When running
R CMD BATCH [options] filename.r
I want to control where the output is printed. I can suppress the creation of the .Rout file with
R CMD BATCH [options] filename.r /dev/null
but is it possible to direct the output to the screen? Like when I run it by
R [options] < filename.r
?
Guess you're on linux. Tried already to redirect to /dev/console ?
Edit -add info from the comments -:
/dev/console apparently doesn't work, /dev/tty does. Depending on the system, /dev/tty0 might be an option too
Cheers
Try Rscript or R --no-save < filename.R:
biocoreap1:Desktop vinceb$ Rscript test.R
test
biocoreap1:Desktop vinceb$ R --no-save < test.R
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
[...]
[Previously saved workspace restored]
> cat('test\n')
test
>
You can maybe do both at the same time (creating the file and printing on screen) if you run R CMD BATCH [options] filename.r and then tail -f filename.Rout
Related
In the past I have used R CMD BATCH to execute R code from the command line on a Linux server. The syntax I used was
R CMD BATCH --no-save --no-restore rcode.r output.txt
The above code writes console output to output.txt which can be monitored as the script is running. Is this also possible with Rscript? I would prefer to use Rscript since I have heard that R CMD BATCH is deprecated.
To clarify my original question, R CMD BATCH writes all console output, including messages, warnings, and print() statements, to output.txt. In contrast Rscript rcode.r > output.txt writes only the print()ed output to the text file and everything else to the terminal. How can I replicate the behavior of R CMD BATCH with Rscript?
I discovered after some digging that, at least on the Linux system I'm using, Rscript is just a convenience function. If you call
Rscript --verbose foobar.r
you will see the underlying call is:
running
'/usr/lib/R/bin/R --no-echo --no-restore --file=foobar.r'
This means that --no-echo is baked into Rscript.
Therefore the solution is to run
/usr/lib/R/bin/R --no-restore --file=foobar.r > output.txt
where the --no-echo is removed, and the output is redirected to a text file as suggested by #MrFlick. The commands will be echoed in addition to the output.
You can create a new alias for Rscript if you want --no-echo to be removed by default. For example, in my .bashrc file I have the following:
function Rscript2() { R --no-restore --file="$1"; }
export -f Rscript2
Now, in my Slurm batch job scripts, I can run Rscript2 file.R to get the desired behavior: all R console output is included in the slurm-*.out files.
Just redirect the output to a file like you would with any other command line output
Rscript rcode.r > output.txt
I am looking for a way to put a breakpoint during an execution of an R script either using Rscript script.R or R --vanilla --silent -f script.R.
I'd expect that R --vanilla --slave -e 'browser()' would not just output Called from: top level and exit, but instead break and open the Browse[1]> > shell.
Is there a way to achieve that in R using browser(), debugger(), etc?
I am using Rscript to run an R script but I get a lot of output on my screen. Can I run Rscript in silent mode (meaning without any screen output)?
Several options come to mind:
within R: use sink() to divert output to a file, see help(sink)
on the shell: Rscript myscript.R 2>&1 >/dev/null
edit the code :)
on Linux, use our littler frontend as it runs in --slave mode by default :)
Options 3 is the most involved but possibly best. You could use a logging scheme where you print / display in "debug" or "verbose" but not otherwise. I often do that, based on a command-line toggle given to the script.
You can redirect the output with
Rscript myscript.R >& >/dev/null (linux)
or
Rscript myscript.R >$null (windows)
or use R directly:
R --quiet --vanilla < myscript.R
or
R CMD BATCH myscript.R
(That last version writes the output to a file myscript.Rout)
One more option: if you want to separate the output and the error message into different files, which makes it easier to identify the problems, you can use the command on the shell:
Rscript myscript.R >a.Rout 2>a.Rerr
This will write the program output to a.Rout and the error messages to a.Rerr. Note that the files of a.Rout and a.Rerr should be removed beforehand, to avoid an error.
I am a bit lost when dealing with installing and using R. I installed R 3.0.1 from source and did the ./configure, make, make check, and make install as suggested. However I tried running R but it said that R wasn't in the /usr/bin folder. So I then copied the entire R-3.0.1/bin directory into my /usr/bin directory using cp. Now I'm getting a few errors regarding /usr/bin/env when trying to use RScript on a hello_world.R script I wrote from the O'Reilly R In a Nutshell book I store in a file hello_world.R the contents are below:
#! /usr/bin/env RScript
print("Hello World!");
Simple enough, but when I try to load it I get the following error:
$ ./hello_world.R
/usr/bin/env: RScript: No such file or directory
I'm not sure if this is a PATH problem or something, but when I search in my /usr/bin directory I do see the RScript file in there along with (R, BATCH, and the others associated with R programming language). Any help is greatly appreciated. Cheers.
You may be using an invalid command line option for Rscript in your shebang line.
For instance ...
#!/usr/bin/env RScript --vanilla
remove "--vanilla" (or other offending option) and rerun your script
#!/usr/bin/env RScript
I know you didn't put this in your example, but the solution may help others searching for the same issue.
Again, the good solution to this problem is very simple and clearly explained in the man page of env. The script should use the env command to invoke Rscript and not Rscript directly:
#!/usr/bin/env Rscript
some R code now...
But a script like this will read the user's .Rprofile among other things. When we want to have a vanilla R session (in order to start with a clean and controlled R), we must pass the option --vanilla. If you try something like
#!/usr/bin/env Rscript --vanilla
some R code now...
env will take the string Rscript --vanilla a the command to execute and will inevitably return the error message
/usr/bin/env: ‘Rscript --vanilla’: No such file or directory
In env's man page, there is an option called -S for splitting the strings. Its role is exactly to solve the problem above and use the first string Rscript as the command name, and the following strings (like --vanilla) as options to pass to Rscript.
The solution is therefore:
#!/usr/bin/env -S Rscript --vanilla
some R code now...
Put in the shebang line of your script #!/usr/bin/Rscript and it should work.
As a side remark if you want to keep up-to-date with the R versions from CRAN and not relying on the native R of your Linux distro (Ubuntu) then add the following line in your apt sources:
deb http://my_favorite_cran_mirror/bin/linux/ubuntu raring/
After that you can always use the apt system to install R which -I would agree with Jake above- it should be the preferable way to install R.
*Change the my_favorite_cran_mirror with a valid CRAN mirror that is close to you.
#! /usr/bin/env RScript
print("Hello World!");
Simple enough, but when I try to load it I get the following error:
$ ./hello_world.R
/usr/bin/env: RScript: No such file or directory
Here u make mistake is that instead of RScript write Rscript.
The syntax will be
#! /usr/bin/env Rscript
print("Hello World!");
Then run it it will work (y) all the best.
$./hello_world.R
I arrived at this question trying to understand this error message on a cluster computer where I did not have control over the R installation.
In general, when I converted Rscript in my makefile to /usr/bin/Rscript the error message no longer occurred.
I have some scripts that I run using R's batch mode.
/usr/bin/R CMD BATCH --vanilla --no-timing ~/scripts/R/sess_dur.R
I redirect the output to a file using:
> sink("~/scripts_output/R_output.txt",append=TRUE)
The problem is that when I run this script, files are created with the same name of the script and the "out" suffix (sess_dur.Rout).
There is some way to tell R not to generate these files?
Have you tried something like:
R CMD BATCH --vanilla --no-timing ~/scripts/R/sess_dur.R /dev/null