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  • #1

    Unable to install Bioconductor packages with biocLite...

    Hi,

    I'm very new to R/Bioconductor. Presently I'm trying to fetch and install BioC packages using the biocLite route, but it's stumbling. Here's the error I get:

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

    Could somebody please suggest a way out? I'm on Windows 7 and behind a proxy server (no username/pwd authentication required though).

    Thanks a lot and good day!
    Tags: None
  • #2
    I wonder if your proxy is screwing things up. You can download that file, double check that it's not corrupted, and then try sourcing it directly. What version of R are you using (just post the output of sessionInfo() ).

    Comment

    • #3
      Thanks for replying, dpryan. But I'm not sure I understand you correctly. Which file are you referring to? btw I'm on R v3.0.1:

      > sessionInfo()
      R version 3.0.1 (2013-05-16)
      Platform: i386-w64-mingw32/i386 (32-bit)

      locale:
      [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252
      [3] LC_MONETARY=English_India.1252 LC_NUMERIC=C
      [5] LC_TIME=English_India.1252

      attached base packages:
      [1] stats graphics grDevices utils datasets methods base

      Thanks again.

      Comment

      • #4
        The file I'm referring to is biocLite.R. You can just download it directly and double check it, since that's what's producing the error.

        Comment

        • #5
          I downloaded the biocLite.R file to a local folder and then tried running it directly. Seems like an html problem:

          > biocLite("NOISeq")
          Line starting '<HTML><HEAD> ...' is malformed!, using
          'http://bioconductor.org/packages/2.12/bioc'
          Error: Line starting '<HTML><HEAD> ...' is malformed!

          Is there something obvious I'm missing?
          Thanks.

          Comment

          • #6
            whatever is being downloaded contains HTML tags, so it is not the correct file. do not use a browser and 'save page', rather download it directly, or open the document in the browser and copy out the text.

            Comment

            • #7
              Hi rxzlmn,

              Actually that's what I did (so hard to understand the html tags...), I just opened the biocLite.R file in Firefox and then copy-pasted it into Notepad++.

              Comment

              • #8
                Error in updating biocLite() package

                Hi There..

                I have installed R version 3.0.2 when i am trying to update bioconducter packages i am geting following error

                > source("http://bioconductor.org/biocLite.R")
                Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
                > biocLite()
                BioC_mirror: http://bioconductor.org
                Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
                Warning message:
                installed directory not writable, cannot update packages 'foreign', 'spatial',
                'survival'

                I have change the installed directory permission also but still i am geting this error.
                can anyone help to find out the error..

                Thanks..

                Comment

                • #9
                  You can try to run R via sudo and see if the problems persist.

                  Comment

                  • #10
                    Thanks... rboettcher

                    It worked for me..

                    Comment

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