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Using Bioconductor RRS feed

  • Question

  • I ran an R script for using Bioconductor (http://www.bioconductor.org/install/)

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

    But, got this error:

      Error 0063: The following error occurred during evaluation of R script:

     ---------- Start of error message from R ----------
     cannot open the connection


     cannot open the connection
     ----------- End of error message from R -----------

    What's the recommended way to use Bioconductor on Azure ML?

    Thanks,

    Sunday, April 26, 2015 8:17 AM

Answers

  • Hi Naoto,

    Perhaps you might now need to download the R package along with the dependencies of that R package into a zip file and then import them into the 'Execute R script' module.

    Hope this works.

    Thanks,
    Jaya.

    • Proposed as answer by neerajkh_MSFT Tuesday, May 5, 2015 4:04 AM
    • Marked as answer by Hai Ning Monday, May 11, 2015 9:45 PM
    Tuesday, April 28, 2015 8:32 PM

All replies

  • Hi Naoto,

    Currently in Azure ML, we do not have all the R packages pre-installed. However you can bring in any R package via the third port in the 'Execute-R Script' module as shown below. 

    To see a list of packages pre-installed, you can quickly write this script into the 'Execute-R Script' module.

    data <- data.frame(installed.packages())
    # Select data.frame to be sent to the output Dataset port
    maml.mapOutputPort("data");

    To install a new package along with the dependencies you can bring in a zip file as shown below:

    #Installing a new package in R
    install.packages("src/foo/DBI.zip", lib = ".", repos = NULL, verbose = TRUE)
    success <- library("DBI", lib.loc = ".", logical.return = TRUE, verbose = TRUE)

    Could you check to see if this works with your R packages? 

    Thanks,
    Jaya.

    Sunday, April 26, 2015 1:39 PM
  • Thanks for your reply, Jaya.

    I tried two things.

    1. I just copied the content of http://bioconductor.org/biocLite.R to R script module.
    Result:

    [ModuleOutput] Warning: unable to access index for repository http://www.bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.1 [ModuleOutput] [ModuleOutput] 'biocLite.R' failed to install 'BiocInstaller', use [ModuleOutput] [ModuleOutput] 'install.packages("BiocInstaller", [ModuleOutput] [ModuleOutput] repos="http://www.bioconductor.org/packages/2.14/bioc")'

    2. Tried the code suggested in #1, and got this result:

    [ModuleOutput] Warning: unable to access index for repository http://www.bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.1 [ModuleOutput]

    So, probably, I need to download the archive file of BiocInstaller package, and install as you suggested.

    Monday, April 27, 2015 3:54 PM
  • Hi Naoto,

    Perhaps you might now need to download the R package along with the dependencies of that R package into a zip file and then import them into the 'Execute R script' module.

    Hope this works.

    Thanks,
    Jaya.

    • Proposed as answer by neerajkh_MSFT Tuesday, May 5, 2015 4:04 AM
    • Marked as answer by Hai Ning Monday, May 11, 2015 9:45 PM
    Tuesday, April 28, 2015 8:32 PM