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

[Alex Mestiashvili]

The issue seem to be solved, the new version is uploaded to unstable.

Thank you and have a nice weekend.
Alex


On 02/29/2016 08:03 AM, Michael Crusoe wrote:
> 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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>
>
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