5 months ago by
The warning in this code
> config <- "https://bioconductor.org/config.yaml"
Error in file(con, "r") :
cannot open the connection to 'https://bioconductor.org/config.yaml'
In addition: Warning message:
In file(con, "r") :
URL 'https://bioconductor.org/config.yaml': status was 'Peer certificate cannot be authenticated with given CA certificates'
indicates that your computer did not recognize the certificate bioconductor.org offers to prove that you are actually communicating with Bioconductor. The certificate is from Go Daddy, a trusted authority, so it likely means that your computer is not configured to recognize this certificate. It would be highly desirable for you to address this issue on your computer, so that for instance you can download Bioconductor packages over secure https, but instructions for this are likely to be highly idiosyncratic and specific to your computer.
I've created a patch to BiocManager that will 'fall back' from https:// to http:// when reading the 'config.yaml' file. It would be great if you could try it out by starting a new R session and perhaps first installing the 'remotes' package
and then the patched version of BiocManager
You will likely also need to specify through standard means that you want to use an http connection for packages, from Bioconductor and perhaps also from CRAN
options(BioC_mirror = "http://bioconductor.org", repos="http://cran.r-project.org")
I strongly encourage you to address the underlying problem, which is the configuration of your computer to accept the Go Daddy certificate.
Please follow, including indicating whether this was successful, on the issue at https://github.com/Bioconductor/BiocManager/issues/32 .