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