Installing first bioconductor package fails on the first attempt, but then succeeds on the second

[dvg-p4]

In a project where no bioconductor packages have been installed yet, I attempt to install one:

> renv::install("bioc::IRanges")
Retrieving 'https://cloud.r-project.org/src/contrib/BiocManager_1.30.20.tar.gz' ...
        OK [file is up to date]
Installing BiocManager [1.30.20] ...
        OK [built from source in 2.8 seconds]
Moving BiocManager [1.30.20] into the cache ...
        OK [moved to cache in 33 milliseconds]
* Installed 1 package in 3.2 seconds.
Error: package 'IRanges' is not available
Traceback (most recent calls last):
7: renv::install("bioc::IRanges")
6: retrieve(names(remotes))
5: handler(package, renv_retrieve_impl(package))
4: renv_retrieve_impl(package)
3: renv_available_packages_latest(package)
2: stopf("package '%s' is not available", package)
1: stop(sprintf(fmt, ...), call. = call.)

Note that renv seems to realize that it needs to first install BiocManager (and does so successfully) but then errors out and claims that the package of interest is not available. However, if I then try again, it succeeds:

> renv::install("bioc::IRanges")
Retrieving 'https://bioconductor.org/packages/3.14/bioc/src/contrib/IRanges_2.28.0.tar.gz' ...
        OK [downloaded 445 Kb in 0.29 seconds]
Retrieving 'https://bioconductor.org/packages/3.14/bioc/src/contrib/BiocGenerics_0.40.0.tar.gz' ...
        OK [downloaded 44.9 Kb in 0.25 seconds]
Retrieving 'https://bioconductor.org/packages/3.14/bioc/src/contrib/S4Vectors_0.32.4.tar.gz' ...
        OK [downloaded 652.9 Kb in 0.32 seconds]
Installing BiocGenerics [0.40.0] ...
        OK [built from source in 5.5 seconds]
Moving BiocGenerics [0.40.0] into the cache ...
        OK [moved to cache in 33 milliseconds]
Installing S4Vectors [0.32.4] ...
        OK [built from source in 21 seconds]
Moving S4Vectors [0.32.4] into the cache ...
        OK [moved to cache in 44 milliseconds]
Installing IRanges [2.28.0] ...

Expected behavior: This works on the first try

Observed behavior: It errors out on the first try, as above

Workaround: Just run it twice (or explicitly initialize the project with bioconductor)

Vaguely relatedly, it would be nice if this vignette also explained the renv::install("bioc::[package]") syntax--had to google around a bit to figure that out.

[zkamvar]

We are also experiencing this issue. I have tested the workaround locally and found that it indeed solves the issue. I am currently running a (not small) integration test to make sure it works remotely: https://github.com/zkamvar/workbench-integration-test/actions/runs/4598105565/jobs/8124053218

[kevinushey]

Thanks for the bug report! This should be fixed up now.

[zkamvar]

To confirm: one solution for this is to install {BiocManager} before running renv::install("bioc::[package]")?

[kevinushey]

Yes indeed, that effectively works around the issue.