[Debian-med-packaging] Bug#835720: salmon: FTBFS: BAMQueue.tpp:88:29: error: no matching function for call to 'spdlog::logger::warn()'

[Andreas Tille]

Hi Sascha,

On Wed, Sep 07, 2016 at 02:21:14PM +0100, Sascha Steinbiss wrote:
> 
> It was a missing build-dependency on libboost-timer-dev. I also added the necessary build-deps on libdivsufsort and libsparsehash, see git.

Thanks for fixing.
 
> However, the build still fails with:
> 
> In file included from /build/salmon-0.7.1+ds1/include/UtilityFunctions.hpp:5:0,
>                  from /build/salmon-0.7.1+ds1/include/SBModel.hpp:7,
>                  from /build/salmon-0.7.1+ds1/src/SBModel.cpp:1:
> /build/salmon-0.7.1+ds1/include/SalmonUtils.hpp:32:27: fatal error: RapMapUtils.hpp: No such file or directory
> 
> which suggests that salmon also uses parts of the previous embedded or downloaded RapMap source tree to build salmon, not just the binary.
> I’m not familiar enough with RapMap’s intended use to decide whether we should introduce a rapmap-dev package given that it doesn’t seem to build a library. Any hints?

Possible quick-n-dirty, solution: Just add a code copy of
RapMapUtils.hpp either as quilt patch or in debian/rapmap and copy over
in build process.  This might help us whether the new version would
really fix the original build issue of #835720.

Proper solution is probably to contact upstream (I think its the same
for rapmap and salmon) how to sensibly solve this issue.

Kind regards

      Andreas.

-- 
http://fam-tille.de