I have used Bioconductor packages before without any issue installing them, but I just upgraded to R v 4.1.0 and I am unable to connect to the URL . I think the issue is with R, but I'm not sure at this point (I can install non-bioconductor packages with no problem).
If I try to install a Bioconductor package manually:
if (!requireNamespace("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
Warning: unable to access index for repository https://cran.fhcrc.org/src/contrib:
cannot open URL 'https://cran.fhcrc.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.fhcrc.org/bin/macosx/contrib/4.1:
cannot open URL 'https://cran.fhcrc.org/bin/macosx/contrib/4.1/PACKAGES'
Warning message:
package ‘BiocManager’ is not available for this version of R
If I try to install through the R package installer:
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
Warning: unable to access index for repository http://www.bioconductor.org/packages/3.13/extra/bin/macosx/contrib/4.1:
cannot open URL 'http://www.bioconductor.org/packages/3.13/extra/bin/macosx/contrib/4.1/PACKAGES'
Warning: unable to access index for repository http://www.bioconductor.org/packages/3.13/extra/bin/macosx/contrib/4.1:
cannot open URL 'http://www.bioconductor.org/packages/3.13/extra/bin/macosx/contrib/4.1/PACKAGES'
Warning: unable to access index for repository https://cran.fhcrc.org/bin/macosx/contrib/4.1:
cannot open URL 'https://cran.fhcrc.org/bin/macosx/contrib/4.1/PACKAGES'
Warning: dependencies ‘GO.db’, ‘SparseM’, ‘matrixStats’, ‘ALL’, ‘hgu95av2.db’, ‘hgu133a.db’, ‘xtable’ are not available
trying URL 'http://www.bioconductor.org/packages/3.13/bioc/bin/macosx/contrib/4.1/topGO_2.44.0.tgz'
Content type 'application/x-gzip' length 2123289 bytes (2.0 MB)
==================================================
downloaded 2.0 MB
The downloaded binary packages are in
/var/folders/46/f4bybyjd599ghrw6dsdmlkgc0000gn/T//RtmphkrHGb/downloaded_packages
Warning: unable to access index for repository http://www.bioconductor.org/packages/3.13/extra/bin/macosx/contrib/4.1:
cannot open URL 'http://www.bioconductor.org/packages/3.13/extra/bin/macosx/contrib/4.1/PACKAGES'
sessionInfo( )
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.0 tools_4.1.0