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

[Andreas Tille]

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.

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