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comses / miracle

Repeatable data analysis workflows for computational models
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DeployR working directory not correctly set #61

Closed warmdev closed 8 years ago

warmdev commented 8 years ago

DeployR working directory is not set when running a script (line 35 of tasks.py), thus it always use DEFAULT_WORKING_DIRECTORY, which is luxedemo by default (line 13 in deployr.py). This causes rhea scripts unable to run.

warmdev commented 8 years ago

Issue persists but is related to how R scripts are loaded to DeployR. Currently all R scripts in the src folder (including any subfolder) are loaded to DeployR into the same directory (DeployR does not support more than one level of subdirectory).

This is not an issue for luxedemo as it does not have any subfolder under src, but it causes rhea scripts to fail, as most scripts there use a library script ut_did.R in the src/lib folder.

Solution: either require that there is no subfolder under src, or use deployrExternal to refer to any files under subfolders.

warmdev commented 8 years ago

The flat folder solution does not work (DeployR cannot source files in the repository directory, only files in the project directory). Will need to require user to use deployrExternal to declare any sourced files. Updated https://github.com/comses/miracle-example-projects to reflect this.