Session options not passed to pak `remote` process

[qouoq]

I just understood that options(BioC_mirror = 'https://example.com/bioconductor') is seen within the pak remote process when I run my R session from $HOME (where my .Rprofile resides), but not from another place. (So that pak::repo_get() reflects the option in a console started from $HOME but not another directory, while pak:::repo_get_internal() shows as expected wherever the session is started from.)

R_BIOC_MIRROR environment variable works around the issue, so no problem, but that's a disconcerting behavior (took me a few months before I figured out).

The topic is the same as #412 as far as I understand, I'm thinking it's better to open a new issue that's more openly about this behavior than adding a comment at that issue. If that's not useful, please let this new issue rest (my hope being that the keywords about bioc mirror may help anyone facing that particular situation).

Beyond, I'm rather lost with the subprocess.R code, but I'd be glad given some pointer to try to better understand what's at stake, and somehow try to contribute in some manner?

[gaborcsardi]

Most options are now passed to the subprocess. R_BIOC_MIRROR still isn't, so I'll keep this open.