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

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

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