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

2017-09-25 Thread Steffen Möller
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

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

2017-09-25 Thread Andreas Tille
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

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

2017-09-21 Thread Phil Wyett
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

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

2017-09-21 Thread Andreas Tille
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

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

2017-09-21 Thread Phil Wyett
On Thu, 2017-09-21 at 15:12 +0200, Andreas Tille wrote: > Hi Phil, > > thanks for your attempt to help. > > On Thu, Sep 21, 2017 at 12:15:50PM +0100, Phil Wyett wrote: > > 1. Parallel build. > > > > // Diff starts  on line below. > > diff --git a/debian/rules b/debian/rules > > index

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

2017-09-21 Thread Andreas Tille
Hi Phil, thanks for your attempt to help. On Thu, Sep 21, 2017 at 12:15:50PM +0100, Phil Wyett wrote: > 1. Parallel build. > > // Diff starts on line below. > diff --git a/debian/rules b/debian/rules > index 7919361..b536ce7 100755 > --- a/debian/rules > +++ b/debian/rules > @@ -11,7 +11,7 @@

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

2017-09-21 Thread Phil Wyett
On Thu, 2017-09-21 at 12:15 +0100, Phil Wyett wrote: > On Thu, 2017-09-21 at 08:27 +0200, Andreas Tille wrote: > > Hi Steffen, > > > > On Wed, Sep 20, 2017 at 10:52:55PM +0200, Steffen Möller wrote: > > > > ... > > > > Error testing example > > > > --- tests/example6.out 2017-09-20

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

2017-09-21 Thread Phil Wyett
On Thu, 2017-09-21 at 08:27 +0200, Andreas Tille wrote: > Hi Steffen, > > On Wed, Sep 20, 2017 at 10:52:55PM +0200, Steffen Möller wrote: > > > ... > > > Error testing example > > > --- tests/example6.out 2017-09-20 13:07:01.0 + +++ > > > example6.out 2017-09-20 13:13:53.186064608

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

2017-09-21 Thread Andreas Tille
Hi Steffen, On Wed, Sep 20, 2017 at 10:52:55PM +0200, Steffen Möller wrote: > > ... > > Error testing example > > --- tests/example6.out 2017-09-20 13:07:01.0 + +++ example6.out > > 2017-09-20 13:13:53.186064608 + @@ -1 +1,5 @@ - > > gi|110640213|ref|NC_008253.1| 2852852 8:T>A

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

2017-09-20 Thread Steffen Möller
On 20.09.17 15:44, Andreas Tille wrote: > [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:

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

2017-09-20 Thread Andreas Tille
[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