Cannot download from behind proxy

[Luke-Symes-Tsy]

My Windows computer, with R 4.4.2, uses a proxy to access the internet.

Using options(download.file.method = "wininet"), I can successfully run install.packages("zip"). However, running pak::pkg_install("zip") fails with:

Error: 
! error in pak subprocess
Caused by error in `download.file(url, tmp, quiet = TRUE)`:
! cannot open URL 'http://bioconductor.org/config.yaml'

For example:

It seems like pak is not recognising the download.file.method option? I am using pak 0.8.0 from CRAN.

[gaborcsardi]

pak does not use download.file() and does not use download.file.method. This is a bug that is possibly fixed in the devel version, you can install it like this:
https://pak.r-lib.org/reference/install.html#nightly-builds

[Luke-Symes-Tsy]

I tracked down the issue to pkgcache trying to update the Bioconductor metadata. pkgcache essentially calls pkgcache:::bioconductor$.internal$read_url("http://bioconductor.org/config.yaml") which uses download.file.

However, the issue seems to be that pak does not tell callr (which runs pkgcache etc) to use the user's .Rprofile - it defaults to user_profile = "project" which looks for a project-specific .Rprofile:

pak/R/subprocess.R

Line 143 in 683f1be

user_profile = if (Sys.getenv("RENV_PROJECT") != "") FALSE else "project"

If I create a project-specific .Rprofile with the right options, then pak::pkg_install("zip") works (after a session restart):

Sys.setenv(ALL_PROXY = ":@<proxy_url>:<proxy_port>")
options(download.file.method = "curl")

What I think should be happening, is if a project-specific .Rprofile does not exist, we should default to user_profile = TRUE which tells callr to use R_PROFILE_USER or ~/.Rprofile if it exists:

user_profile = if (Sys.getenv("RENV_PROJECT") != "") FALSE else if (file.exists(".Rprofile")) "project"  else TRUE

Note: I tested the latest devel version of pak and avoided the Bioconductor error (since Bioconductor is now turned off by default); however my ALL_PROXY setting was still not being picked up from my user ~/.Rprofile, but was from a project-specific .Rprofile.