Revamp tests

[csdaw]

This is a large PR that moves camprotR from using testthat 2nd edition to the 3rd edition. The benefits of this are primarily that if function outputs change, now the diffs are human readable.

This PR includes the following changes:

• check-bioc Github Actions workflow has been updated to the latest Bioconductor release.
• Most tests have been rewritten (they are now 'snapshot' tests).
• Now vdiffr package is used to compare the expected output of plotting functions to a snapshot references.
• camprotR now requires testthat version >= 3.0.0
• New packages added to 'Suggests' which are required for tests: vdiffr >= 1.0.0, withr
• get_ccp_crap() has been moved from R/make_fasta.R to R/download_ccp_crap.R because that's where I kept looking for it.
• Small bugfixes in make_fasta() and check_uniprot_release() and crap.Rmd vignette to avoid error in Ubuntu CI workflow.
• The following datasets have been added to camprotR (still need proper documentation):
  • pep_silac_p0 = peptideGroups.txt output from unlabelled MOLM-13 whole cell lysate.
  • pep_silac_p4 = peptideGroups.txt output from a whole cell lysate generated from a 1:1 mix of R0K0 and R10K8 MOLM-13 cells which had been labelled for 4 passages.
  • psm_silac_p4 = PSMs.txt output from a whole cell lysate generated from a 1:1 mix of R0K0 and R10K8 MOLM-13 cells which had been labelled for 4 passages.
• Added an argument to add_PTM_positions() to fix a tiny bug.
• The inst/testdata folder and its contents have been deleted. Now the files required for testing at automatically generated and removed at testing time.
• The cRAP_20190401.fasta file has been replaced with a gzipped version.
• The cRAP_FullIdentifiers.fasta.gz file has been removed and the reference to it in the TMT vignette has been changed to the other cRAP file.
• Gzipped version of the GPM cRAP fasta and the MaxQuant contaminants fasta have been added to inst/extdata.

Note that estimate_incorporation() and the functions in R/go.R have had their tests deleted in this branch. Tests for these functions will be added back in other PRs.

[csdaw]

Trying to access the url ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta is causing the build of crap.Rmd vignette to fail on Ubuntu.

Need to make some changes to cRAP vignette.

[csdaw]

Actually it was calls to http::GET() causing CI failure for Ubuntu, due to issues introduced in Ubuntu 20.04 (see here for details and the workaround I have used).