Build time test for recent commit of kineticstools
Hi Afif,
I have updated the packaging of kineticstool after using git mode in
d/watch. Unfortunately the build-time test runs into an error:
...
test_private_api (test_inputs.TestSplitDataset) ... SKIP: Missing test data directory
Test for known modifications near the start of H. pylori genome ... SKIP: Missing test data directory
test_internal.test_basic ... ok
test_internal.test_path ... ERROR
test_internal.test_path_with_prefixed_chem ... ERROR
test_internal.test_getResourcePathSpec ... ERROR
SKIP: /pbi/dept/secondary/siv/testdata/kineticsTools or /pbi/dept/secondary/siv/references/Helicobacter_pylori_J99 not available
test_run_e2e (test_tool_contract.TestIpdSummary) ... SKIP: /pbi/dept/secondary/siv/testdata/kineticsTools or /pbi/dept/secondary/siv/references/Helicobacter_pylori_J99 not available
test_run_e2e (test_tool_contract.TestIpdSummaryChunk) ... SKIP: FIXME
test_run_e2e (test_tool_contract.TestSummarizeModifications) ... SKIP: /pbi/dept/secondary/siv/testdata/kineticsTools or /pbi/dept/secondary/siv/references/Helicobacter_pylori_J99 not available
======================================================================
ERROR: test_internal.test_path
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
TypeError: test_path() takes exactly 1 argument (0 given)
======================================================================
ERROR: test_internal.test_path_with_prefixed_chem
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
TypeError: test_path_with_prefixed_chem() takes exactly 1 argument (0 given)
======================================================================
ERROR: test_internal.test_getResourcePathSpec
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
TypeError: test_getResourcePathSpec() takes exactly 1 argument (0 given)
----------------------------------------------------------------------
Ran 27 tests in 49.601s
FAILED (SKIP=18, errors=3)
Pos: 3, TplStrand: 0
Got ctx: NGGGCGGCGACCTCG
Lut prediction: 0.692615
Gbm prediction: 0.692615
Gbm prediction fast: 0.692615
Gbm pred via predictIpdFuncModel: 0.692615
Methylated prediction: NGGGJGGCGACCTCG -> 0.809961
Methylated prediction: NGGGCGGCGJCCTCG -> 0.481690
Methylated prediction fast: NGGGJGGCGACCTCG -> 0.809961
Methylated prediction fast: NGGGCGGCGJCCTCG -> 0.481690
...
Pos: 34, TplStrand: 0
Got ctx: ATGAAAATTTTCCGG
Lut prediction: 1.700875
Gbm prediction: 1.700875
Gbm prediction fast: 1.700875
Gbm pred via predictIpdFuncModel: 1.700875
Methylated prediction: ATGAHAATTTTCCGG -> 9.737025
Methylated prediction: ATGAAAATTHTCCGG -> 2.211950
Methylated prediction fast: ATGAHAATTTTCCGG -> 9.737025
Methylated prediction fast: ATGAAAATTHTCCGG -> 2.211950
[{'LLR': 44.9363980691445, 'tpl': 14982, 'Mask': [-5, 0], 'modification': 'm6A', 'strand': 0, 'QMod': 195.15629718037397}, {'LLR': 0.7833812384793148, 'tpl': 15040, 'Mask': [-1, 3], 'modification': 'm6A', 'strand': 1, 'QMod': 5.036355656230437}, {'LLR': 45.588426682175815, 'tpl': 14991, 'Mask': [-5, 0, 1], 'modification': 'm6A', 'strand': 1, 'QMod': 197.98802146719927}, {'LLR': 12.04025630132049, 'tpl': 14997, 'Mask': [-8, -5, 1, 2, 3], 'modification': 'm4C', 'strand': 1, 'QMod': 52.290194354679265}, {'LLR': 5.787841909938088, 'tpl': 14996, 'Mask': [-6, -3, 1, 2], 'modification': 'm4C', 'strand': 1, 'QMod': 25.14956702352173}]
E: pybuild pybuild:338: test: plugin distutils failed with: exit code=1: cd /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build; python2.7 -m nose -v test
dh_auto_test: pybuild --test -i python{version} -p 2.7 returned exit code 13
Any idea how to fix this?
Kind regards
Andreas.
--
http://fam-tille.de
Reply to: