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niemasd / FAVITES

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)
GNU General Public License v3.0
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PANGEA doesn't work in Docker image #8

Closed niemasd closed 6 years ago

niemasd commented 6 years ago

Configuration File

.travis_tests/test_PANGEA.json

Unexpected Behavior

/---------------------------------------------------------------------\
| FAVITES - FrAmework for VIral Transmission and Evolution Simulation |
|                            Version 1.0.3                            |
|                         Niema Moshiri 2017                          |
\---------------------------------------------------------------------/
========================   Simulation Process  ========================
Loading contact network...Traceback (most recent call last):
  File "/FAVITES/run_favites.py", line 75, in <module>
    MF.modules['Driver'].run('/'.join(expanduser(abspath(argv[0])).split('/')[:-1]), ORIG_CONFIG)
  File "/FAVITES/modules/Driver_Default.py", line 109, in run
    GC.cn_edge_list = MF.modules['ContactNetworkGenerator'].get_edge_list()
  File "/FAVITES/modules/ContactNetworkGenerator_PANGEA.py", line 58, in get_edge_list
    check_output([GC.Rscript_path,PANGEA_command_script], stderr=open(devnull,'w'))
  File "/usr/lib/python3.5/subprocess.py", line 626, in check_output
    **kwargs).stdout
  File "/usr/lib/python3.5/subprocess.py", line 708, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['Rscript', 'FAVITES_PANGEA_COMMAND.R']' returned non-zero exit status 1
niemasd commented 6 years ago

Fixed in 1.1.0