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patr1ckm

civis-compute's Issues

Rscript + default packages

For R, we should change the default Rscript command to

Rscript --default-packages=methods,datasets,utils,grDevices,graphics,stats [file.R]

This saves some heartache because methods isn't loaded by default. This replicates exactly the default packages loaded in an interactive R session.

R support

Thanks for this! I tried it out with a simple R script called test.R that just contains 2 + 2.

civis-compute submit test.R
civis-compute status 8050758

The log is:

log file:
  [2017-11-10T19:33:41.000Z] Queued
  [2017-11-10T19:33:42.000Z] Running
  [2017-11-10T19:33:43.000Z] Dedicating resources
  [2017-11-10T19:33:45.000Z] Downloading code and container
  [2017-11-10T19:33:46.000Z] Executing script
  [2017-11-10T19:33:46.000Z] Traceback (most recent call last):
  [2017-11-10T19:33:46.000Z]   File "/usr/local/bin/civis", line 11, in <module>
  [2017-11-10T19:33:46.000Z]     sys.exit(main())
  [2017-11-10T19:33:46.000Z]   File "/usr/local/lib/python2.7/dist-packages/civis/cli/__main__.py", line 334, in main
  [2017-11-10T19:33:46.000Z]     cli = generate_cli()
  [2017-11-10T19:33:46.000Z]   File "/usr/local/lib/python2.7/dist-packages/civis/cli/__main__.py", line 229, in generate_cli
  [2017-11-10T19:33:46.000Z]     spec = retrieve_spec_dict()
  [2017-11-10T19:33:46.000Z]   File "/usr/local/lib/python2.7/dist-packages/civis/cli/__main__.py", line 201, in retrieve_spec_dict
  [2017-11-10T19:33:46.000Z]     modified_time = os.path.getmtime(_CACHED_SPEC_PATH)
  [2017-11-10T19:33:46.000Z]   File "/usr/lib/python2.7/genericpath.py", line 62, in getmtime
  [2017-11-10T19:33:46.000Z]     return os.stat(filename).st_mtime
  [2017-11-10T19:33:46.000Z] OSError: [Errno 2] No such file or directory: '/root/.civis_api_spec.json'
  [2017-11-10T19:33:47.000Z] Memory statistics are unavailable
  [2017-11-10T19:33:47.000Z] Error on job: Process ended with an error, exiting: 1.
  [2017-11-10T19:33:47.000Z] Failed

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