Issue installing Cardinal in R

[Catherine Rawlins]

Hello,

Every time I try to follow the instructions on the bioconductor and/or cardinal msi website the command line says "Warning message:package ‘Cardinal’ is not available (as a binary package for R version 3.1.3)" and I got the same messge with R version 3.0.3. Is there a specific version of R I should be using? What is the main different between Rtools and R?

Thank you,

Catie Rawlins

[kbemis]

Hi Catie,

Cardinal is currently only available on the development version of Bioconductor, which requires the development version of R. If you install the development version of R from CRAN (scroll down to "other builds" on the download page), and then follow the Bioconductor installation instructions, it should work.

Cardinal will be included in the next public release of Bioconductor on April 17, at which point it will be installable from an ordinary installation of R.

Rtools includes the tools for developing R packages on Windows, and is only necessary if you are building and installing the package from source. It's not necessary if you are installing from Bioconductor.

I hope this helps.

Kyle

[Catherine Rawlins]

I tried R-Devel build for windows from http://cran.r-project.org/ and used the source code for the bioconductor for Cardinal but it seems like the package is not installing.

I follow the instructions on the Bioconductor website (http://bioconductor.org/packages/devel/bioc/html/Cardinal.html) but I continually get this response:

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

Bioconductor version 3.1 (BiocInstaller 1.17.6), ?biocLite for help

> biocLite("Cardinal")

BioC_mirror: http://bioconductor.org

Using Bioconductor version 3.1 (BiocInstaller 1.17.6), R version 3.3.0.

Installing package(s) ‘Cardinal’

also installing the dependency ‘Biobase’

Warning: unable to access index for repository http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.3

Warning: unable to access index for repository http://bioconductor.org/packages/3.1/data/annotation/bin/windows/contrib/3.3

Warning: unable to access index for repository http://bioconductor.org/packages/3.1/data/experiment/bin/windows/contrib/3.3

Warning: unable to access index for repository http://bioconductor.org/packages/3.1/extra/bin/windows/contrib/3.3

Packages which are only available in source form, and may need

  compilation of C/C++/Fortran: ‘Biobase’ ‘Cardinal’

  These will not be installed

I also tried the GitHub installation instructions with no luck.

I have tried so many different things and many different versions of R and I am not sure what is going wrong!

[kbemis]

It looks like this is due to R 3.2 and Bioconductor 3.1 are both getting ready for release. Bioconductor is expecting R version 3.2, while the development branch of R has moved on to version 3.3.

You can download the test version of R 3.2 for Windows here: http://cran.r-project.org/bin/windows/base/rtest.html

I apologize for the confusion. This should all be fixed and working again next month when Bioconductor 3.1 is released.

Kyle

[Catherine Rawlins]

Good to know it wasn't anything conceptually I was doing wrong. I will try again with R 3.2. Thank you for your help!