This breaks installation of chromVAR, as reported on the Bioconductor 3.23 daily report: https://bioconductor.org/checkResults/3.23/bioc-LATEST/chromVAR/
The fix is easy: simply import nucleotideSubstitutionMatrix from the pwalign package.
Please address as soon as possible.
Note that nucleotideSubstitutionMatrix got formally deprecated in Biostrings in BioC 3.21, then defunct in BioC 3.22, and finally removed from Biostrings in BioC 3.23.
Thank you for your contribution to Bioconductor,
Hervé Pagès
On behalf of the Bioconductor Core Team
This breaks installation of chromVAR, as reported on the Bioconductor 3.23 daily report: https://bioconductor.org/checkResults/3.23/bioc-LATEST/chromVAR/
The fix is easy: simply import
nucleotideSubstitutionMatrixfrom the pwalign package.Please address as soon as possible.
Note that
nucleotideSubstitutionMatrixgot formally deprecated in Biostrings in BioC 3.21, then defunct in BioC 3.22, and finally removed from Biostrings in BioC 3.23.Thank you for your contribution to Bioconductor,
Hervé Pagès
On behalf of the Bioconductor Core Team