Your message dated Fri, 22 Oct 2021 14:48:56 +0000
with message-id <[email protected]>
and subject line Bug#996794: fixed in ncbi-acc-download 0.2.7-2
has caused the Debian Bug report #996794,
regarding ncbi-acc-download: autopkgtest failure with python-biopython
1.79+dfsg-1~0exp0 in experimental
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
996794: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=996794
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: ncbi-acc-download
Version: 0.2.7-1
Severity: important
Tags: ftbfs
Dear Maintainer,
I am trying to assess the side effects of an upgrade of the
package python-biopython to 1.79 to its reverse dependencies.
Pseudo-excuses look alright, except for ncbi-acc-download [1].
[1]: https://release.debian.org/britney/pseudo-excuses-experimental.html
[2]:
https://ci.debian.net/data/autopkgtest/unstable/amd64/n/ncbi-acc-download/15982166/log.gz
The full log [2] shows variations around the following symptom:
__________________ test_download_wgs_parts_supercontig_retry
___________________
req = <requests_mock.mocker.Mocker object at 0x7fc14613fb20>
def test_download_wgs_parts_supercontig_retry(req):
cfg = Config(format="genbank")
supercontig = open(full_path('supercontig.gbk'), 'rt')
req.get(ENTREZ_URL, response_list=[
{"text": u'Whoa, slow down', "status_code": 429, "headers":
{"Retry-After": "0"}},
{"body": open(full_path('supercontig_full.gbk'), 'rt')}
])
outhandle = wgs.download_wgs_parts(supercontig, cfg)
supercontig_full = open(full_path('supercontig_full.gbk'), 'rt')
> assert outhandle.getvalue() == supercontig_full.read()
E AssertionError: assert 'LOCUS ...671808)\n//\n' == 'LOCUS
...ccctaac\n//\n'
E - LOCUS NC_007194 60 bp DNA
linear CON 03-APR-2018
E ? ^^^^^^^
^^ ^^^ ^^
E + LOCUS NC_007194 4918979 bp DNA
linear CON 11-NOV-2009
E ? ^^^^^^^
^^ ^^^ ^^
E DEFINITION Aspergillus fumigatus Af293 chromosome 1, whole
genome shotgun
E sequence.
E ACCESSION NC_007194...
E
E ...Full output truncated (22 lines hidden), use '-vv' to show
test_wgs.py:145: AssertionError
To be honest, I don't know whether this is caused by a bug in
biopython, or if it could be normal from ncbi-acc-download to
issue a slightly different output. Testing against biopython
1.78 does not raise that issue.
Since the test suite is run at build time, ncbi-acc-download
would also fail to build from source if python-biopython were to
be upgraded, hence the tag. Note that I think the package
downloads resources from the Internet during the test at build
time too, so would might be a serious policy violation, but I
haven't checked for sure yet.
Kind Regards,
--
Étienne Mollier <[email protected]>
Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
Sent from /dev/pts/4, please excuse my verbosity.
signature.asc
Description: PGP signature
--- End Message ---
--- Begin Message ---
Source: ncbi-acc-download
Source-Version: 0.2.7-2
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
ncbi-acc-download, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (supplier of updated ncbi-acc-download
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 22 Oct 2021 16:14:30 +0200
Source: ncbi-acc-download
Architecture: source
Version: 0.2.7-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 996794
Changes:
ncbi-acc-download (0.2.7-2) unstable; urgency=medium
.
* Team upload.
* Add biopython1.79.patch. (Closes: #996794)
* Bump standards version to 4.6.0
Checksums-Sha1:
45cd6f122e30dab99783b711dd75dd8f4a099509 2433 ncbi-acc-download_0.2.7-2.dsc
09bf0f1add0335eb48b38b79bbda388ab5332f02 4476
ncbi-acc-download_0.2.7-2.debian.tar.xz
86cf93355c81ce3e8169b244998ad0b4a0cc0b56 8323
ncbi-acc-download_0.2.7-2_amd64.buildinfo
Checksums-Sha256:
291309a9b59d3fc9dac8f4d6a3469c5c7a93c423e68dd25da5f13f4c568e63da 2433
ncbi-acc-download_0.2.7-2.dsc
631607eca8d33e2e4c404968a02997bd37c9f4e99b3319cd035bf73bcc604351 4476
ncbi-acc-download_0.2.7-2.debian.tar.xz
bc73cc4ea30e0a3f676cc6e20acf255db782f38c524efafa36a993fcadc0f6fc 8323
ncbi-acc-download_0.2.7-2_amd64.buildinfo
Files:
faa349b70578bf779781b5c45a1d15e2 2433 science optional
ncbi-acc-download_0.2.7-2.dsc
603534c8e41cbdc997255df8f575b211 4476 science optional
ncbi-acc-download_0.2.7-2.debian.tar.xz
e0202a9c97c4d27235b5d03cbbd81ad2 8323 science optional
ncbi-acc-download_0.2.7-2_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=9RC2
-----END PGP SIGNATURE-----
--- End Message ---
