Your message dated Mon, 05 Oct 2020 15:21:05 +0000
with message-id <e1kpsit-000e76...@fasolo.debian.org>
and subject line Bug#920545: fixed in python-intervaltree-bio 1.0.1-4
has caused the Debian Bug report #920545,
regarding python-intervaltree breaks python-intervaltree-bio autopkgtest
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.
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--
920545: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=920545
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: python-intervaltree, python-intervaltree-bio
Control: found -1 python-intervaltree/3.0.2-1
Control: found -1 python-intervaltree-bio/1.0.1-2
X-Debbugs-CC: debian...@lists.debian.org
Severity: important
User: debian...@lists.debian.org
Usertags: breaks needs-update
Dear maintainers,
With a recent upload of python-intervaltree the autopkgtest of
python-intervaltree-bio fails in testing when that autopkgtest is run
with the binary packages of python-intervaltree from unstable. It passes
when run with only packages from testing. In tabular form:
pass fail
python-intervaltree from testing 3.0.2-1
python-intervaltree-bio from testing 1.0.1-2
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration of
python-intervaltree to testing [1]. Due to the nature of this issue, I
filed this bug report against both packages. Can you please investigate
the situation and reassign the bug to the right package? If needed,
please change the bug's severity.
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://qa.debian.org/excuses.php?package=python-intervaltree
https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-intervaltree-bio/1785537/log.gz
=================================== FAILURES
===================================
________________________________ test_knownGene
________________________________
def test_knownGene():
# To speed up testing, we'll download the file and reuse the
downloaded copy
knownGene_url =
'http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/knownGene.txt.gz'
# Mirror. Slightly faster and more stable, I believe:
knownGene_url =
'http://kt.era.ee/distribute/pyintervaltree/knownGene.txt.gz'
# To speed up testing, we'll download the file and reuse the
downloaded copy
knownGene_file, headers = urlretrieve(knownGene_url)
knownGene_localurl = 'file:///%s' % os.path.abspath(knownGene_file)
knownGene =
GenomeIntervalTree.from_table(url=knownGene_localurl, decompress=True) #
Py3 downloads .gz files to local files with names not ending with .gz
assert len(knownGene) == 82960
> result = knownGene[b'chr1'].search(100000, 138529)
E AttributeError: 'IntervalTree' object has no attribute 'search'
.pc/offline-test-data.patch/tests/genomeintervaltree_test.py:28:
AttributeError
test_knownGene[file:///tmp/autopkgtest-lxc.z3ra1nek/downtmp/build.Szw/src/debian/data/]
base_url =
'file:///tmp/autopkgtest-lxc.z3ra1nek/downtmp/build.Szw/src/debian/data/'
def test_knownGene(base_url):
# To speed up testing, we'll download the file and reuse the
downloaded copy
knownGene_url = base_url + 'knownGene.txt.gz'
# To speed up testing, we'll download the file and reuse the
downloaded copy
knownGene_file, headers = urlretrieve(knownGene_url)
knownGene_localurl = 'file:///%s' % os.path.abspath(knownGene_file)
knownGene =
GenomeIntervalTree.from_table(url=knownGene_localurl, decompress=True) #
Py3 downloads .gz files to local files with names not ending with .gz
assert len(knownGene) == 82960
> result = knownGene[b'chr1'].search(100000, 138529)
E AttributeError: 'IntervalTree' object has no attribute 'search'
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: python-intervaltree-bio
Source-Version: 1.0.1-4
Done: Nilesh Patra <npatra...@gmail.com>
We believe that the bug you reported is fixed in the latest version of
python-intervaltree-bio, 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 920...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <npatra...@gmail.com> (supplier of updated python-intervaltree-bio
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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 05 Oct 2020 18:44:27 +0530
Source: python-intervaltree-bio
Architecture: source
Version: 1.0.1-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Nilesh Patra <npatra...@gmail.com>
Closes: 920545
Changes:
python-intervaltree-bio (1.0.1-4) unstable; urgency=medium
.
* Team Upload.
[ Olivier Sallou ]
* d/tests/control Ignore .pc directory for autopkgtest (Closes: #920545).
.
[ Afif Elghraoui ]
* Remove myself from Uploaders
.
[ Andreas Tille ]
* Add myself to Uploaders
* debhelper-compat 12
* Standards-Version: 4.5.0
* Remove trailing whitespace in debian/changelog
* Explicitly Depends: python3-intervaltree
* Make sure only offline tests are done
.
[ Nilesh Patra ]
* Fix autopkgtests (Closes: #920545)
* debhelper-compat 13 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
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--- End Message ---
