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BioLockJ-Dev-Team / sheepdog_testing_suite

Test suite for BioLockJ development team.
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R error messages are written to file under script/ rather than file under logs #256

Closed IvoryC closed 3 years ago

IvoryC commented 4 years ago

The log reads:

[1] "All MAIN_R_CalculateStats.R functions successfully initialized"
[1] "Execute Task [ Import BioLockJ_Lib.R ]"
Error in writeErrors(errors) : 
  /mnt/efs/pipelines/rhizosphere_fromCounts_2020Jul09/05_R_CalculateStats/script/MAIN_R_CalculateStats.R status --> FAILED!  Error details saved to: /mnt/efs/pipelines/rhizosphere_fromCounts_2020Jul09/05_R_CalculateStats/script/MAIN_R_CalculateStats.R_Failures
Calls: runModule ... prepRun -> executeTask -> checkStatus -> writeErrors
Execution halted

And script/MAIN_R_CalculateStates.R_Failures reads:

Missing R library, please run install.packages("ggpubr") from within R
Error in writeErrors(errors) : 
  /mnt/efs/pipelines/rhizosphere_fromCounts_2020Jul09/05_R_CalculateStats/script/MAIN_R_CalculateStats.R status --> FAILED!  Error details saved to: /mnt/efs/pipelines/rhizosphere_fromCounts_2020Jul09/05_R_CalculateStats/script/MAIN_R_CalculateStats.R_Failures

That message should have been written to the log file; not a flag file.

Also---really need a mechanism to check packages during check dependencies! (sep issue)

IvoryC commented 3 years ago

I believe this has been fixed. When I reviewed a pipeline just now, the error was part of the log file, not part of the _Failed file.