On Wed, Sep 9, 2015 at 12:32 AM Andreas Tille <[email protected]> wrote:
> Hi Michael, > > On Wed, Sep 09, 2015 at 01:00:08AM +0000, Michael Crusoe wrote: > > Hmm... I think we are working with different repositories as there should > > be no 'rc' release candidate part of the version. > > > > http://anonscm.debian.org/cgit/debian-med/khmer.git > > > > I've deleted the extra branches (big-rebase, libkhmerdev) so hopefully > that > > will clear things up. > > Ahh, OK. I'm now working on the master branch. > Great, glad to be on the same page again. > > I also had some fixes for upstream/metadata since I'm not sure who the > parser works with multiline values and converted to a syntax that is > safe. (Please pull.) > Got 'em, they look fine. Thanks! > > Unfortunately it does not build at my side and I wonder why: > <snip> > > I have no idea why this does not work - I never experienced this before > ... perhaps since I never used a << constraint. I commited a patch that > drops this constraint since we can assume that it is fulfilled now at > build time (otherwise the build will probably fail?) and just kept it > for the resulting package depends. > Hmm.. I don't mind them being dropped I guess. > > Unfortunately this is not the only problem. I have one remaining failed > test: > > ... > PYBUILD_SYSTEM=custom \ > PYBUILD_TEST_ARGS="cd {dir}; export > PATH={destdir}/usr/lib/khmer/bin:$PATH ; \ > cd {build_dir}; {interpreter} -m nose --attr \ > '!known_failing,!jenkins,!huge'" dh_auto_test > pybuild --test --test-nose -i python{version} -p 3.4 --dir . > I: pybuild base:170: cd /tmp/buildd/khmer-2.0+dfsg; export > PATH=/tmp/buildd/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin:/usr/sbin:/usr/bin:/sbin:/bin > ; cd /tmp/buildd/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.4/build; python3.4 > -m nose --attr '!known_failing,!jenkins,!huge' > > ................................................................................................................................................................................................................................................................................................................................................................SSSSSSSSSS...........................................................................F.......................................................................................................................................................................... > ====================================================================== > FAIL: khmer.tests.test_scripts.test_abundance_dist_threaded > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest > self.test(*self.arg) > File > "/tmp/buildd/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.4/build/khmer/tests/test_scripts.py", > line 1612, in test_abundance_dist_threaded > assert line == '1,96,96,0.98', line > nose.proxy.AssertionError: 1,96,96,0.96 > -------------------- >> begin captured stdout << --------------------- > running: abundance-dist-single.py in: /tmp/khmertest_78rd1e9r > arguments ['abundance-dist-single.py', '-x', '1e7', '-N', '2', '-k', '17', > '-z', '--threads', '18', '/tmp/khmertest_78rd1e9r/test.fa', > '/tmp/khmertest__98luj3k/test.dist'] > > --------------------- >> end captured stdout << ---------------------- > > ---------------------------------------------------------------------- > Ran 608 tests in 30.787s > > FAILED (SKIP=10, failures=1) > E: pybuild pybuild:262: test: plugin custom failed with: exit code=1: cd > /tmp/buildd/khmer-2.0+dfsg; export > PATH=/tmp/buildd/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin:/usr/sbin:/usr/bin:/sbin:/bin > ; cd /tmp/buildd/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.4/build; python3.4 > -m nose --attr '!known_failing,!jenkins,!huge' > dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.4 --dir . > returned exit code 13 > ... > We just added a known issue for this release about a multithreading issue with `load-graph.py` and I'm betting this test failure is related. The package builds for me just fine but I've added a patch to override that test. Does that patch work for you? > > Kind regards > > Andreas. > > -- > http://fam-tille.de > -- Michael R. Crusoe: Software Research Engineer [email protected] The lab for Data Intensive Biology; University of California, Davis https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe
