[Debian-med-packaging] Bug#879616: bug_879616 [rapmap_autopkgtest]

[Andreas Tille]

Dear Kate,

thanks again for working on the autopkgtest.

On Wed, Jan 10, 2018 at 08:38:32PM +0200, Kalou.Katerina wrote:
> 
> I am currently trying to provide a unit test for rapmap (closing bug n.
> 879616 <879616 at bugs.debian.org>). The test until now, is just :
> 
> 'pkg="rapmap"
> ln -s ~/spdlog/include/spdlog/ ~/${pkg}/include

Hmmm, that's wrong as well as the dependencies you added in
debian/tests/control are wrong.  These packages are Build-Depends
to build the package.  However, the test runs on the just built
package to there is no need to compile any more.
 
> cp -a ${pkg}/* $AUTOPKGTEST_TMP

That's also not the best idea.  For the line below you only need
the test data not the whole source tree.

> rapmap quasiindex -t transcripts.fasta -i sample_quasi_index'

To let this work you need the actual data files.  In "usual"
autopkgtests you take these from the source directory.  However, in
Debian Med we established a method where the user can run the test as a
user example as well.  To approach this I added a new package which
included the example data and adds the run-unit-test to this package
(besides a README.test file).

> However, the build fails giving me the error :
> 'In file included from
> /tmp/autopkgtest.LNHf4Z/build.kpG/real-tree/src/RapMapIndexer.cpp:45:0:
> /tmp/autopkgtest.LNHf4Z/build.kpG/real-tree/include/RapMapUtils.hpp:34:29:
> fatal error: spdlog/fmt/ostr.h: No such file or directory
> compilation terminated.
> src/CMakeFiles/rapmap.dir/build.make:89: recipe for target
> 'src/CMakeFiles/rapmap.dir/RapMapIndexer.cpp.o' failed
> make[4]: *** [src/CMakeFiles/rapmap.dir/RapMapIndexer.cpp.o] Error 1'
> 
> When i manually include a symbolic link to the file as
> ln -s ~/spdlog/include/spdlog/ ~/$rapmap/include
> the build succeeds

As I said this is somehow wrong since in autopkgtest no compilation
is needed.  I removed all this.  (Please also make sure you will not
commit swap files ;-) )
 
> However , when i include that line in the autopkgtest it fails. I have read
> that it is not possible to include symbolic links in an autopkgtest? I will
> keep searching for a solution to this, but any helpful hint would be
> appreciated :)

No idea about this and why this is done.
 
I think to finalise the test it would make sense to compare the test
result with the result that was obtained at compile time.  Would you
mind adding this to confirm that you understood the principle and the
changes I did?

Kind regards

        Andreas.

-- 
http://fam-tille.de