Bug#951222: scikit-learn breaks python-skbio autopkgtest: skbio.stats.distance._permdisp.permdisp
Control: reassign -1 python-skbio On 2020-02-12 20:00:16 +0100 Paul Gevers wrote: > With a recent upload of scikit-learn the autopkgtest of python-skbio > fails in testing when that autopkgtest is run with the binary packages > of scikit-learn from unstable. It passes when run with only packages > from testing. In tabular form: >passfail > scikit-learn from testing0.22.1+dfsg-1 > python-skbio from testing0.5.5-3 > all others from testingfrom testing > > I copied some of the output at the bottom of this report. > > Currently this regression is blocking the migration of scikit-learn 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? As indicated in a previous reply, the test case itself runs fine with scikit-learn 0.22.2.post1+dfsg-5 (and even earlier) when called through pytest. It's only when python-skbio's internal test runner is called that the test fails. Therefore, one can probably safely assume that the issue must originate there. Furthermore, as python-skbio was already removed from testing and therefore, a newer scikit-learn won't be an issue there, I'm reassigning this to python-skbio only, so that scikit-learn can migrate.
Bug#951222: scikit-learn breaks python-skbio autopkgtest: skbio.stats.distance._permdisp.permdisp
On Tue, Mar 31, 2020 at 11:47:40AM +0200, Christian Kastner wrote: > I've been working on fixing the open issues of src:scikit-learn, and > looked into this bug. > > This is odd. When executing the failing test code manually, the output > is just as expected (p = 0.35). The output is also just as expected when > the test suite is run at build time [1], as all tests pass. > > It's only when autopkgtest invokes the tests that this test fails. > > At build time, tests are simply run (by pybuild) with, > python3.x -m pytest > whereas the autopkgtest calls > python3 -m skbio.test > so I assume it has something to do with the latter. > > I did not investigate this further, I just reported this back upstream > to the referenced GitHub issue. > > [1] > https://buildd.debian.org/status/fetch.php?pkg=python-skbio&arch=amd64&ver=0.5.5-7&stamp=1582910349&raw=0 Thanks a lot for checking Andreas. -- http://fam-tille.de
Bug#951222: scikit-learn breaks python-skbio autopkgtest: skbio.stats.distance._permdisp.permdisp
On 2020-02-13 09:31:54 +0100 Andreas Tille wrote: > Control: tags -1 upstream > Control: forwarded -1 https://github.com/biocore/scikit-bio/issues/1693 > > > 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? > > I admit I'm not sure what package needs to be fixed but in any case I've > forwarded the issue to python-skbio upstream to make them aware of this. > My observation is that responses to bug reports of scikit-bio github are > not to be expected in a short time frame. I'm also not sure whether the > upstream tag / forward for python-skbio might hide the issue from > scikit-learn maintainers view - I have no idea where the issue really > needs to be fixed. I've been working on fixing the open issues of src:scikit-learn, and looked into this bug. This is odd. When executing the failing test code manually, the output is just as expected (p = 0.35). The output is also just as expected when the test suite is run at build time [1], as all tests pass. It's only when autopkgtest invokes the tests that this test fails. At build time, tests are simply run (by pybuild) with, python3.x -m pytest whereas the autopkgtest calls python3 -m skbio.test so I assume it has something to do with the latter. I did not investigate this further, I just reported this back upstream to the referenced GitHub issue. [1] https://buildd.debian.org/status/fetch.php?pkg=python-skbio&arch=amd64&ver=0.5.5-7&stamp=1582910349&raw=0
Bug#951222: scikit-learn breaks python-skbio autopkgtest: skbio.stats.distance._permdisp.permdisp
Hi Andreas, On 13-02-2020 09:31, Andreas Tille wrote: > My observation is that responses to bug reports of scikit-bio github are > not to be expected in a short time frame. Please be aware that if the issue is really with python-skbio, than the way autoremovals work with these kind of bugs against both packages will mean that it's python-skbio that will be removed from testing (as is my intention). So you have time until autoremoval removes your package from testing. Paul signature.asc Description: OpenPGP digital signature
Processed: Re: Bug#951222: scikit-learn breaks python-skbio autopkgtest: skbio.stats.distance._permdisp.permdisp
Processing control commands: > tags -1 upstream Bug #951222 [src:scikit-learn, src:python-skbio] scikit-learn breaks python-skbio autopkgtest: skbio.stats.distance._permdisp.permdisp Added tag(s) upstream. > forwarded -1 https://github.com/biocore/scikit-bio/issues/1693 Bug #951222 [src:scikit-learn, src:python-skbio] scikit-learn breaks python-skbio autopkgtest: skbio.stats.distance._permdisp.permdisp Set Bug forwarded-to-address to 'https://github.com/biocore/scikit-bio/issues/1693'. -- 951222: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=951222 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
Bug#951222: scikit-learn breaks python-skbio autopkgtest: skbio.stats.distance._permdisp.permdisp
Control: tags -1 upstream Control: forwarded -1 https://github.com/biocore/scikit-bio/issues/1693 > 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? I admit I'm not sure what package needs to be fixed but in any case I've forwarded the issue to python-skbio upstream to make them aware of this. My observation is that responses to bug reports of scikit-bio github are not to be expected in a short time frame. I'm also not sure whether the upstream tag / forward for python-skbio might hide the issue from scikit-learn maintainers view - I have no idea where the issue really needs to be fixed. Kind regards Andreas. -- http://fam-tille.de
Bug#951222: scikit-learn breaks python-skbio autopkgtest: skbio.stats.distance._permdisp.permdisp
Source: scikit-learn, python-skbio Control: found -1 scikit-learn/0.22.1+dfsg-1 Control: found -1 python-skbio/0.5.5-3 Severity: serious Tags: sid bullseye X-Debbugs-CC: debian...@lists.debian.org User: debian...@lists.debian.org Usertags: breaks needs-update Dear maintainers, With a recent upload of scikit-learn the autopkgtest of python-skbio fails in testing when that autopkgtest is run with the binary packages of scikit-learn from unstable. It passes when run with only packages from testing. In tabular form: passfail scikit-learn from testing0.22.1+dfsg-1 python-skbio from testing0.5.5-3 all others from testingfrom testing I copied some of the output at the bottom of this report. Currently this regression is blocking the migration of scikit-learn 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? More information about this bug and the reason for filing it can be found on https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation Paul PS: scikit-learn also FTBFS on several architectures. [1] https://qa.debian.org/excuses.php?package=scikit-learn https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-skbio/4266056/log.gz === FAILURES === __ [doctest] skbio.stats.distance._permdisp.permdisp ___ 129 ... ['s1', 's2', 's3', 's4', 's5', 's6']) 130 >>> grouping = ['G1', 'G1', 'G1', 'G2', 'G2', 'G2'] 131 132 Run PERMDISP using 99 permutations to caluculate the p-value: 133 134 >>> from skbio.stats.distance import permdisp 135 >>> import numpy as np 136 >>> #make output deterministic, should not be included during normal use 137 >>> np.random.seed(0) 138 >>> permdisp(dm, grouping, permutations=99) Differences (unified diff with -expected +actual): @@ -4,5 +4,5 @@ number of groups 2 test statistic 1.03296 -p-value 0.35 +p-value 0.29 number of permutations 99 Name: PERMDISP results, dtype: object signature.asc Description: OpenPGP digital signature
