Bug #10881
Updated by Ward Vandewege over 7 years ago
<pre>
cwltool INFO: /home/tfmorris/venv/bin/arvados-cwl-runner 863280201573355f380c59226015373885b50617 1.0.20170112194703, arvados-python-client 0.1.20170112173420, cwltool 1.0.20170112185927
2017-01-13_01:58:09 e51c5-8i9sb-q0w9end7q7mszgc 18554 docker image hash is 9974f6d72cf4a57923b0c4c3ecbaf58c9af43c35b2003e3ad765de69fa314f7c
2017-01-13_01:58:42 e51c5-8i9sb-q0w9end7q7mszgc 18554 0 stderr Using Arvados SDK version 0.1.20170112173420
2017-01-13_01:58:43 e51c5-8i9sb-q0w9end7q7mszgc 18554 0 stderr Traceback (most recent call last):
2017-01-13_01:58:43 e51c5-8i9sb-q0w9end7q7mszgc 18554 0 stderr File "/tmp/crunch-job/src/crunch_scripts/cwl-runner", line 13, in <module>
2017-01-13_01:58:43 e51c5-8i9sb-q0w9end7q7mszgc 18554 0 stderr arvados_cwl.crunch_script.run()
2017-01-13_01:58:43 e51c5-8i9sb-q0w9end7q7mszgc 18554 0 stderr File "/usr/lib/python2.7/dist-packages/arvados_cwl/crunch_script.py", line 35, in run
2017-01-13_01:58:43 e51c5-8i9sb-q0w9end7q7mszgc 18554 0 stderr logger.info(arvados_cwl.versionstring())
2017-01-13_01:58:43 e51c5-8i9sb-q0w9end7q7mszgc 18554 0 stderr File "/usr/lib/python2.7/dist-packages/arvados_cwl/__init__.py", line 495, in versionstring
2017-01-13_01:58:43 e51c5-8i9sb-q0w9end7q7mszgc 18554 0 stderr arvcwlpkg = pkg_resources.require("arvados-cwl-runner")
2017-01-13_01:58:43 e51c5-8i9sb-q0w9end7q7mszgc 18554 0 stderr File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 745, in require
2017-01-13_01:58:43 e51c5-8i9sb-q0w9end7q7mszgc 18554 0 stderr needed = self.resolve(parse_requirements(requirements))
2017-01-13_01:58:43 e51c5-8i9sb-q0w9end7q7mszgc 18554 0 stderr File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 639, in resolve
2017-01-13_01:58:43 e51c5-8i9sb-q0w9end7q7mszgc 18554 0 stderr raise DistributionNotFound(req)
2017-01-13_01:58:43 e51c5-8i9sb-q0w9end7q7mszgc 18554 0 stderr pkg_resources.DistributionNotFound: futures>=3.0.5
2017-01-13_01:58:43 e51c5-8i9sb-q0w9end7q7mszgc 18554 0 stderr srun: error: compute2: task 0: Exited with exit code 1
2017-01-13_01:58:43 e51c5-8i9sb-q0w9end7q7mszgc 18554 0 child 18967 on compute2.1 exit 1 success=
</pre>
New dependency on python-futures, apparently. So where is it coming from?
<pre>
(venv)...$ pipdeptree -r -p futures
Warning!! Cyclic dependencies found:
* SPARQLWrapper => rdflib => SPARQLWrapper
* rdflib => SPARQLWrapper => rdflib
------------------------------------------------------------------------
futures==3.0.5
- cwltest==1.0.20161227194859 [requires: futures>=3.0.5]
- cwltool==1.0.20170112185927 [requires: cwltest>=1.0.20161227194859]
- arvados-cwl-runner==1.0.20170112194703 [requires: cwltool==1.0.20170112185927]
</pre>
Huh, it's there in the python packages, no problem.
But we don't package futures in deb/rpm and the distribution packages debs are missing the dependency (here, for example, is the ubuntu1204 version of cwltest):
<pre>
shell.e51c5:~# apt-cache show python-cwltest
Package: python-cwltest
Version: 1.0.20161227194859-2
License: Apache 2.0
Vendor: none
Architecture: all
Maintainer: Ward Vandewege <ward@curoverse.com>
Installed-Size: 23
Depends: python-schema-salad (>= 1.14), python-typing (>= 3.5.2), python-junit-xml (>= 1.7), python2.7
Section: default
Priority: extra
Homepage: https://github.com/common-workflow-language/cwltest
Description: Common workflow language testing framework
Description-md5: 4071a470dc6bcdbae7fb8dd3f5e6863b
Filename: pool/trusty/main/p/python-cwltest/python-cwltest_1.0.20161227194859-2_all.deb
MD5sum: 1defaa6918fe3dccb6c090233b6b840b
SHA1: 01b49291cb6ca07cfa526641bd3b52ecb92ae928
SHA256: e973b583333df03817b87d49cfb9011eda0c5a7427bc81a730d4a80066c9882b
Size: 10722
...
</pre>
So... fpm bug?