> > > > Hello! > > > > I have written autopkgtests for yanagiba[1] and unc-fish[2]. > > > > The yanagiba package seems to fail the ci pipeline. The error seems to be > > from - > > > > dpkg: yanagiba-build-deps: dependency problems, but configuring anyway as > > you requested: > > yanagiba-build-deps depends on dh-python; however: > > Package dh-python is not installed. > > yanagiba-build-deps depends on python3-setuptools; however: > > Package python3-setuptools is not installed. > > yanagiba-build-deps depends on python3-pandas; however: > > Package python3-pandas is not installed. > > yanagiba-build-deps depends on python3-biopython; however: > > Package python3-biopython is not installed. > > yanagiba-build-deps depends on python3-nanomath; however: > > Package python3-nanomath is not installed. > > => For yanagiba > > Not quite, the error instead comes from: > > dpkg-source: error: unwanted binary file: debian/tests/data/data.fastq.gz > dpkg-source: error: detected 1 unwanted binary file (add it in > debian/source/include-binaries to allow its inclusion). > > So whenever you include "binaries" (with sources) in d/tests/data or > d/<any-directory> > you need to allow its inclusion via d/source/include-binaries. Here it > is just a compressed file, hence should be fine > > Other than that, copyright was wrong. There should not be a space before > ":" > (colon) and after Files, i.e. it has to be "Files: ..." and not "Files : > ...." > > And "Team Upload" need to be the top entry, not somewhere in the middle. > Fixed all of these and pushed. > > Actually, there is a tool called lintian[3] which helps find out these > things, and every package should be as much lintian clean as possible. > > Although it is best to run it locally and check, > It also shows up in the salsa-CI - although it passes, but that is > usually not enough. The bare minimum is to fix error + warnings. There > can be determined w/ statements beginning with "W:" > as an example, in your salsa CI log[4] for unc-fish, this is a warning > > "W: unc-fish source: no-nmu-in-changelog" > > yanagiba is almost ready, since you downloaded data from ncbi database, > can you write a script for fetching data by running it? > Just like the way I did it for pilercr[5] > I don't have a good idea of navigating this file at the right location > Note that doing this is ``optional``, and let me know if it cannot be done
I have pushed the get-test-data script. Could you please have a look at it? Thank you! > > => Now, For unc-fish: > > Looks fine, but as you might notice, this package is not in the archive > yet. > The reason is the TODO mentioned in d/changelog: > > """ > TODO: Find reason for failure: > $ /usr/lib/unc-fish/fish -b blocks.txt -B simpleblocks.txt -g > grids.txt -C contigs.txt > Segmentation fault > """ > > I modified this command placing all relevant files in the directory I > amd running it, and I get: > > $ unc-fish -f control.txt -b blocks.txt -B simpleblocks.txt -g grids.txt > -C contigs.txt > > corrupted size vs. prev_size > [1] 30290 abort unc-fish -f control.txt -b blocks.txt -B > simpleblocks.txt -g grids.txt -C > > I did not take a deeper look at it, can you check once? > > Also, @Andreas, why is test data stored in "/var/lib/fish" and not > "/usr/share/doc...."? This looks > sort of weird, is that really intended? > > > [1] https://salsa.debian.org/med-team/yanagiba > > [2] https://salsa.debian.org/med-team/unc-fish > [3]: https://wiki.debian.org/HowToPackageForDebian#Lintian > [4]: https://salsa.debian.org/med-team/unc-fish/-/jobs/1782347 > [5]: > https://salsa.debian.org/med-team/pilercr/-/blob/master/debian/tests/get-test-data > > Nilesh > ᐧ
