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Question: problems regarding installing TEQC package
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gravatar for xiang.zuo
7 days ago by
xiang.zuo0
xiang.zuo0 wrote:

Hello,

I am installing the bioconductor package name TEQC(http://www.bioconductor.org/packages/release/bioc/html/TEQC.html), but something is wrong, here is the detailed error information. I tried to google this error, but cannot solve the problem. Could you please help me?

> if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> BiocManager::install("TEQC", version = "3.8")
Error: Bioconductor version cannot be validated; no internet connection?

 

ADD COMMENTlink modified 5 days ago by Martin Morgan ♦♦ 22k • written 7 days ago by xiang.zuo0

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.

ADD REPLYlink modified 7 days ago • written 7 days ago by shepherl ♦♦ 870

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")

 

ADD REPLYlink written 7 days ago by Martin Morgan ♦♦ 22k

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’
ADD REPLYlink modified 5 days ago by Martin Morgan ♦♦ 22k • written 6 days ago by xiang.zuo0

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

ADD REPLYlink written 6 days ago by xiang.zuo0
0
gravatar for Martin Morgan
5 days ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

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 .

ADD COMMENTlink modified 5 days ago • written 5 days ago by Martin Morgan ♦♦ 22k
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