Question

R program (bioconductor)

0

Entering edit mode

9.7 years ago

bioinfo ▴ 60

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?

R • 4.6k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by bioinfo ▴ 60

Ram · Answer 1 · 2015-03-05

3

Entering edit mode

9.7 years ago

Devon Ryan 104k

"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.

ADD COMMENT • link 9.7 years ago by Devon Ryan 104k

2

Entering edit mode

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

ADD REPLY • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by Martin Morgan ★ 1.6k

Ram · Answer 2 · 2015-03-05

1

Entering edit mode

9.7 years ago

alesssia ▴ 580

Try:

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

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by alesssia ▴ 580