The warning in this code
> config <- "https://bioconductor.org/config.yaml"
> readLines(config)
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
install.packages("remotes")
and then the patched version of BiocManager
remotes::install_github("Bioconductor/BiocManager", ref="feature/http-fallback")
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 .
The Error seems to suggest that you did not have internet connection at the time you tried this function. Can you ensure that you are connected to the internet and try again? Could you also include your
sessionInfo()if you continue to have errors after checking the internet connection.The underlying problem is like from
config <- "https://bioconductor.org/config.yaml" readLines(config)Do those lines work for you? Can you also report the result of
packageVersion("BiocManager")Thanks for your reply
> config <- "https://bioconductor.org/config.yaml" > readLines(config) 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' packageVersion("BiocManager") [1] ‘1.30.3’Thanks！Ｉ have checked the Internet and nothing is wrong.
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.1