Bug #10881
Updated by Ward Vandewege almost 8 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 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?