fatal error: cannot execute 'cc1': execvp: Permission denied

Question

I created a conda environment on a HPC node and want to install a R package called "ape" but got a fatal error message.

when I run install.packages"ape"

I got the error message x86_64-conda-linux-gnu-cc: fatal error: cannot execute 'cc1': execvp: Permission denied.

I installed the gcc by conda install -c conda-forge gxx_linux-64 but it still doesn't work.

I don't have permission to use apt-get install gcc since I am not an admin of the HPC. What can I do to fix this? Any recommendations will be appreciated.

Thank you.

that works. Thank you for your recommendation. – Fang Yuan Jan 26 '23 at 15:06 — Fang Yuan, Jan 26 '23 at 15:06
Converted the Comment to an Answer since that helped. – merv Feb 08 '23 at 03:45 — merv, Feb 08 '23 at 03:45

score 1 · Answer 1 · answered Feb 08 '23 at 03:45

1

I recommend not using install.packages, instead install the Conda Forge package r-ape (see https://stackoverflow.com/a/60767530/570918). Also, you get the amazing bonus that everything is precompiled (super fast install, especially if using mamba).

answered Feb 08 '23 at 03:45

merv

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fatal error: cannot execute 'cc1': execvp: Permission denied

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