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<div class="moz-cite-prefix">The issue seem to be solved, the new
version is uploaded to unstable.<br>
<br>
Thank you and have a nice weekend.<br>
Alex<br>
<br>
<br>
On 02/29/2016 08:03 AM, Michael Crusoe wrote:<br>
</div>
<blockquote
cite="mid:CAD=WrcKQPkG3T1bHUwpdy+RtCVfETiaKTCSFaD8gNGWAXboKNg@mail.gmail.com"
type="cite">
<pre wrap="">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.
Īn Lun, 29 feb. 2016, 04:45 Ben Langmead, <a class="moz-txt-link-rfc2396E" href="mailto:langmea@cs.jhu.edu"><langmea@cs.jhu.edu></a> a scris:
</pre>
<blockquote type="cite">
<pre wrap="">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
</pre>
<blockquote type="cite">
<pre wrap="">On Feb 18, 2016, at 3:09 AM, Andreas Tille <a class="moz-txt-link-rfc2396E" href="mailto:andreas@an3as.eu"><andreas@an3as.eu></a> wrote:
Hi Ben,
when trying to build the latest version of Bowtie2 I was running into
some build errors I described here:
</pre>
</blockquote>
<pre wrap=""><a class="moz-txt-link-freetext" href="https://lists.alioth.debian.org/pipermail/debian-med-packaging/2016-February/039567.html">https://lists.alioth.debian.org/pipermail/debian-med-packaging/2016-February/039567.html</a>
</pre>
<blockquote type="cite">
<pre wrap="">
I've got this answer from a Debian Med team member:
On Thu, Feb 18, 2016 at 12:56:12AM +0100, Gert Wollny wrote:
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">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:
</pre>
</blockquote>
<pre wrap="">
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.
</pre>
</blockquote>
<pre wrap="">
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.
--
<a class="moz-txt-link-freetext" href="http://fam-tille.de">http://fam-tille.de</a>
</pre>
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<pre wrap="">
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<pre wrap="">
</pre>
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