Add missing R dependencies

[fgvieira]

Added missing R dependencies.

[dlaehnemann]

I am not sure any of this should be necessary. What was the root problem that motivated these additions?

[dlaehnemann]

I just tried the following and it worked for me, including stating that it is Performing Bayesian estimates. So maybe this is some artefact of a conda setup somewhere? Or some other weird side effects?

mamba create -n mapdamage2 mapdamage2=2.2.1
conda activate mapdamage2
mapDamage --input test.sorted.bam --reference genome.fasta --folder test --rescale-out test.rescaled.bam

[fgvieira]

ok, so it seems it was because of a conflict between R packages.
It seems that, even though R and R packages are installed through conda, the R_LIBS variables takes precedence if it is defined.

Either way, I've removed the patch version and pinned it to minor version only.
best

[dlaehnemann]

Ah, yeah. Thanks for the patience and keeping on digging on your end. This does seem messy, judging for the (stalling) attempts to fix this in conda:
conda-forge/r-base-feedstock#65

[dlaehnemann]

This minimal change obivously makes sense, so I'll merge it!

[mbargull]

It seems that, even though R and R packages are installed through conda, the R_LIBS variables takes precedence if it is defined.

Ah, the PYTHONPATH of the R world. Yes, that makes sense; I hadn't thought about that!
@fgvieira, thank you very much for the followup -- that's quite helpful for debugging future issues of other users!