install via devtools::install_github([...]) tries to install dependencies from outdated Bioconductor v3.18

[ymahlich]

A fresh install of spammR via

library(devtools)
devtools::install_github('pnnl-compbio/spammR',build_vignettes = TRUE,force=TRUE)

tries to install dependencies from Bioconductor 3.18 instead of 3.20 (the current version) even if an up to date BiocManager is installed. This potentially results in multiple dependencies failing to install if packages aren't available for the processor architecture. Example warnings:

Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/macosx/big-sur-arm64/contrib/4.4:
  cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/macosx/big-sur-arm64/contrib/4.4:
  cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/macosx/big-sur-arm64/contrib/4.4:
  cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.18/workflows/bin/macosx/big-sur-arm64/contrib/4.4:
  cannot open URL 'https://bioconductor.org/packages/3.18/workflows/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.18/books/bin/macosx/big-sur-arm64/contrib/4.4:
  cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES'
Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘zlibbioc’ ‘XVector’
  ‘SparseArray’ ‘DelayedArray’ ‘S4Arrays’ ‘IRanges’ ‘S4Vectors’ ‘GenomicRanges’ ‘impute’ ‘limma’

After manual install of the listed libraries via a manual call of BiocManager::install() (which pulls from the up-to-date repositories) spammR installs properly (assuming leapR is installed prior and BiocStyle has been installed as well - see also issue #35 )