[Debian-med-packaging] Bug#1036743: Bug#1036743: kleborate: debsums reports modified files after apt-get upgrade && apt-get dist-upgrade

[Étienne Mollier]

Hi all,

Andreas Beckmann, on 2023-05-25:
> during a test with piuparts I noticed debsums reporting modified files
> after a 2-stage upgrade from bullseye to bookworm:
>   apt-get upgrade
>   apt-get dist-upgrade
> (It does not happen if only a single-stage apt-get dist-upgrade is used)
> 
> kleborate gets upgraded during the first stage, 'apt-get upgrade'.
> 
> >From the attached log (scroll to the bottom...):
> 
> 2m4.4s ERROR: FAIL: debsums reports modifications inside the chroot:
>   /usr/lib/python3/dist-packages/kleborate/data/CARD_v3.1.13.fasta.ndb
>   /usr/lib/python3/dist-packages/kleborate/data/CARD_v3.1.13.fasta.ntf
>   /usr/lib/python3/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta.ndb
>   /usr/lib/python3/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta.ntf
>   /usr/lib/python3/dist-packages/kleborate/data/MgrB_and_PmrB.fasta.ndb
>   /usr/lib/python3/dist-packages/kleborate/data/MgrB_and_PmrB.fasta.ntf
>   /usr/lib/python3/dist-packages/kleborate/data/OmpK.fasta.ndb
>   /usr/lib/python3/dist-packages/kleborate/data/OmpK.fasta.ntf
>   /usr/lib/python3/dist-packages/kleborate/data/QRDR_120.fasta.ndb
>   /usr/lib/python3/dist-packages/kleborate/data/QRDR_120.fasta.ntf
>   /usr/lib/python3/dist-packages/kleborate/data/clb_alleles.fasta.ndb
>   /usr/lib/python3/dist-packages/kleborate/data/clb_alleles.fasta.ntf
>   /usr/lib/python3/dist-packages/kleborate/data/iro_alleles.fasta.ndb
>   /usr/lib/python3/dist-packages/kleborate/data/iro_alleles.fasta.ntf
>   /usr/lib/python3/dist-packages/kleborate/data/iuc_alleles.fasta.ndb
>   /usr/lib/python3/dist-packages/kleborate/data/iuc_alleles.fasta.ntf
>   /usr/lib/python3/dist-packages/kleborate/data/rmpA2.fasta.ndb
>   /usr/lib/python3/dist-packages/kleborate/data/rmpA2.fasta.ntf
>   /usr/lib/python3/dist-packages/kleborate/data/rmp_alleles.fasta.ndb
>   /usr/lib/python3/dist-packages/kleborate/data/rmp_alleles.fasta.ntf
>   /usr/lib/python3/dist-packages/kleborate/data/wzi.fasta.ndb
>   /usr/lib/python3/dist-packages/kleborate/data/wzi.fasta.ntf
>   /usr/lib/python3/dist-packages/kleborate/data/ybt_alleles.fasta.ndb
>   /usr/lib/python3/dist-packages/kleborate/data/ybt_alleles.fasta.ntf

I'm not sure what's up, but I could reproduce a very similar
issue by installing kleborate 2.0.1-1 from bullseye on sid, and
this resulted to same or similar mismatches:

$ dpkg --verify kleborate
??5??????   /usr/lib/python3/dist-packages/kleborate/data/CARD_v3.0.8.fasta.ndb
??5??????   /usr/lib/python3/dist-packages/kleborate/data/CARD_v3.0.8.fasta.ntf
??5??????   /usr/lib/python3/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta.ndb
??5??????   /usr/lib/python3/dist-packages/kleborate/data/Klebsiella_pneumoniae.fasta.ntf
??5??????   /usr/lib/python3/dist-packages/kleborate/data/MgrB_and_PmrB.fasta.ndb
??5??????   /usr/lib/python3/dist-packages/kleborate/data/MgrB_and_PmrB.fasta.ntf
??5??????   /usr/lib/python3/dist-packages/kleborate/data/OmpK.fasta.ndb
??5??????   /usr/lib/python3/dist-packages/kleborate/data/OmpK.fasta.ntf
??5??????   /usr/lib/python3/dist-packages/kleborate/data/QRDR_120.fasta.ndb
??5??????   /usr/lib/python3/dist-packages/kleborate/data/QRDR_120.fasta.ntf
??5??????   /usr/lib/python3/dist-packages/kleborate/data/clb_alleles.fasta.ndb
??5??????   /usr/lib/python3/dist-packages/kleborate/data/clb_alleles.fasta.ntf
??5??????   /usr/lib/python3/dist-packages/kleborate/data/iro_alleles.fasta.ndb
??5??????   /usr/lib/python3/dist-packages/kleborate/data/iro_alleles.fasta.ntf
??5??????   /usr/lib/python3/dist-packages/kleborate/data/iuc_alleles.fasta.ndb
??5??????   /usr/lib/python3/dist-packages/kleborate/data/iuc_alleles.fasta.ntf
??5??????   /usr/lib/python3/dist-packages/kleborate/data/rmpA2.fasta.ndb
??5??????   /usr/lib/python3/dist-packages/kleborate/data/rmpA2.fasta.ntf
??5??????   /usr/lib/python3/dist-packages/kleborate/data/rmp_alleles.fasta.ndb
??5??????   /usr/lib/python3/dist-packages/kleborate/data/rmp_alleles.fasta.ntf
??5??????   /usr/lib/python3/dist-packages/kleborate/data/wzi.fasta.ndb
??5??????   /usr/lib/python3/dist-packages/kleborate/data/wzi.fasta.ntf
??5??????   /usr/lib/python3/dist-packages/kleborate/data/ybt_alleles.fasta.ndb
??5??????   /usr/lib/python3/dist-packages/kleborate/data/ybt_alleles.fasta.ntf

Installation of kleborate from sid and testing shown no issues.
Installation of kleborate from bullseye on bullseye is okay too.
I suspect this is related to the following code snippet in
postinst, where a change in makeblastdb output format from
bullseye to bookworm could have caused a mismatch:

        for fasta in /usr/lib/python3/dist-packages/kleborate/data/*.fasta ; do
            makeblastdb -dbtype nucl -in "$fasta" > /dev/null
        done

I haven't checked closely yet, but I suspect the .ndb and .ntf
should be removed from the .deb and rely entirely on mkaeblastdb
to produce the files.  Looking that up…

Have a nice day,  :)
-- 
Étienne Mollier <emollier at emlwks999.eu>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/3, please excuse my verbosity.
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