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

[Ben Langmead]

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