bioconductor packages: 3.8 -> 3.10

[timsears]

Motivation for this change

Bioconductor packages are out of date by over a year. Want to build bioinformatics environments without relying on conda.

Things done

• followed instructions from the nix documentation.
• updated the *-packages.nix files in r-modules/ Added 27 workflows packages from bioconductor and updated the machinery to track them.
• ran nix-build test-evaluation.nix --dry-run. Succeeds on linux, fails on darwin.
• Edited many of the customizations in r-modules/default.nix.
• Removed defunct packages.
• Added a test suite that I ran manually in r-modules/test-package-build.nix Tested an environment that uses rstudio and a number of packages. The tested packages all build, except for a few that are now marked as broken.

This PR probably supersedes #81307, except it does not bump R from 3.6.3 to 3.6.3

• Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
• Built on platform(s)
  • NixOS
  • macOS
  • other Linux distributions
• Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
• Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
• Tested execution of all binary files (usually in ./result/bin/)
• Determined the impact on package closure size (by running nix path-info -S before and after)
• Ensured that relevant documentation is up to date
• Fits CONTRIBUTING.md.

[andir]

Any good reason to keep the old hash around?

[timsears]

Thanks. No. I will get rid of it in an updated PR shortly. Just to note, updating the hash had no effect on the R packages that depend on bwdigets, They are all still broken. The updated PR will mark them all as broken.

[timsears]

Superseded by PR #85522