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Fix test failure from defunct cigarRangesAlongReferenceSpace() - #125
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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.
kriemo
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Sep 16, 2026
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.
kriemo
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Sep 27, 2026
* Fix R CMD check WARNING and NOTE from deprecated scuttle functions and 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.
* Fix test failure from defunct cigarRangesAlongReferenceSpace() (#125)
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.
* Fix find_scde_sites test for scran::combineMarkers() returning a List
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>
* Rename combineMarkers() summary.dEF column to dEF in find_scde_sites()
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>
* bump path version
---------
Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>
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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.