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

On Thu, 2017-09-21 at 22:42 +0200, Andreas Tille wrote:

On Thu, Sep 21, 2017 at 07:00:27PM +0200, Steffen Möller wrote:

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?

If I use debuild on a machine running testing bowtie builds fine and doese not segfault.   So either the difference is in testing <-> unstable or build on local machine <-> pbuilder chroot.

Kind regards

      Andreas.

Hi,

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#

Regards

Phil

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