Re: khmer 2.0 released, package ready for sponsoring
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.
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.)
Unfortunately it does not build at my side and I wonder why:
ource -i.git -I.git -i.git -I.git --before-build khmer-2.0+dfsg
dpkg-buildpackage: host architecture amd64
dpkg-checkbuilddeps: Unmet build dependencies: python3-screed (<< 1.0)
dpkg-buildpackage: warning: build dependencies/conflicts unsatisfied; aborting
dpkg-buildpackage: warning: (Use -d flag to override.)
E: Failed autobuilding of package
I: user script /var/cache/pbuilder/build/cow.25342/tmp/hooks/C99_failed_build starting
Installing convenience apps: bash less bash-completion
/# apt-cache policy python3-screed
python3-screed:
Installed: (none)
Candidate: 0.9-1
Version table:
0.9-1 0
500 http://http.debian.net/debian/ sid/main amd64 Packages
pkg-buildpackage: warning: build dependencies/conflicts unsatisfied; aborting
/# apt-get install python3-screed
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following extra packages will be installed:
python3-bz2file
The following NEW packages will be installed:
python3-bz2file python3-screed
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 71.4 kB/79.1 kB of archives.
After this operation, 264 kB of additional disk space will be used.
Do you want to continue? [Y/n]
Get:1 http://http.debian.net/debian/ sid/main python3-screed all 0.9-1 [71.4 kB]
Fetched 71.4 kB in 1s (43.5 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package python3-bz2file.
(Reading database ... 19683 files and directories currently installed.)
Preparing to unpack .../python3-bz2file_0.98-1_all.deb ...
Unpacking python3-bz2file (0.98-1) ...
Selecting previously unselected package python3-screed.
Preparing to unpack .../python3-screed_0.9-1_all.deb ...
Unpacking python3-screed (0.9-1) ...
Setting up python3-bz2file (0.98-1) ...
Setting up python3-screed (0.9-1) ...
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.
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
...
Kind regards
Andreas.
--
http://fam-tille.de
Reply to: