Hi Nadiya, thanks for your work on this. It seems you've hit a non-trival example but that's no problem but rather a challenge, right?
At first I've fixed debian/changelog. It seems you always called dch -i which is for each call bumping the Debian release. Please use the -i option only once. Even better use dch --team since this adds the "Team upload" entry which marks the upload in a way that lintian (the Debian policy checker) does not claim that the changelog owner is not listed as Uploader in debian/control. Please git pull to see the result. On Thu, Mar 23, 2017 at 09:55:37PM -0700, Nadiya Sitdykova wrote: > I've added tests of examples from here > https://ginolhac.github.io/mapDamage/#a5 But only two of them works fine. Hmm, I admit I get a strange error even here: mapDamage -i rescale_test/pe_test/pe.sam -r rescale_test/pe_test/ref.fa Started with the command: /usr/bin/mapDamage -i rescale_test/pe_test/pe.sam -r rescale_test/pe_test/ref.fa Reading from 'rescale_test/pe_test/pe.sam' Writing results to 'results_pe/' pdf results_pe/Fragmisincorporation_plot.pdf generated No length distributions are available, plotting length distribution only works for single-end reads Error: Seqtk failed: [Errno 2] No such file or directory I applied all patches via quilt push -a and checked for occurences of seqtk via: mapdamage(master) $ grep -Riw Seqtk | grep -v -e "^\." -e "^debian" mapdamage/composition.py: path_to_seqtk = mapdamage.rscript.construct_path("seqtk",folder="seqtk") mapdamage/composition.py: sys.stderr.write("Error: Seqtk failed: %s\n" % (error,)) bin/mapDamage: fpath_seqtk = '/usr/bin/seqtk' bin/mapDamage: sys.stderr.write("Seqtk executable not accessible; mapDamage has not\n" So it seems that in mapdamage/composition.py the path to seqtk is not properly assembled. Would you mind checking this? > Other two "Cannot use --<option> with missing R-libraries", so it seems > they need recommended r-cran-rcppgsl package. I created simple stand-alone > test with this package in depends to demonstrate that something goes wrong > with installing RcppGSL. I looked at the source code here > https://anonscm.debian.org/cgit/debian-med/mapdamage.git/tree/mapdamage/Rscripts/stats/checkLibraries.R > and > it looks like after package installation "library(RcppGSL)" doesn't load > library correctly. Hmmm, GSL rings a bell for me. There was a gsl library transistion. Are you using a current Debian testing or unstable system? If not that might be the cause of the issue. May be you explain more verbosely what exactly you mean by "doesn't load library correctly"? I get $ mapDamage --check-R-packages All R packages are present After checking mapdamage/rscript.py what R packages are really checked I added some R packages as real Depends. I personally follow the strategy to use Depends if a package is needed to run the full test suite. While I actually learned from your commits that you can work around this via "needs-recommends" (its nice to learn when mentoring ;-) ) I'm sure users really want to have the full functionality. In summary please do the following: 1. Check why seqtk is not found in mapdamage/composition.py my guess is that the current quilt patch is incomplete. 2. If the R test keeps on failing please provide more information Thanks again for your work on this Andreas. PS: Regarding the time delay you mentioned in your other mail: That's fine - we have team members in different time zones. :-) -- http://fam-tille.de