I'm writing a bash script (to be called from the terminal -- on a Linux system) that creates a log-file prior to initiating an 'rscript' using some simple user input. I'm however running into problems in controlling what messages are included in the log file (or sent to the terminal), and can't find any solution for excluding one specific R package-load message:
Package WGCNA 1.66 loaded.
In other words I need a way to (only) silence this specific message, which is printed when the WGCNA package is successfully loaded.
I will try to keep the code non-specific to hopefully make it easier to follow.
The below block is a skeleton (excluding some irrelevant code), and will be followed by some different variants I've tried. Where, originally i tried controlling the output from the R script using sink() and suppressPackageStartupMessages(), which - I thought - should have been enough.
bash script:
#!/usr/bin/env bash
read RDS
DATE=`date +%F-%R`
LOG=~/path/log/$DATE.log
touch $LOG
export ALLOW_WGCNA_THREADS=4
Rscript ~/path/analysis.R $RDS $DATE $LOG
R script:
#!/usr/bin R
# object set-up
rds.path <- "~/path/data/"
temp.path <- "~/path/temp/"
pp.data <- readRDS(paste0(rds.path, commandArgs(T)[1]))
file.date <- paste0(commandArgs(T)[2], "_")
# set up error logging
log.file <- file(commandArgs(T)[3], open="a")
sink(log.file, append=TRUE, type="message")
sink(log.file, append=TRUE, type="output")
# main pkg call
if(suppressPackageStartupMessages(!require(thePKG))){
stop("\nPlease follow the below link to install the requested package (thePKG) with relevant dependencies\n https://link.address")
}
# thePKG method call
cat("> Running "method"\n", append=TRUE)
module <- method(thePKG_input = pp.data, ppi_network = ppi_network)
# reset sink and close file connection
sink(type="message")
sink(type="output")
close(log.file)
This doesn't output anything to the terminal (which is good), including the following in the log-file:
Package WGCNA 1.66 loaded.
> Running "method"
Error: added error to verify that it's correctly printed to the file
I want to keep my log files as clean and on point as possible (and avoid clutter in the terminal), and therefor wish to remove the package-load message. I've tried the following...
i. Omitting the sink() call from the R script, and adding
&>> $LOG
to the bash 'Rscript' call. Resulting in the same file output as above.
ii. Same as i but substituting suppressPackageStartupMessages() with suppressMessages(), which results in the same file output as above.
iii. Same as i but added
... require(thePKG, quietly=TRUE)
in the R script # main pkg call, with the same results.
These where the potential solutions I came across, and tried in different variations with no positive results.
I also wondered if the WGCNA package was loaded "outside" of the !require-loop of thePKG, since it's not affected by suppressMessages() for that call. But, introducing an intentional error (which terminated the process) prior to the if-require(thePKG)-call removed the message -- hinting at its initiation inside the loop. I also tried calling WGCNA by itself at the start of the R script, with an added suppressMessages() to it, but that didn't work either. The export function used in the bash script doesn't effect the outcome (to my knowledge) and removing it extends the load message to include the following (truncated to save space):
Package WGCNA 1.66 loaded.
Important note: It appears that your system supports multi-threading, but it is not enabled within WGCNA in R.
To allow multi-threading within WGCNA with all available cores, use allowWGCNAThreads() within R. Use disableWGCNAThreads() to disable threading if necessary.
(...)
I'm aware that I could send the output (only) to /dev/null, but there's other output printed to the file (e.g. > Running "method") that I still want.
Does anyone have a suggestion for how to remove this message? I'm very new to programming in R, and just started using Linux (Ubuntu LTS), so please keep that in mind when answering.
Thanks in advance.
I could gather the following execution flow from your question:
Bash_Script ----> R_Script ----> Output_to_terminal (and also a log file probably)
For the requirements stated, following commands (in bash) could help you:
grep - This command helps you search for patterns
Pipe (|) - This is an operator in Linux which helps you redirect output of one command as input to another for further processing (For eg. A | B )
tee - This command takes any input and forwards it to a file + standard output (terminal)
So, you could mix and match the above commands in your bash file to get the desired output:
You can extend
Rscript ~/path/analysis.R $RDS $DATE $LOG
with
Rscript ~/path/analysis.R "$RDS" "$DATE" "$LOG" | grep -v "Package WGCNA" | tee "output.log"
What each command does ?
a) | -> This redirects output of preceding command as input to the next. It's more of a connector
b) grep -> Normally used to search for patterns. In this example, we use it with -v option to do a invert-match instead i.e. search for everything except Package WGCNA
c) tee -> This writes output to terminal + also redirects the same to a log file name, passed as argument. You could skip this command altogether, if not needed