[Bioc-devel] Request to de-deprecate ChIPQC

[Rory Stark]

Dear Bioconductor core team,

I'm writing to request de-deprecation of the ChIPQC package.

ChIPQC was deprecated because its Nozzle.R1 CRAN dependency was
archived and no longer installable, causing R CMD INSTALL to fail.


*I've committed a fix (version 1.49.1, on the devel branch,
commitc4b49cd) *that
removes advanced reporting but keeps the computation of all of the metrics.
This fix:

1. Formally deprecates the ChIPQCreport() function per Bioconductor's
standard 3-cycle deprecation guidelines. ChIPQCreport() now calls
.Deprecated() and returns invisibly; man/ChIPQC-deprecated.Rd points users
at the QC accessor methods (QCmetrics, etc.) and plotting of
individual metrics in the help files.

2. Removes Nozzle.R1 from Imports: and NAMESPACE.

3. Preserves the original ChIPQCreport.R implementation verbatim at
inst/legacy/report.r for possible future revival on a different
report-generation backend.

4. Fixes a latent Collate: field issue surfaced by R 4.6's strict
enforcement, plus several pre-existing R CMD check NOTEs.

R CMD check is clean: 0 ERRORs, 0 WARNINGs; 3 short NOTEs remain, all
pre-existing and unrelated to the deprecation work. These are tracked for
follow-up and don't affect package functionality. The core QC functionality
to compute metrics — ChIPQC(), ChIPQCsample(), QCmetrics(),
coveragehistogram(), crosscoverage(), etc. — is unaffected and fully
functional.

Note: because ChIPQC is currently marked as deprecated, it doesn't
appear in the public devel build report. The CHECK status reported above is
from macOS (aarch64-apple-darwin23, R 4.6 / Bioc 3.24), including building
the vignette. I also
verified Linux aarch64 cross-platform compatibility against
bioconductor/bioconductor_docker:devel: all 22 R/Bioc dependencies install
cleanly, the package loads (with the .onAttach deprecation banner firing as
expected), and ChIPQCsample() runs end-to-end producing valid QC output.

I have not removed PackageStatus: Deprecated or the .onAttach() deprecation
banner — those changes await your approval.

Please let me know if you need any further information, or if I should push
these fixes to the release branch.

Thank you,
Rory Stark
bioconductor using starkhome.com

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