Issues with "chanw0/MRS" R package and dependencies

Question

[emi-smiley]

I initailly started off wanted to download the "chanw0/MRS" R package.. then I had a hard time with dependencies (sigh)

1. BiocManager::install("ANCOMBC")

Error: package or namespace load failed for ‘ANCOMBC’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘scater’

So then I tried to install scater based on online instructions

1. BiocManager::install("scater")

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")'
for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
Installing package(s) 'scater'
also installing the dependency ‘densvis’

Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.rds': 'https://bioconductor.org/packages/3.17/books/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.gz': HTTP status was '404 Not Found'Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘densvis’

So then I tried to install densvis

3.BiocManager::install("densvis")

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")'
for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
Installing package(s) 'densvis'
Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.rds':HTTP status was '404 Not Found'Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES'Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.17/books/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.17/books/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.gz': HTTP status was '404 Not Found'Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘densvis’

I have gcc installed via home-brew on my Mac (Sonoma V14.2.1) and my R version is 4.3.1.

Any help for ANY of the steps above would be a huge help! Thanks :)

Answer 1

[emi-smiley]

For anyone else with this issue, I needed to update my version of BiocManager and all the BiocManager packages thereafter ... sigh