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nanxstats / Rcpi

💊 Molecular informatics toolkit with integration of bioinformatics and cheminformatics tools for drug discovery
https://nanx.me/Rcpi/
Artistic License 2.0
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Use pwalign for pairwise sequence alignment if Biostrings >= 2.72.0 #23

Closed nanxstats closed 3 months ago

nanxstats commented 3 months ago

In Bioconductor 3.19 and Biostrings >= 2.72.0, the pairwise sequence alignment facilities are moved into the pwalign package. For maximum compatibility, this PR detects the installed Biostrings version at runtime and decides which package to use for pairwiseAlignment(), without introducing pwalign as an additional hard dependency.

nanxstats commented 3 months ago

The r-oldrel (R 4.3.x) check is failing because rjson 0.2.22 (released on 2024-08-20) now depends on R >= 4.4.0.

Since Bioconductor version bundles with the R version, all things released in Bioconductor >= 3.19 are built on R >= 4.4.x, this should not be a problem.

The GitHub Actions check will pass once R 4.5.0 is released and R 4.4.x becomes r-oldrel.