Update R, Bioconductor, and anndata to the current versions

[jashapiro]

Now that R 4.2.1 is available through conda-forge, I have updated the environment use that, which allowed updating to Bioconductor 3.15, which allowed anndata 0.8.0.

Many R packages were updated in the meantime, so the renv.lock file has many changes.

On an Intel machine, you should be able to combine the environment updates with installation and just run

snakemake --use-conda --forceall --cores 4

to test all changes (with whatever core count you want).

On an Apple Silicon mac, you will need to start with

CONDA_SUBDIR=osx-64 snakemake --use-conda --conda-create-envs-only -c2 build_renv

followed by the command above.

Expect a long run time the first time as R packages are rebuilt!

[sjspielman]

On an Apple mac, you will need to start with

M1 :)

[sjspielman]

Can confirm this built (about 48 minutes with --c3)! I'm now testing the snakemake in this updated environment.

[sjspielman]

Ran the full snakefile, no errors! 🎉

[allyhawkins]

Was also able to build and run the Snakefile without any issue 👍