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<zimoun>rekado_: so, does your answer mean you will take care about Bioconductor upgrade with the same move of the CRAN upgrade?
***civodul` is now known as civodul
<rekado_>zimoun: sorry for being unclear; no, I just wanted to make you aware of the pending CRAN mass upgrade, so that we can avoid conflicts.
<rekado_>I’ll try to finish this today, and then you’re welcome to base your Bioconductor upgrade on top of that work.
<rekado_>here’s an HPC job script to launch RStudio Server in a container:
<rekado_>it’s super ugly because RStudio resets environment variables, so with that “env > ~/.Renviron” trick we make it load all those variables again.
<rekado_>the manifest looks like this:
<rekado_>it’s a decent foundation that lets people run “install.packages” as if on a traditional system
<civodul>--share=/gnu/store looks gross :-)
<rekado_>it is, but it also makes the use of guix.install from within R possible
<rekado_>we can’t know in advance what directories under /gnu/store will be needed, and we can’t map new directories into a running container
<rekado_>this has actually been a great source of disappointment to me.
<rekado_>it would seem obvious to allow an outside process to map additional directories into an existing mount namespace, but I haven’t been able to make it work.
<PurpleSym>rekado_: We have a patch to propagate environments into RStudio sessions:
<rekado_>civodul: should actually be --expose=/gnu/store, but it’s only marginally better
<rekado_>PurpleSym: good to know!
<rekado_>zimoun: I’ll skip the upgrade of r-dt; too much JavaScript for one day.
<zimoun>rekado_: Thanks for your answer.
***liberalartist is now known as philip1