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 <[email protected]>
Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
Sent from /dev/pts/3, please excuse my verbosity.
signature.asc
Description: PGP signature
