Thanks and sorry for the slow reply. I have finally seen the error myself. I think it should be fixed in commit d697f23.
Best, Johannes --- Dr. rer. nat. Johannes Köster Centrum Wiskunde & Informatica Harvard Medical School http://johanneskoester.bitbucket.org -------- Original Message -------- Subject: Random failures in test suite of snakemake [Bug#848820: snakemake: FTBFS randomly (failing tests)] Local Time: December 22, 2016 9:46 AM UTC Time: December 22, 2016 8:46 AM From: andr...@an3as.eu To: Johannes Köster <johannes.koes...@tu-dortmund.de>, Kevin Murray <kdmf...@gmail.com> 848...@bugs.debian.org Hi Johannes, the Debian Med team is packaging snakemake for Debian (thanks for this nice tool by the way). We received a bug report that one test of the unit test suite fails randomly (3 times out of 100 tries). The essence of the provided build logs which are linked at the bug page[1] is the follwing: ====================================================================== ERROR: tests.tests.test_symlink_temp ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/<<BUILDDIR>>/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build/tests/tests.py", line 301, in test_symlink_temp run(dpath("test_symlink_temp"), shouldfail=True) File "/<<BUILDDIR>>/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build/tests/tests.py", line 105, in run rmtree(tmpdir) File "/usr/lib/python3.5/shutil.py", line 478, in rmtree onerror(os.rmdir, path, sys.exc_info()) File "/usr/lib/python3.5/shutil.py", line 476, in rmtree os.rmdir(path) OSError: [Errno 39] Directory not empty: '/<<BUILDDIR>>/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build/.test0k8le5n3' but you might like to inspect the complete log at your preference. My current course of action will be to simply disable this test for the moment. Kind regards Andreas. [1] https://bugs.debian.org/848820 ----- Forwarded message from Santiago Vila <sanv...@unex.es> ----- Date: Mon, 19 Dec 2016 23:46:36 +0100 (CET) From: Santiago Vila <sanv...@unex.es> To: Debian BTS <sub...@bugs.debian.org> Subject: Bug#848820: snakemake: FTBFS randomly (failing tests) X-Debian-PR-Message: report 848820 X-Debian-PR-Package: src:snakemake X-Debian-PR-Keywords: X-Debian-PR-Source: snakemake Package: src:snakemake Version: 3.9.0+dfsg-1 Severity: serious Dear maintainer: I tried to build this package with "dpkg-buildpackage -A" (which is what the "Arch: all" autobuilder would do to build it) but it failed: -------------------------------------------------------------------------------- [...] debian/rules build-indep dh build-indep --with python3,sphinxdoc --buildsystem=pybuild dh_testdir -i -O--buildsystem=pybuild dh_update_autotools_config -i -O--buildsystem=pybuild dh_autoreconf -i -O--buildsystem=pybuild dh_auto_configure -i -O--buildsystem=pybuild I: pybuild base:184: python3.5 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/<<BUILDDIR>>/snakemake-3.9.0+dfsg' dh_auto_build I: pybuild base:184: /usr/bin/python3 setup.py build running build [... snipped ...] 2 four 2 one 2 three 2 two 9 snakemake.logging: INFO: rule one: input: a output: 1.a wildcards: sample=a snakemake.logging: INFO: snakemake.logging: INFO: rule one: input: b output: 1.b wildcards: sample=b snakemake.logging: INFO: snakemake.logging: INFO: 1 of 9 steps (11%) done snakemake.logging: INFO: rule two: input: 1.a output: 2.a wildcards: sample=a snakemake.logging: INFO: snakemake.logging: INFO: 2 of 9 steps (22%) done snakemake.logging: INFO: rule two: input: 1.b output: 2.b wildcards: sample=b snakemake.logging: INFO: snakemake.logging: WARNING: Removing temporary output file 1.a. snakemake.logging: INFO: 3 of 9 steps (33%) done snakemake.logging: ERROR: WorkflowError: File 2.a seems to be a broken symlink. snakemake.logging: WARNING: Waiting at most 3 seconds for missing files. --------------------- >> end captured logging << --------------------- ---------------------------------------------------------------------- Ran 70 tests in 36.186s FAILED (errors=1) Error in job two while creating output file 2.b. MissingOutputException in line 9 of /<<BUILDDIR>>/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build/tests/test_symlink_temp/Snakefile: Missing files after 3 seconds: 2.b E: pybuild pybuild:276: test: plugin distutils failed with: exit code=1: cd /<<BUILDDIR>>/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build; python3.5 -m nose tests dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.5 returned exit code 13 debian/rules:16: recipe for target 'build-indep' failed make: *** [build-indep] Error 25 dpkg-buildpackage: error: debian/rules build-indep gave error exit status 2 -------------------------------------------------------------------------------- This is just how the build ends. I attach three different build logs. They happened while trying to build the package 100 times, so the failure rate is about 3%. If you try to reproduce this, please try a lot of times. Thanks. _______________________________________________ Debian-med-packaging mailing list debian-med-packag...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging ----- End forwarded message ----- -- http://fam-tille.de