Fix BioC 3.23 compatibility: pwalign, C++14, jaspar_db docs#128
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AliciaSchep wants to merge 35 commits into
Open
Fix BioC 3.23 compatibility: pwalign, C++14, jaspar_db docs#128AliciaSchep wants to merge 35 commits into
AliciaSchep wants to merge 35 commits into
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Also re-roxygenize.
These functions were moved from Biostrings to pwalign in BioC 3.19 and removed from Biostrings in BioC 3.23. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Set CXX_STD=CXX14 in Makevars and update SystemRequirements since RcppArmadillo now requires C++14 - Add jaspar_db parameter to getJasparMotifs.Rd to match code Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
Biostringsimports withpwalignfornucleotideSubstitutionMatrixand
stringDist, which were moved topwalignin BioC 3.19 and removedfrom
Biostringsin BioC 3.23pwaligntoImportsinDESCRIPTIONCXX_STD = CXX14insrc/Makevarsand updateSystemRequirementssince
RcppArmadillonow requires C++14jaspar_dbparameter ingetJasparMotifs.Rd(added by feat: allow different jaspar DB sources #114but missing from the Rd file)
Test plan
R CMD check --no-manual --no-vignettespasses locally with no ERRORs