[Debian-med-packaging] C++ problems when upgrading bowtie2

[Michael Crusoe]

Thank you Ben for the update. Andreas is offline for a few weeks but we
will swiftly update the Debian package once the release is ready.

În Lun, 29 feb. 2016, 04:45 Ben Langmead, <langmea at cs.jhu.edu> a scris:

> Hi Andreas,
>
> We spent some time this last week diagnosing and fixing this issue.  We
> hope to post a new release of Bowtie 2 very soon that both includes the
> parallel index-building feature, and compiles properly with TBB.
>
> Best,
> Ben
>
> > On Feb 18, 2016, at 3:09 AM, Andreas Tille <andreas at an3as.eu> wrote:
> >
> > Hi Ben,
> >
> > when trying to build the latest version of Bowtie2 I was running into
> > some build errors I described here:
> >
> >
> https://lists.alioth.debian.org/pipermail/debian-med-packaging/2016-February/039567.html
> >
> > I've got this answer from a Debian Med team member:
> >
> > On Thu, Feb 18, 2016 at 12:56:12AM +0100, Gert Wollny wrote:
> >>> could anybody with more C++ knowledge than me have a look at my last
> >>> bowtie2 commits of the new upstream version which throws the
> >>> following
> >>> problems:
> >>
> >> without digging too deep into the code it seems that the TBB thread
> >> implementation is not working properly, i.e. the without TBB they use a
> >> thread implementation that resides withing the tthread namespace, and
> >> without TBB, they include the TBB headers, but don't take care of the
> >> fact that now all thread related classes reside in the tbb namespace.
> >>
> >> If you remove the WITH_TBB=1 part from debian/rules than it builds.
> >
> > Since using WITH_TBB is explicitly recommended inside the MANUAL I'd
> > like to discuss other options how to build Bowtie2 2.2.7 - and I guess
> > you are also interested to learn that building this code with gcc 5.3.1
> > causes trouble.
> >
> > Kind regards and thanks for providing Bowtie2 as free software
> >
> >    Andreas.
> >
> > --
> > http://fam-tille.de
>
>
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