install problem with R/bioconductor

[sanwen]

Dear all,
I use linux system. I try to use Myrna, it need to work with R/Bioconductor. I have trouble when install Bioconductor.
In an R command window, I type the following:
source("http://bioconductor.org/biocLite.R")

But it shows:
Error in source("http://bioconductor.org/biocLite.R");
http://bioconductor.org/biocLite.R:1:1: unexpected '<'
1; <
^


I don't known why? Can anybody help me? Thanks a lot!

[adamdeluca]

try a wget from your linux machine.

wget http://bioconductor.org/biocLite.R

Do you get a file like this?

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

biocLite <- function(pkgs, groupName="lite", ...)
{
    if (missing(pkgs))
        biocinstall(groupName=groupName, ...)
    else
        biocinstall(pkgs=pkgs, groupName=groupName, ...)
}

[sanwen]

try a wget from your linux machine.

wget http://bioconductor.org/biocLite.R

Do you get a file like this?

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

biocLite <- function(pkgs, groupName="lite", ...)
{
    if (missing(pkgs))
        biocinstall(groupName=groupName, ...)
    else
        biocinstall(pkgs=pkgs, groupName=groupName, ...)
}

Hi adamdeluca, yes, i get a file biocLite.R, and then, how to install? I am sorry that i am not familiar with linux

[Zigster]

Dear all,
I use linux system. I try to use Myrna, it need to work with R/Bioconductor. I have trouble when install Bioconductor.
In an R command window, I type the following:
source("http://bioconductor.org/biocLite.R")

But it shows:
Error in source("http://bioconductor.org/biocLite.R");
http://bioconductor.org/biocLite.R:1:1: unexpected '<'
1; <
^


I don't known why? Can anybody help me? Thanks a lot!

are you behind an http-proxy?

[sanwen]

are you behind an http-proxy?

Maybe not. I use Putty to login a super computer server (linux system).

[adamdeluca]

If the server is behind an http proxy, it could be inserting text into the R code that is being retrieved with the source() call. The invalid '<' first character just screams HTML. That's why I had you try the wget command.

[sanwen]

I have solved the problem.
Thank adamdeluca and Zigster 's warm heart

[adamdeluca]

Please post your solution for future reference.

[Robin]

install bioconductor in R

I have the exactly problems here. When I run source command in R, and I got the error message as follow:

> source("http://bioconductor.org/biocLite.R")
Error in file(file, "r", encoding = encoding) :
cannot open the connection
In addition: Warning message:
In file(file, "r", encoding = encoding) :
unable to resolve 'bioconductor.org'

When I run wget command on my Linux machine, and I got the same output as follow:

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

biocLite <- function(pkgs, groupName="lite", ...)
{
if (missing(pkgs))
biocinstall(groupName=groupName, ...)
else
biocinstall(pkgs=pkgs, groupName=groupName, ...)
}


What is the problem here? Can you give me some help?

Thank
R

[ioatomis]

I had the same problem as above when using Rstudio launched from a launcher on a Linux machine

> source("http://bioconductor.org/biocLite.R")
Error in source("http://bioconductor.org/biocLite.R") :
http://bioconductor.org/biocLite.R:1:1: unexpected '<'
1: <
^

The problem was the proxy settings - I had already set the proxy in my .bashrc

export http_proxy=http://[proxy]

and when launching R or Rstudio from a console I had no problems.

[vikas dahiya]

installation problem in Bioconductor

Hi all,
I am facing a problem in installing bioconductor when i am typing source("http://bioconductor.org/biocLite.R") command in R 3.0.2. the error is shown below:

Error in file(filename, "r", encoding = encoding) :
cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
unable to resolve 'bioconductor.org'

Pleeees help me out.

[dpryan]

Is the computer connected to the internet?

[vikas dahiya]

Yes, devon ryan. It was connected with internet.

[vikas dahiya]

Sorry !! I didn't mention that I am working on windows and not on linux.

[dpryan]

Presumably you're behind a firewall or proxy of some sort. Contact your local network administrator.