Commit 24f67a24 authored by Joerg Buescher's avatar Joerg Buescher
Browse files

tryCatch around tidy up part in qqq_auto_integrate

parent fcb5e23f
......@@ -186,20 +186,25 @@ print('passed git check')
# for documentation purposes append session info to log. do this at the end because it's a messy read.
cat(as.character(sessionInfo()), file=prm$log_con)
# Call sample postprocessing if in pipeline mode
if (!(as.character(Sys.info()[["user"]]) == 'rstudio')){
rm(list = ls()) # empty workspace to avoid out of memory options
gc()
# system("chmod 777 overviewheatmap.pdf", intern=FALSE, wait=FALSE)
system("python3 /code/msweb/metabolomics/help/sample_postprocessing.py", intern=FALSE, wait=FALSE)
}
# cat('\nSettings overview: \n')
# cat(as.character(prm),file=prm$log_con)
print ('qqq_auto_integrate complete.')
tryCatch({
# Call sample postprocessing if in pipeline mode
if (!(as.character(Sys.info()[["user"]]) == 'rstudio')){
rm(list = ls()) # empty workspace to avoid out of memory options
gc()
# system("chmod 777 overviewheatmap.pdf", intern=FALSE, wait=FALSE)
system("python3 /code/msweb/metabolomics/help/sample_postprocessing.py", intern=FALSE, wait=FALSE)
}
# cat('\nSettings overview: \n')
# cat(as.character(prm),file=prm$log_con)
print ('qqq_auto_integrate complete.')
# tidy up
setwd(originalwd)
par(pardefault)
# tidy up
setwd(originalwd)
par(pardefault)
}, error = function(err) {
# if tidying up doesn't work, well too bad.
})
} # endfunction
......
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