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  • install problem with R/bioconductor

    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!

  • #2
    try a wget from your linux machine.
    Code:
    wget http://bioconductor.org/biocLite.R
    Do you get a file like this?
    Code:
    source("http://bioconductor.org/getBioC.R")
    
    biocLite <- function(pkgs, groupName="lite", ...)
    {
        if (missing(pkgs))
            biocinstall(groupName=groupName, ...)
        else
            biocinstall(pkgs=pkgs, groupName=groupName, ...)
    }

    Comment


    • #3
      Originally posted by adamdeluca View Post
      try a wget from your linux machine.
      Code:
      wget http://bioconductor.org/biocLite.R
      Do you get a file like this?
      Code:
      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

      Comment


      • #4
        Originally posted by sanwen View Post
        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?
        --
        Jeremy Leipzig
        Bioinformatics Programmer
        --
        My blog
        Twitter

        Comment


        • #5
          Originally posted by Zigster View Post
          are you behind an http-proxy?
          Maybe not. I use Putty to login a super computer server (linux system).

          Comment


          • #6
            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.

            Comment


            • #7
              I have solved the problem.
              Thank adamdeluca and Zigster 's warm heart

              Comment


              • #8
                Please post your solution for future reference.

                Comment


                • #9
                  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

                  Comment


                  • #10
                    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.

                    Comment


                    • #11
                      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.

                      Comment


                      • #12
                        Is the computer connected to the internet?

                        Comment


                        • #13
                          Yes, devon ryan. It was connected with internet.

                          Comment


                          • #14
                            Sorry !! I didn't mention that I am working on windows and not on linux.

                            Comment


                            • #15
                              Presumably you're behind a firewall or proxy of some sort. Contact your local network administrator.

                              Comment

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