R program (bioconductor)

Question

[bioinfo]

Hi

While I was connecting the bioconductor packages I got an error

source ("http://www.bioconductor.org/biocLite.R")
Error in file(filename, "r", encoding = encoding) :
  cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  unable to connect to 'www.bioconductor.org' on port 80.

Any suggestion how to rectify it?

Answer 1

[Devon Ryan]

"unable to connect to 'www.bioconductor.org' on port 80." means that R can't connect to the bioconductor website. This is a networking issue that only your local IT can solve. I should note that a "common" cause of this is running R scripts on cluster nodes that are firewalled from the internet.

[Martin Morgan]

It may also be R-specific, especially on Windows. See setInternet2() and section 2.19 of the R for Windows FAQ.

Answer 2

[alesssia]

Try:

source("http://bioconductor.org/biocLite.R")