Why is R unable to access index for repository of bioconductor

Question

When trying to install bioconductor (for installing phyloseq package) I get several warning and error messages

I got a new harddrive few days ago so I had to reinstall all programs including R with all the packages I usally need. Everything worked fine until I tried bioconductor.

I am using the rcommended code which worked out for me before: source('http://bioconductor.org/biocLite.R') biocLite('phyloseq')

The error message I get is:

Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.6.0 (2019-04-26). installation path not writeable, unable to update packages: cluster, nlme Updating packages 'bipartite' Warning: unable to access index for repository https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.6:
cannot open URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.6/PACKAGES

So apparently there are several problems?

1. Some packages cant be updated due to wrong libpath and
2. R is not able the open the bioconductor hompage

Thanks for your suggestions!

Answer 1

Bioconductor is tied to particular versions of R. You're trying to use a version of Bioconductor (3.7) on a version of R (3.6) that does not match. There is a map between versions, but the underlying problem is that you're using your R-3.5 libraries hoping that they'll work in R-3.6. You should instead 'start over' with an R-3.6 specific installation. In addition, 'BiocInstaller' has been replaced with BiocManager; your 'recommended code' is out of date, as shown on package landing pages.

If you want to continue using your previous library installation (note that this is a one-way street -- you're giving up on your usable R-3.5 installation), try removing ALL versions of the BiocVersion and BiocInstaller packages. .

remove.packages(c("BiocVersion", "BiocInstaller")) # repeat 'till all removed

Either starting with a new library or after removing previous versions of BiocVersion / BiocInstaller, install BiocManager from CRAN

install.packages("BiocManager")

and go about your business

BiocManager::install("phyloseq")

Make sure to validate your installation, so that you do not mix packages from different Bioconductor versions

BiocManager::valid()

Check out current package landing pages, e.g., for phyloseq, or the installation page.