Hi Kevin,
thanks for pushing pristine-tar. Unfortunately I get a build error in a
sid chroot (created by pbuilder):
...
Finished job 0.
4 of 3 steps (133%) done
.EE
======================================================================
ERROR: tests.tests.test_default_remote
----------------------------------------------------------------------
Traceback (most recent call last):
File "/build/snakemake-3.13.3/.pybuild/pythonX.Y_3.5/build/snakemake/remote/S3.py", line 22, in <module>
from filechunkio import FileChunkIO
ImportError: No module named 'filechunkio'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/build/snakemake-3.13.3/.pybuild/pythonX.Y_3.5/build/tests/tests.py", line 536, in test_default_remote
default_remote_prefix="test-remote-bucket")
File "/build/snakemake-3.13.3/.pybuild/pythonX.Y_3.5/build/tests/tests.py", line 87, in run
config=config, **params)
File "/build/snakemake-3.13.3/.pybuild/pythonX.Y_3.5/build/snakemake/__init__.py", line 323, in snakemake
default_remote_provider)
File "/usr/lib/python3.5/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 986, in _gcd_import
File "<frozen importlib._bootstrap>", line 969, in _find_and_load
File "<frozen importlib._bootstrap>", line 958, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 673, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 697, in exec_module
File "<frozen importlib._bootstrap>", line 222, in _call_with_frames_removed
File "/build/snakemake-3.13.3/.pybuild/pythonX.Y_3.5/build/snakemake/remote/S3Mocked.py", line 15, in <module>
from snakemake.remote.S3 import RemoteObject as S3RemoteObject, RemoteProvider as S3RemoteProvider
File "/build/snakemake-3.13.3/.pybuild/pythonX.Y_3.5/build/snakemake/remote/S3.py", line 25, in <module>
"need to be installed to use S3 remote() file functionality. %s" % e.msg)
snakemake.exceptions.WorkflowError: The Python 3 packages 'boto' and 'filechunkio' need to be installed to use S3 remote() file functionality. No module named 'filechunkio'
======================================================================
ERROR: tests.tests.test_run_namedlist
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/build/snakemake-3.13.3/.pybuild/pythonX.Y_3.5/build/tests/tests.py", line 539, in test_run_namedlist
run(dpath("test_run_namedlist"))
File "/build/snakemake-3.13.3/.pybuild/pythonX.Y_3.5/build/tests/tests.py", line 66, in run
with tempfile.TemporaryDirectory(prefix=".test", dir=os.path.abspath(".")) as tmpdir:
File "/usr/lib/python3.5/posixpath.py", line 362, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
======================================================================
FAIL: tests.tests.test_script
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/build/snakemake-3.13.3/.pybuild/pythonX.Y_3.5/build/tests/tests.py", line 317, in test_script
run(dpath("test_script"))
File "/build/snakemake-3.13.3/.pybuild/pythonX.Y_3.5/build/tests/tests.py", line 91, in run
assert success, "expected successful execution"
AssertionError: expected successful execution
-------------------- >> begin captured logging << --------------------
snakemake.logging: WARNING: Provided cores: 3
snakemake.logging: WARNING: Rules claiming more threads will be scaled down.
snakemake.logging: WARNING: Job counts:
count jobs
1 2
1 3
1 4
1 all
4
snakemake.logging: INFO:
snakemake.logging: INFO: rule 3:
output: test.in
jobid: 3
snakemake.logging: INFO:
snakemake.logging: INFO: rule 4:
output: test.html
jobid: 1
snakemake.logging: INFO:
snakemake.logging: ERROR: Error in job 4 while creating output file test.html.
snakemake.logging: ERROR: RuleException:
CalledProcessError in line 32 of /build/snakemake-3.13.3/.pybuild/pythonX.Y_3.5/build/tests/test_script/Snakefile:
Command 'Rscript -e 'rmarkdown::render("/build/snakemake-3.13.3/.pybuild/pythonX.Y_3.5/build/tests/test_script/scripts/.snakemake.3125nv4v.test.Rmd", output_file="/build/snakemake-3.13.3/.pybuild/pythonX.Y_3.5/build/.testkk3zpbdz/test.html", quiet=TRUE, params = list(rmd="/build/snakemake-3.13.3/.pybuild/pythonX.Y_3.5/build/tests/test_script/scripts/.snakemake.3125nv4v.test.Rmd"))'' returned non-zero exit status 1
File "/build/snakemake-3.13.3/.pybuild/pythonX.Y_3.5/build/tests/test_script/Snakefile", line 32, in __rule_4
File "/usr/lib/python3.5/concurrent/futures/thread.py", line 55, in run
snakemake.logging: WARNING: Will exit after finishing currently running jobs.
snakemake.logging: INFO: Finished job 3.
snakemake.logging: INFO: 1 of 4 steps (25%) done
snakemake.logging: WARNING: Will exit after finishing currently running jobs.
snakemake.logging: ERROR: Exiting because a job execution failed. Look above for error message
--------------------- >> end captured logging << ---------------------
----------------------------------------------------------------------
Ran 87 tests in 51.630s
FAILED (errors=2, failures=1)
E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd /build/snakemake-3.13.3/.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
Kind regards
Andreas.
--
http://fam-tille.de