Using Bioconductor

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,

Answer 1

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.

Answer 2

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.

Answer 3

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.