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Modernization: repair man-page mojibake, extend biocViews - #6
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- Repair UTF-8 transcoding damage ("??" artifacts) in 32 dataset man
pages: separator spaces, author names (de Reynies, Garcia-Alcalde,
Bandres, Agesen, ...), journal references, copyright marks, and
statistical symbols (p = , R^2, uM, polymerase epsilon), using ASCII
equivalents.
- biocViews: add ColonCancerData, MicroarrayData, RNASeqData, GEO.
- Remove the empty FULLVcuratedCRCData_counts.csv placeholder.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- Merge the "(continued)" NEWS section into the 2.46.0 heading so news() shows one block per version. - "(c) 2011 AACR" spacing; add missing spaces that predate the mojibake (journal names run into years, missing comma spaces). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Copilot review overview
🟡 Changes recommended
The new NEWS entry is assigned to version 2.46.0 while the package is being released as 2.45.5.
Review effort: Balanced
Findings: 1
Open (1)
What changed in this PR
Repairs corrupted dataset documentation, expands Bioconductor metadata, removes an empty placeholder, and bumps the package version.
Changes:
- Restores ASCII equivalents for damaged names, citations, and symbols across 32 man pages.
- Adds colorectal cancer, microarray, RNA-seq, and GEO biocViews.
- Removes an obsolete empty CSV placeholder.
| File | Description |
|---|---|
NEWS.md |
Documents metadata and documentation updates. |
DESCRIPTION |
Bumps version and expands biocViews. |
inst/extdata/FULLVcuratedCRCData_counts.csv |
Removes empty placeholder. |
man/TCGA.RNASeqV2.READ_eset.Rd |
Restores POLE terminology. |
man/TCGA.RNASeqV2_eset.Rd |
Restores POLE terminology. |
man/TCGA.READ_eset.Rd |
Restores POLE terminology. |
man/TCGA.COAD_eset.Rd |
Restores POLE terminology. |
man/GSE45270_eset.Rd |
Repairs contributor formatting. |
man/GSE4526_eset.Rd |
Repairs citation formatting. |
man/GSE4045_eset.Rd |
Repairs citation formatting. |
man/GSE3964_eset.Rd |
Repairs citation formatting. |
man/GSE39582_eset.Rd |
Restores statistical notation and author name. |
man/GSE33113_eset.Rd |
Repairs citation formatting. |
man/GSE3294_eset.Rd |
Repairs citation formatting. |
man/GSE28702_eset.Rd |
Repairs citation formatting. |
man/GSE27544_eset.Rd |
Restores contributor names. |
man/GSE26906_eset.Rd |
Repairs citation formatting. |
man/GSE26682.GPL96_eset.Rd |
Restores units, notation, and names. |
man/GSE26682.GPL570_eset.Rd |
Restores units, notation, and names. |
man/GSE2630_eset.Rd |
Restores contributor names. |
man/GSE24550.GPL5175_eset.Rd |
Restores author and citation text. |
man/GSE24549.GPL5175_eset.Rd |
Restores contributor names. |
man/GSE21815_eset.Rd |
Repairs contributor formatting. |
man/GSE21510_eset.Rd |
Restores copyright and citation text. |
man/GSE18105_eset.Rd |
Repairs citation formatting. |
man/GSE17538.GPL570_eset.Rd |
Repairs citation formatting. |
man/GSE17537_eset.Rd |
Repairs citation formatting. |
man/GSE17536_eset.Rd |
Repairs citation formatting. |
man/GSE16125.GPL5175_eset.Rd |
Repairs citation formatting. |
man/GSE14333_eset.Rd |
Repairs citation formatting. |
man/GSE14095_eset.Rd |
Repairs citation formatting. |
man/GSE13067_eset.Rd |
Repairs citation formatting. |
man/GSE12945_eset.Rd |
Repairs citation formatting. |
man/GSE12225.GPL3676_eset.Rd |
Repairs journal spacing and citation text. |
man/GSE11237_eset.Rd |
Repairs citation formatting. |
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| * Removed `external_data_store.txt` and `Namespace: auto`; explicit | ||
| NAMESPACE exporting only `curatedCRCData()`. | ||
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| ## DOCUMENTATION AND METADATA |
Member
Author
|
The version mismatch is intentional Bioconductor convention: in devel, maintainers bump only z (2.45.3 → .4 → .5), and the core team bumps to 2.46.0 at the 3.24 release, so NEWS is written against the release version users will actually install. Per-z NEWS headings would splinter one release's changes into half a dozen micro-sections. Leaving as is. 🤖 Drafted with Claude Code |
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Follow-up pass deferred from #5 (not release-critical):
FULLVcuratedCRCData_counts.csvplaceholder; also fix pre-existing missing spaces (journal names run into years).R CMD checkStatus: OK.🤖 Generated with Claude Code