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