renv::restore() failing to download packages - potentially due to differences in R versions

[luizalmeida93]

Hi,

I have a laptop where I conducted all of my statistical analysis 2 years ago. It has R version 4.0.3; hence, Bioconductor is limited to version 3.12 and Biocmanager 1.30.10. I stopped working on it and migrated to a desktop, which is running R 4.2.0 (Bioconductor 3.15.2 and Biocmanager 1.30.19). I had to re-run an analysis, and it gave me slightly different results comparing both systems. This is the moment I realized I needed renv.

Now, I installed renv on both machines, and I am trying to "migrate" the laptop scripts to the desktop. When trying to run renv::restore() on my desktop, using a lock.file for a specific project from the laptop, renv can't install the packages. This is what I did:

1. created a new folder and a project in R (on my desktop)
2. ran renv::init()
3. ran renv::restore(lockfile = "backup_renv.lock")
4. Console is asking if I want to install BiocManager [1.30.22]. I say "Yes", but this is already a red flag as this version does not match my lock.file
5. Console then shows all packages in the lock.file and proceeds to install them.
6. A few get installed, but a bunch have these errors:

Warning: failed to find binary for 'ggrepel 0.9.1' in package repositories
Warning: failed to find source for 'ggrepel 0.9.1' in package repositories
Warning: error downloading 'https://bioconductor.org/packages/3.12/bioc/src/contrib/Archive/ggrepel/ggrepel_0.9.1.tar.gz' [curl: (22) The requested URL returned error: 404]

I have the hypothesis that the difference in R versions is the cause of my issue. I tried installing Biocmanager 1.30.10 and Bioconductor 3.12 before running renv::restore(). Biocmanager installs as expected, but when running BiocManager::install(version = "3.12") I get an error that this version is not compatible with my R version. It seems that R is ok-ish regarding backward compatibility, but Bioconductor is not ok at all running older versions unless you have older R as well.

Does this make sense or am I doing something wrong?

edit1: attached the lock.file as a text file.
backup_renv_text.txt

edit2:
I tested using renv::init(bioconductor = "3.12") to see if it would solve the problem. It did not work when followed by renv::restore(lockfile = "backup_renv.lock"); however, if I use renv::install(), for example renv::install("bioc::[email protected]") then it successfully install the package that would otherwise not be installed by renv::restore().

[kevinushey]

ggrepel 0.9.1 should be available in the CRAN archive, so I'm surprised this isn't working... it should be unrelated to whether or not you're using Bioconductor.

[luizalmeida93]

Personally, I was intrigued by the fact that renv::restore() cannot install the package, but running renv::install("bioc::[email protected]") worked perfectly.

Do you need any other info that could help pinpoint the issue?

I still have the laptop with the package versions that were working perfectly; thus, I was considering the "cellar" function available in Renv. My question is, how to back up the packages from the laptop? I was considering the whole library folder (as displayed by .libPaths()); however, they are not in .zip or .tar. If I simply zip each and every one of those folders, would that be accepted by cellar?