hide bash chunk execution with terminal rmarkdown::render run

[splaisan]

I have this small bash chunk which runs OK but outputs to the terminal when I run my Rmd from command line

R --slave -e "infile='extracted.fq.gz'; rmarkdown::render('Plot_FastqStats.Rmd', 'pdf_document', quiet=TRUE)"

How can I make it silent and just doing it job without echo'ing?

I have already set a bunch of things in the Rmd but still get the output below

opts_chunk$set(error=FALSE,
               message=FALSE, 
               warning=FALSE, 
               eval=TRUE,
               echo=FALSE,
               include=FALSE,
               results = "hide",
               fig.cap=".",
               fig.show="asis",
               fig.keep="high",
               fig.width=3,
               fig.hight=3,
               cache=FALSE,
               comment=NA,
               progress = FALSE, 
               verbose = FALSE)

my chunk of bash code

'''{bash, include=FALSE, results='hide'}

# declare a custom bash function
function getstats ()
{
if [ $# == 1 ]; then
  name=$(basename $1)
  zcat $1 | bioawk -c fastx -v varn=${name} 'BEGIN{FS="\t"; OFS="\t"; print "Name","Len","GC%","meanQ"}{print varn,length($seq),gc($seq),meanqual($qual)}' > data/counts.txt;
 else
     echo "# give a fastq.gz file as argument";
     return;
 fi
}

# apply the function to a fastq.gz input file
getstats $infile
'''

• Example of a run with verbose output despite all settings to FALSE/hide

R --slave -e "infile='extracted.fq.gz'; rmarkdown::render('Plot_FastqStats.Rmd', 'pdf_document', quiet=TRUE)"

running: bash  -c "
# declare a custom bash function
function getstats ()
{
if [ \$# == 1 ]; then
  name=\$(basename \$1)
  zcat \$1 | bioawk -c fastx -v varn=\${name} 'BEGIN{FS=\"\\t\"; OFS=\"\\t\"; print \"Name\",\"Len\",\"GC%\",\"meanQ\"}{print varn,length(\$seq),gc(\$seq),meanqual(\$qual)}' > data/counts.txt;
 else
     echo \"# give a fastq.gz file as argument\";
     return;
 fi
}

# apply the function to a fastq.gz input file
getstats \$infile"
Parsed with column specification:
cols(
  Name = col_character(),
  Len = col_double(),
  `GC%` = col_double(),
  meanQ = col_double()
)

[cderv]

Hi,

For such questions or issue, please next time, provide a reproducible example to work on. It is asked in the issue template you deleted.

This is more a question here than an issue I guess.

If you just want to suppress stdout and stderr in your linux terminal, you can use some linux tricks
about /dev/null

Small reprex:

---
title: "test"
output: md_document
---

```{bash message=FALSE, include=FALSE}
echo "chunk1"
```

put this in a test.Rmd then run

Rscript -e "rmarkdown::render('test.Rmd', quiet = TRUE)"

You'll have some outputs because non R engines print some messages to R output, currently by design I guess (from the source code in bloc_exec to explain what is going on.

Rscript -e "rmarkdown::render('test.Rmd', quiet = TRUE)">/dev/null 2>&1

This will print nothing in terminal. Does it work for you ?

[splaisan]

Thanks a lot for the detailed answer and sorry for not providing a working example. You confirmed that the code cannot be made really quiet from inside which was my underlying question. I will suppress verbosity at bash level as you suggest. Thanks again for your time

[cderv]

message, warning and error chunk option are there to decide if you want to keep it in rendered output with R code result or send back to console. I am not sure non R engines respect those options currently. I guess supporting quiet option for non R engine could be added but I am still in doubt if it should be done :

• It is kind of more secure to have some infos on what is going on when non R related
• Message can be suppress directly in console if necessary.

Will see what other think about this

[splaisan]

I agree, i only had this verbosity issue with bash chunks (with all verbosity options to false). With r chunks i can control without problem. I can live with this though, I was seeking perfection. ;-)

[yihui]

The chunk option message = FALSE works in this case now. Thanks for the report!

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