On 29/07/21 09:40 PM, Shruti Sridhar wrote:
> 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
=> 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
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