I have 2 R scripts in the sub-folders of folder1, and ran the following script. "No such file or directory" error was returened for the R scripts. Does anyone know how to solve this problem? Thanks
Bash script:
#! /usr/bin/env Rscript
for dir in folder1/* ; do
Rscript script1.R
Rscript script2.R
done
Are script1.R and script2.R inside the subdirectories of folder1? If so, try this:
#! /bin/bash
for dir in folder1/* ; do
Rscript "$dir"/script1.R
Rscript "$dir"/script2.R
done
Another way to run all R scripts inside folder1 is to use find:
find folder1 -type f -name "*.R" -exec Rscript {} \;
You #! specifies R, not bash. And your loop is wrong.
Maybe try this:
#!/bin/bash Rscript
for dir in folder1/script*.R ; do
echo "Now running $dir"
Rscript folder1/$dir
done
You never changed the directory, so you should either switch to the new subfolder before executing the scripts or execute them using the full path.
Thus, try to replace
Rscript script1.R
Rscript script2.R
either by
cd folder1/$dir; Rscript script1.R; cd -
cd folder1/$dir; Rscript script2.R; cd -
or
Rscript folder1/$dir/script1.R
Rscript folder1/$dir/script2.R
Also, your shebang is wrong, it should be
#!/bin/bash
or something similar if you want your script to be a shell script. Right now it is executed as an R script.
