Re: bug_879616 [rapmap_autopkgtest]

[Andreas Tille <andreas@an3as.eu>]

Dear Kate,

On Wed, Jan 10, 2018 at 08:38:32PM +0200, Kalou.Katerina wrote:
> Dear all,
> 
> Happy New Year! :)

Thanks, same to you.
 
> I am currently trying to provide a unit test for rapmap (closing bug n.
> 879616 <879616@bugs.debian.org>). The test until now, is just :
> 
> 'pkg="rapmap"
> ln -s ~/spdlog/include/spdlog/ ~/${pkg}/include
> 
> if [ "$AUTOPKGTEST_TMP" = "" ] ; then
>   AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
>   trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
> fi
> 
> cp -a ${pkg}/* $AUTOPKGTEST_TMP
> rapmap quasiindex -t transcripts.fasta -i sample_quasi_index'
> 
> However, the build fails giving me the error :
> 'In file included from
> /tmp/autopkgtest.LNHf4Z/build.kpG/real-tree/src/RapMapIndexer.cpp:45:0:
> /tmp/autopkgtest.LNHf4Z/build.kpG/real-tree/include/RapMapUtils.hpp:34:29:
> fatal error: spdlog/fmt/ostr.h: No such file or directory
> compilation terminated.
> src/CMakeFiles/rapmap.dir/build.make:89: recipe for target
> 'src/CMakeFiles/rapmap.dir/RapMapIndexer.cpp.o' failed
> make[4]: *** [src/CMakeFiles/rapmap.dir/RapMapIndexer.cpp.o] Error 1'
> 
> When i manually include a symbolic link to the file as
> ln -s ~/spdlog/include/spdlog/ ~/$rapmap/include
> the build succeeds
> 
> 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 :)

Could you please commit your changes to Git to enable me having a look
at the code.  Otherwise I might misunderstand what you wrote.

Thanks for working on this

      Andreas.

-- 
http://fam-tille.de