Installing packages from bioc-dev.cancerdatasci.org

bioc-dev.cancerdatasci.org is the proposed replacement for bioconductor.org — a new serving stack built on Cloudflare R2 and Workers (see the overview for the design). It is not a mirror site in the usual sense: mirroring is just how it is populated today, so that its content can be verified byte-for-byte against production while the new stack is evaluated. It carries the complete package repositories for every Bioconductor release — software, annotation, experiment data, workflows, and books, for both the current release (3.23) and devel (3.24) — synced hourly from the same source that publishes to bioconductor.org and checksum-verified against it weekly.

You can install packages from it today, with two lines of R. Trying it — and telling us what breaks, if anything — is exactly the help we need.

Quick start

options(BioC_mirror = "https://bioc-dev.cancerdatasci.org")
BiocManager::install("GEOquery")

That’s it. BiocManager builds every repository URL from the BioC_mirror option, so all five repository types come from the mirror; CRAN dependencies still come from CRAN as usual.

Make it stick across sessions

Add the option to your ~/.Rprofile:

options(BioC_mirror = "https://bioc-dev.cancerdatasci.org")

Verify what you’re pointed at

BiocManager::repositories()

Every Bioconductor URL in the output should start with https://bioc-dev.cancerdatasci.org. To confirm an install came from the mirror, run it verbosely — the download URLs are printed as they’re fetched.

Optional: full independence from bioconductor.org

BiocManager fetches one small config file (version map) from bioconductor.org even when a mirror is set. The mirror carries that file too, so to exercise the mirror with bioconductor.org completely out of the loop:

Sys.setenv(BIOCONDUCTOR_CONFIG_FILE = "https://bioc-dev.cancerdatasci.org/config.yaml")
options(BioC_mirror = "https://bioc-dev.cancerdatasci.org")

This is only needed for testing that independence; for normal use the two-line quick start is enough.

What to expect

  • Identical content. The mirror is byte-for-byte: same package versions, same tarballs, same checksums as bioconductor.org, at most an hour behind. If BiocManager::install() behaves differently against the mirror in any way, that is a bug we want to hear about.
  • Same URLs, different host. Landing pages, vignettes, and archives all work with bioconductor.org replaced by bioc-dev.cancerdatasci.org in any URL.
  • It may be faster, especially outside the US: content is served from Cloudflare’s edge rather than a single AWS region.

Reverting

Remove the options() line (and the Sys.setenv line if you added it), restart R, and you are back on bioconductor.org. Nothing about your installed packages needs to change — the packages themselves are identical.

Reporting problems

Anything surprising — an install that fails, a checksum mismatch, a slow or missing file, a page that renders wrong — is worth reporting, however small. Send it to Sean Davis (seandavi@gmail.com) with the R output and, if possible, the failing URL.