yoda:/tmp/buildd/bowtie-1.2.1.1+dfsg#
> Thanks for the attempt to reproduce.  I tried to ignore the test results
> at build time and installed the resulting package on my local machine.
> Now the segfaults are not happening any more.  That's really strange.  I
> do not think that the issue is caused due to a broken chroot (I'm
> actually using cowbuilder not pbuilder) since I can reproduce the
> problem on three different machines.
>
> Besides the build problem I need to ask the bioinformaticans on the
> Debian Med list about changes in the output of bowtie.  If I run the
> test suite with the freshly installed package I get things like:
>
>
> Error testing example
> --- tests/example1.out  2017-09-04 14:11:54.115569050 +0200
> +++ example1.out        2017-09-23 07:41:11.214221005 +0200
> @@ -1,5 +0,0 @@
> --      gi|110640213|ref|NC_008253.1|   148810  10:A>G,13:C>G
> --      gi|110640213|ref|NC_008253.1|   2852852 8:T>A
> --      gi|110640213|ref|NC_008253.1|   4930433 4:G>T,6:C>G
> --      gi|110640213|ref|NC_008253.1|   905664  6:A>G,7:G>T
> -+      gi|110640213|ref|NC_008253.1|   1093035 2:T>G,15:A>T
>
>
> I wonder whether some bioinformatican could at least reproduce this and
> could comment on the test suite.
>
> For general Debian Mentors I'll leave the question for more ideas why
> the program segfaults inside pbuilder (at that time including debugging
> symbols) but runs when installing the package on a real machine and
> what I could do to track this down.


This is exactly what I get. I think this needs to be discussed with
upstream.

Cheers,

Steffen