The package was deprecated in 3.23 and removed from 3.24 you are correct that they currently do not appear or are building on devel. Please push your changes to RELEASE_3_23 branch. Once it builds there cleanly without ERROR we will undeprecate the package.
Lori Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <[email protected]> on behalf of Rory Stark <[email protected]> Sent: Tuesday, May 5, 2026 4:09 PM To: [email protected] <[email protected]> Subject: [Bioc-devel] Request to de-deprecate ChIPQC 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 [email protected] [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://secure-web.cisco.com/1wBYc5E2aE1o79oPW3AtGbLgVh1z3an9Xrg5GZlapfhzqs1y2tydJvkwjHvL9eubrHl9SJfd8RiIw8iI-5JuMcr3Yfvf3mX1-K_LF4OoyRYiZqE6MjL3QBmGdUwSoPNgX7GLNqwONvXmPJBkcpcOPrzvJWI8B5DdSmlvQQ_7xwq0pq__bqlcTJfT-sp5NdEVXTSPVJmoZ2HdQkoYSCnjrDIf1aoIFI9oWqa5VNNHNOHaxWhzxojtwTsPcCh6urojCkUoqvtJ6Jd36oEtgXnBAJczxTZM6wOoNM6bAnnWeTLSHSiOBhmMa8BBh1mwg6c0k/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]]
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