I am running two different commands to run two different R Scripts and one of it is generating log and other is not. I am unable to figure out why .. any pointers would be appreciated
Working and generating log/error
Rscript main.R '2021=Jun_2021.xlsx&2021=May_2021.xlsx' 2> output/test_err.txt | tee output/test_log.txt
Executes Script but Not generating log/error
Rscript main.R '2021=TESTFILE.xlsm&Param1=INZ01¶m2=Test' 2> output/test_err.txt | tee output/test_log.txt
as it turned out, i had a script to cleanup the output folder and was deleting these .txt files in the process.
Appreciate your inputs guys, thanks.
Related
I have multiple scripts naming R001.r, R002.r, and so on. I need to schedule them so that they run in a sequential manner one after the other. What would be the best approach to do this.
I think you want to wrap your r scripts in a caller sh file and then invoke it through terminal. Here is what I would do.
Open up a terminal or any text editor available and fill it up with the following commands:
Rscript R0001.r
Rscript R0002.r
Rscript R0003.r
...
Save this file into something like call_my_scripts. You can then execute it via standard unix shell commands as follows:
./call_my_scripts
This will run sequentially by definition. Make sure you give exec permissions to the file before you invoke it as follows:
chmod u+x call_my_scripts
I am running a script that starts as follows:
#!/usr/bin/env Rscript
#./geneiase -t static -i mydata.tab
If I run the script on my data directly in the command line, it starts without errors or warnings.
But the program is very demanding computationally so I need to submit my jobs to a cluster using a job scheduler called Slurm.
When I write the exact same expression (as in the second paragraph) within the batch job file, and then I submit the job using sbatch, it is immediatelly terminated and does not return any error or output that can help me understand the problem.
I think it has to do with having Rscript in $PATH, but even though I added the directory where Rscript is located to $PATH by: PATH=$PATH:path/to/R/build/R-3.4.0/lib64/R/bin, the problem remains.
Is there a way that I can make Rscript be run in a Slurm batch job?
You'll need to keep the environment of your SLURM script as bash
#!/bin/bash
Since you can run your R script from the command line, it likely means the path to R is already included in your $PATH. On the command line, you might already do something like:
Rscript ./path-to-script/script
To run R from within your SLURM script, it's the same as running from the command line:
Rscript ./path-to-script/script
I'm trying to follow the conventional method to trigger R scripts through batch like
RScript Example.R
but what i look to is some way to run multiple R scripts through a batch file.
I tried to do use Start command to open multiple sessions but that doesn't work either. (RScript START ex1.R START ex2.R)
PS complete noob to batch files.
On Windows - if you want to run them in parallel make sure you add start in yoyr batch (.bat) script. Otherwise Example2.R waits for Example1.R to complete etc.
start RScript Example1.R
start RScript Example2.R
...
If you're using sh to launch your scripts, this could do it.
cd /path_to_script1/
sh script1.sh &
cd /path_to_script2/
sh script2.sh &
cd /path_to_script3/
sh scipt2.sh &
This launches parallel R sessions (one for each script) so careful with memory and CPU use. Each script file contains Rscript command.
Simply save the RScript commands in a Windows batch file (.bat) then double-click the file in directory or call it via command line. Below assumes RScript is an environment variable.
Batch file (type below in Notepad and save with extension .bat, not default .txt)
cd "C:\Path\To\Scripts"
RScript Example1.R
RScript Example2.R
RScript Example3.R
RScript Example4.R
RScript Example5.R
CMD Command line
call myRScriptBatchFile.bat
PowerShell Command line
cmd.exe /c myRScriptBatchFile.bat
I'm running, using crontab, an R/Shiny WebApp. The crontab expression looks like this:
#reboot R -e 'shiny::runApp(...)' | tee /var/log/shiny-server.log
I've also tried
#reboot R -e 'shiny::runApp(...)' &> /var/log/shiny-server.log
but does the same: It prints to the file the header when you initialize R from shell. But it doesn't print any text about the page, i.e. when it loads, when it uploads something, when it crashes...
Do you know how to pipe the output of the logs of the WebApp to the file?
Thank you
I have been searching in the web and I didn't find any solution.
Instead, I changed the philosophy. I generated myself some logs from inside the Shiny app with the help of the sink() function.
Thank you.
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.