Error in mbWorkflow if babel dir is incorrect

MassBank / RMassBank

Playground for experiments on the official http://bioconductor.org/packages/devel/bioc/html/RMassBank.html

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Error in mbWorkflow if babel dir is incorrect #95

Closed schymane closed 9 years ago

schymane commented 9 years ago

If the Babel dir in the settings is incorrect, this currently results in an error at mbWorkflow Step 6 (generate molfiles) - whereas if no babel dir is given, we can still produce structures. We should be able to catch this error and go back to the default (ugly) structures. In the end we should look into replacing our dependency on OpenBabel as mentioned in #90

mbworkflow_error_step6

schymane commented 9 years ago

Three options:

try to auto-detect babel
catch error and default back to CACTUS
Access Babel through R #90

ermueller commented 9 years ago

Fixed in ee161fb

schymane commented 9 years ago

Leaving #90 as enhancement, this can be closed