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Question: source(biocLite.R) leads to this error >>> Peer certificate cannot be authenticated with given CA certificates
0
gravatar for jol.espinoz
15 months ago by
jol.espinoz10
jol.espinoz10 wrote:

I'm trying to use `BioConductor` with my `R` installed through `conda`. 

 

I get this error:

```

jespinozlt-osx:~ jespinoz$ which R
/Users/jespinoz/anaconda/bin/R
jespinozlt-osx:~ jespinoz$ R

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin11.0.0 (64-bit)

> source("https://bioconductor.org/biocLite.R")
Error in file(filename, "r", encoding = encoding) :
  cannot open connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  URL 'https://bioconductor.org/biocLite.R': status was 'Peer certificate cannot be authenticated with given CA certificates'

```

ADD COMMENTlink modified 15 months ago by Martin Morgan ♦♦ 20k • written 15 months ago by jol.espinoz10
0
gravatar for Martin Morgan
15 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

I guess a minimal reproducible example is file("https://bioconductor.org/biocLite.R"). I don't think it's a problem with Bioconductor's certificates, but instead that libcurl (the default method for https) is not finding the CA certificates bundle. I don't know whether this is influenced by your anaconda or not, and if it is I don't have any suggestions.

You could try curl -I https://bioconductor.org/biocLite.R from the command line. If that fails then the task is to get an updated CA certificate bundle in the right location for cURL.

A work-around is to use http: rather than https, but that's not a very good idea.

ADD COMMENTlink written 15 months ago by Martin Morgan ♦♦ 20k

I tried http and was getting the same problem :( when I get back to my computer I will try the curl method.  Using R w/ conda is a little buggy. 

ADD REPLYlink written 15 months ago by jol.espinoz10

Try also options(useHTTPS=FALSE) with the http:// url. 

ADD REPLYlink written 15 months ago by Martin Morgan ♦♦ 20k

I didn't get an error when I ran the `curl` line but I'm getting that my `R` version isn't compatible with `biocLite`

> options(useHTTPS=FALSE)

> source("http://bioconductor.org/biocLite.R")
Warning: unable to access index for repository https://bioconductor.org/packages/3.3/bioc/src/contrib:
  cannot download all files
'biocLite.R' failed to install 'BiocInstaller', use
  'install.packages("BiocInstaller",
  repos="https://bioconductor.org/packages/3.3/bioc")' or
  'install.packages("BiocInstaller",
  repos="http://bioconductor.org/packages/3.3/bioc")'
Warning message:
package ‘BiocInstaller’ is not available (for R version 3.3.1)
ADD REPLYlink modified 15 months ago • written 15 months ago by jol.espinoz10

Does the suggestion to

options(useHTTPS=FALSE)
install.packages("BiocInstaller", repos="http://bioconductor.org/packages/3.3/bioc")

get BiocInstaller installed, and biocLite() install default packages?

ADD REPLYlink written 15 months ago by Martin Morgan ♦♦ 20k
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