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-ci@lists.debian.org Severity: important User: debian-ci@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'
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