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EOSC-LOFAR / prefactor-cwl

CWL version of prefactor
MIT License
3 stars 3 forks source link

make run-udocker gives AttributeError: type object '_io.BytesIO' has no attribute 'StringIO' on ManjaroLinux #30

Closed HannoSpreeuw closed 5 years ago

HannoSpreeuw commented 5 years ago

lsb_release -a ---> LSB Version: n/a Distributor ID: ManjaroLinux Description: Manjaro Linux Release: 18.0.0-rc Codename: Illyria

git clone git@github.com:EOSC-LOFAR/prefactor-cwl.git
cd prefactor-cwl make small make run-udocker ..... ..... Info: installing from: http://repo.indigo-datacloud.eu/repository/indigo/2/centos7/x86_64/tgz/udocker-1.1.1.tar.gz Traceback (most recent call last): File "some_path/udocker/prefactor-cwl/.virtualenv/bin/udocker", line 6663, in sys.exit(Main().start()) File "some_path/udocker/prefactor-cwl/.virtualenv/bin/udocker", line 6651, in start exit_status = self.execute() File "some_path/udocker/prefactor-cwl/.virtualenv/bin/udocker", line 6631, in execute cmds"install" File "some_path/udocker/prefactor-cwl/.virtualenv/bin/udocker", line 6300, in do_install status = utools.install(force) File "some_path/udocker/prefactor-cwl/.virtualenv/bin/udocker", line 1265, in install tarball_file = self._download(tarball) File "some_path/udocker/prefactor-cwl/.virtualenv/bin/udocker", line 1154, in _download (hdr, dummy) = self.curl.get(tarball_url, ofile=tarball_file) File "some_path/udocker/prefactor-cwl/.virtualenv/bin/udocker", line 4413, in get return self._geturl.get(args, kwargs) File "some_path/udocker/prefactor-cwl/.virtualenv/bin/udocker", line 4501, in get buf = cStringIO.StringIO() AttributeError: type object '_io.BytesIO' has no attribute 'StringIO' [job ndppp_prep_cal] Job error: Error collecting output for parameter 'msout': steps/ndppp_prep_cal.cwl:164:7: Did not find output file with glob pattern: '[u'calibrated.MS']' [job ndppp_prep_cal] completed permanentFail Workflow cannot make any more progress. Final process status is permanentFail make: [Makefile:48: run-udocker] Error 1

mr-c commented 5 years ago

Change the first line of .virtualenv/bin/udocker to read python2 instead of plain python or install from the devel branch on GitHub:

  curl https://raw.githubusercontent.com/indigo-dc/udocker/devel/udocker.py > udocker
  chmod u+rx ./udocker
  ./udocker install
HannoSpreeuw commented 5 years ago

Thanks. I chose the first option. Fixed.