Commit d422a0f3 authored by Joerg Buescher's avatar Joerg Buescher
Browse files

adding troubleshooting output

parent cbf2c19a
......@@ -17,9 +17,11 @@ qqq_auto_integrate <- function(nowfolder = "", parameters = list()) {
# Set working directory (in Testmode)
if (nowfolder == '') {
print('setting nowfolder')
nowfolder <- getwd()
}else{
if(dir.exists(nowfolder)){
print('setting nowfolder2')
setwd(nowfolder)
}else{
cat(paste0(nowfolder," directory doesn't exist!"))
......@@ -33,6 +35,7 @@ qqq_auto_integrate <- function(nowfolder = "", parameters = list()) {
# Initialize prm (global settings)
prm <- initialize_prm()
print('initialize complete')
# update prm from local settings in mzML folder
update_prm_path <- paste0(nowfolder,"/update_prm.xlsx")
......@@ -52,7 +55,7 @@ qqq_auto_integrate <- function(nowfolder = "", parameters = list()) {
prm[[paranames[ip]]] <- parameters[[paranames[ip]]]
}
}
print('prm update complete')
if(!prm$runninglocal){ # if running on server
sink(prm$log_con, append=TRUE) # output errors and messages to log file
}
......@@ -85,7 +88,7 @@ qqq_auto_integrate <- function(nowfolder = "", parameters = list()) {
}, error = function(err) {
# not in docker container used for development, do nothing
})
print('passed git check')
# Reset working directory
setwd(nowfolder)
......
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