add many more tests and R ports

[danielnachun]

This PR should cover almost all testable notebooks save for twoone:

• STAR because the executable is broken on macOS (I'm still working on this)
• gregor because the database seems to be missing from the MWE

[jaempawi]

Tested this branch (015e513) end-to-end on the BU SCC (RHEL 8, glibc 2.28), 8 cores via the batch scheduler.

Results: test_scripts 60/60 green; test_notebooks 134/139.

Three findings, all environment-level rather than test bugs:

1. pixi.toml needs a newer pixi than the error suggests. The new inline form platforms = [{ platform = "linux-64", glibc = "2.17" }, "osx-arm64"] fails to parse in pixi 0.57.0 with a bare "expected a string, found table" pointing at line 5, which is a confusing failure mode. 0.75.0 parses it fine. Worth documenting a minimum pixi version in the README, since CI always gets the latest via setup-pixi and won't catch this.

2. Three tools can't run on glibc 2.28. This affects real analyses, not just tests. test_rnaseqc_call, test_grm_loco_workflow and test_rsem_index all fail at dynamic-link time before executing any pipeline logic. objdump shows rnaseqc, gcta and rsem-extract-reference-transcripts each require GLIBC_2.38.

Note the manifest declares glibc = "2.17", so these builds are being selected despite advertising a floor they don't honor (likely upstream packaging metadata). Either way, the protocol currently can't run RNA-SeQC, GCTA or RSEM on RHEL 8 clusters from this environment.

3. The preprocessCore threading workaround is needed outside CI too. test_sesame and test_minfi fail in quantile normalization with ERROR; return code from pthread_create() is 22. Minimal reproducer: Rscript -e 'library(preprocessCore); normalize.quantiles(matrix(rnorm(100), 10))'. Rebuilding with configure.args = "--disable-threading" makes both pass immediately (verified: 2 passed). Since ci.yml flags that rebuild as CI-only and unsafe for production, it'd be worth either pinning a build that works or documenting the constraint. Right now methylation calling is broken on this platform out of the box.

[danielnachun]

@jaempawi I identified the cause for the package issues you identified here and they should all be fixed now. I was wondering if the preprocessCore issue would show up in a real environment and since it did, I went ahead and repackaged it on my channel. It should work now because I remove the workaround in the CI commands and it passed here.

I will update the README to reflect that a newer pixi is needed. Thankfully pixi can be updated with pixi self-update, which I will add to the README.

Please go ahead and retest everything now and let's see if it all works this time.