[Bug]: Install R packages "tidy graph" and "graph" on Rockfish cluster before running `Rscript build/local_install.R`

[twallema]

Label

documentation

Priority Label

low priority

Describe the bug/issue

Issue

• Following the "how to run on the Rockfish cluster guide"

• Trying to run the chunk:

  
  cd /scratch4/struelo1/flepimop-code/$USER
  export FLEPI_PATH=$(pwd)/flepiMoP
  cd $FLEPI_PATH
  git checkout main
  git pull
  conda activate flepimop-env # normally already done, but in case.

install gempyor and the R module. There should be no error, please report if not.

Sometimes you might need to run the next line two times because inference depends

on report.generation, which is installed later because of alphabetical order.

(or if you know R well enough to fix that 😊)

Rscript build/local_install.R # warnings are ok; there should be no error. pip install --no-deps -e flepimop/gempyor_pkg/

- Returns an error in the installation of the R packages, it says:

```bash
ERROR: dependencies ‘ggraph’, ‘tidygraph’ are not available for package ‘flepicommon’

• I think, similar to the "Quick Start Guide" page, before running Script build/local_install.R the user should install some R packages,

R
> install.packages(c("ggraph","tidygraph"))

• So technically the block in the docs should be,

cd /scratch4/struelo1/flepimop-code/$USER
export FLEPI_PATH=$(pwd)/flepiMoP
cd $FLEPI_PATH
git checkout main
git pull
conda activate flepimop-env # normally already done, but in case.

#install gempyor and the R module. There should be no error, please report if not.
# Sometimes you might need to run the next line two times because inference depends
# on report.generation, which is installed later because of alphabetical order.
# (or if you know R well enough to fix that 😊)

# install dependencies ggraph and tidy graph
R
> install.packages(c("ggraph","tidygraph"))
> quit()

Rscript build/local_install.R # warnings are ok; there should be no error.
pip install --no-deps -e flepimop/gempyor_pkg/

• But perhaps this can be added in the installation? @saraloo @Jose

Environment, if relevant

Rockfish cluster, Rocky Linux release 8.8 (Fedora)

[pearsonca]

Should probably approach the R setup as an environment management problem, much like the approach for Python using conda. It seems like there is an renv folder - but this local_install script doesn't seem to leverage that approach?

I've got an example of doing that sort of thing in github.com/cmmid/paramix/blob/main/inst/install.R

[TimothyWillard]

Now superseded by build/hpc_install_or_update.sh.