fix(rstudio): Resolve container errors and improve env handling#13
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pansapiens wants to merge 1 commit into
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fix(rstudio): Resolve container errors and improve env handling#13pansapiens wants to merge 1 commit into
pansapiens wants to merge 1 commit into
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This commit addresses several issues encountered when running the rstudio.sh script. The script would fail under two conditions: 1. If `conda` was not initialized, the `conda deactivate` command would error out. This has been removed as it's not essential for the script's operation. 2. The `apptainer exec` command was using an incorrect syntax for the `--env` flag, passing a comma-separated list instead of individual `key=value` pairs. This commit corrects the `--env` flag usage and introduces `--cleanenv` to ensure a predictable environment within the container. Additionally, the RStudio server would fail to start because it couldn't find the host user inside the container. This is resolved by bind-mounting the host's `/etc/passwd` and `/etc/group` files in read-only mode.
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This commit addresses several issues encountered when running the rstudio.sh script.
The script would fail under two conditions:
condawas not available, theconda deactivatecommand would raise a non-zero exit code. This has been removed as it's not essential for the script's operation any longer.apptainer execcommand was using an incorrect syntax for the--envflag, passing a comma-separated list instead of individualkey=valuepairs.This commit corrects the
--envflag usage and introduces--cleanenvto ensure a predictable environment within the container. Additional env vars, including RENV_PATHS_CACHE have been added.Additionally, in some cases the RStudio server would fail to start because it couldn't find the host user inside the container. This is resolved by bind-mounting the host's
/etc/passwdand/etc/groupfiles in read-only mode.Fixes #6