I have a bash script where I use singularity exec to run a program from inside the container. I want to call this script in R using the system() function. Everything works fine until Singularity needs to access a file named singularity.conf located in /usr/local/etc/singularity. The problem is that R cannot find the singularity directory in /etc, resulting in this error:
"FATAL: While initializing: couldn't parse configuration file /usr/local/etc/singularity/singularity.conf: open /usr/local/etc/singularity/singularity.conf: no such file or directory."
I have already checked in the terminal, and the /etc directory contains the singularity directory, which contains the singularity.conf file. I used the chmod command to grant all permissions to everyone regarding the singularity directory. Despite these actions, the problem persists. When I try to view the /etc directory with the system("ls -alh /usr/local/etc") function, it appears to be empty, so I cannot access the singularity directory in /etc.
Can somebody help me?
Thank you.