[Debian-med-packaging] Bug#733352: Bowtie and tophat fail to build with seqan >= 1.4

[Andreas Tille]

Hi David,

On Tue, Mar 04, 2014 at 11:17:21AM +0100, Weese, David wrote:
> 
> > Ognyan Kulev promised a patch for bowie
> 
> Ok, can you please paste my last mail (with the instructions) at https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=733398 to help him.

I'm pretty sure that Ognyan is aware of the information since he was
responding to the bug report.  (I also add the address of the tophat
bug to keep others informed.)
 
> >> - seems to be const problem
> >> - the constructor of a seqan::Gaps<..., Alloc> was called with a const String and requires a non-const String
> >> - from just the error report I can't say how to fix it
> > 
> > Would a full build log which is more verbose than
> > 
> >   https://bugs.debian.org/733352
> > 
> > help to create a patch?
> > 
> 
> Not really. What I need is to reproduce your exact build environment to reproduce the exact error and provide a patch.

The exact build environment can be createt quite easily on a Debian (or
also Ubuntu machine).  You create a pbuilder environment via

   pbuilder --create sid

fetch the package source

   apt-get source tophat

cd to the unpacked dir and say

   pdebuild

Which builds the package inside the pbuilder chroot.  If you need more
detailed information I'd be happy to providvide it.

Kind regards

      Andreas.

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