Fix R CMD check WARNING and NOTE f - #126
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…d Rd link anchors
scuttle::normalizeCounts()/summarizeAssayByGroup() used in find_scde_sites()
are deprecated as of scuttle 1.22 (Bioc 3.24 devel) in favor of
scrapper::normalizeRnaCounts.se()/aggregateAcrossCells.se(), which raised
"Found the following significant warnings" during R CMD check. Migrate to
scrapper, matching the "sum" statistic and group-labeled columns of the old
output (verified numerically identical against scuttle via the shared
underlying primitives). Add a find_scde_sites() test, since none existed.
Also add explicit package anchors (e.g. [GRanges][GenomicRanges::GRanges])
to roxygen \link{} targets flagged by "Rd \link{} targets missing package
anchors" across annot_snps.Rd, calc_AEI.Rd, calc_edit_frequency.Rd,
find_de_sites.Rd, find_scde_sites.Rd, make_de_object.Rd, pileup_cells.Rd,
and pileup_sites.Rd.
The remaining compiled-code NOTE (assert/stderr/stdout/abort/exit symbols
in raer.so) originates from the statically linked Rhtslib/htslib archive,
not raer's own C sources, and isn't addressable here.
GenomicAlignments >= 1.49.1 (Bioc 3.24 devel) made cigarRangesAlongReferenceSpace() defunct in favor of cigars_as_ranges_along_ref() from the new cigarillo package, which broke the "filtering for indel events works" test on the Bioc devel build. Switch the test to use cigarillo directly and add it as a Suggests dependency.
scran::combineMarkers() now returns an S4Vectors List rather than a base list, so is.list() returns FALSE and for() cannot iterate over it directly, breaking the "find_scde_sites works" test. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
scran::combineMarkers() prefixes the aggregated effect-size column with "summary." (i.e. summary.dEF instead of dEF), so the documented dEF column promised by find_scde_sites() was never actually produced, failing the "p.value"/"dEF" column check in the find_scde_sites test. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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scuttle::normalizeCounts()/summarizeAssayByGroup() used in find_scde_sites() are deprecated as of scuttle 1.22 (Bioc 3.24 devel) in favor of scrapper::normalizeRnaCounts.se()/aggregateAcrossCells.se(), which raised "Found the following significant warnings" during R CMD check. Migrate to scrapper, matching the "sum" statistic and group-labeled columns of the old output (verified numerically identical against scuttle via the shared underlying primitives). Add a find_scde_sites() test, since none existed.
Also add explicit package anchors (e.g. [GRanges][GenomicRanges::GRanges]) to roxygen \link{} targets flagged by "Rd \link{} targets missing package anchors" across annot_snps.Rd, calc_AEI.Rd, calc_edit_frequency.Rd, find_de_sites.Rd, find_scde_sites.Rd, make_de_object.Rd, pileup_cells.Rd, and pileup_sites.Rd.
The remaining compiled-code NOTE (assert/stderr/stdout/abort/exit symbols in raer.so) originates from the statically linked Rhtslib/htslib archive, not raer's own C sources, and isn't addressable here.