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Question: Bioconductor support for R-3.1.0 on Mavericks (Mac OS X 10.9)
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gravatar for Dan Tenenbaum
3.6 years ago by
Dan Tenenbaum ♦♦ 8.1k
United States
Dan Tenenbaum ♦♦ 8.1k wrote:
Hi all, (This concerns Mac users only; the rest of you do not need to read this.) When R-3.1.0 is released on April 10 you will notice that there are two flavors of R available for download for the Mac: a version built on Snow Leopard (Mac OS 10.6) and a version built on Mavericks (Mac OS X 10.9). The Snow Leopard version of R will work fine on all versions of Mac OS X from 10.6 onward, including Mavericks. Binary Bioconductor packages are NOT yet available for the Mavericks build of R. The two versions are not binary-compatible. If you install the Mavericks version of R, you'll find that you are unable to install Bioconductor packages with biocLite(). You should be able to install packages from source, but this will require that you have a development environment set up, and various system dependencies depending on the packages you're trying to install. This is not recommended. What we do recommend is to use the Snow Leopard version of R. With this version, you'll be able to install Bioconductor packages with biocLite() in the normal manner. We have ordered some new hardware to facilitate building Bioconductor packages on Mavericks. After the hardware has arrived, we'll set up builds on it and verify that they are working properly. At that time we'll make an announcement on the Bioconductor and Bioc-devel lists, and you will then be able to use the Mavericks version of R with Bioconductor. Thanks and please let us know if you have any questions. Dan
ADD COMMENTlink written 3.6 years ago by Dan Tenenbaum ♦♦ 8.1k

Hi

Am new to R and Bioconductor but have tried to examine old posts and FAQ for an answer to my installation question but with no success.

Am running R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" through RStudio Version 0.98.1102 on a Mac OS X 10.10.2. When I try to install Bioconductor and various libraries, I get the following errors.  

Here is the code that you suggest with the accompanying error messages

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

Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help

biocLite()

Error: 'no packages in repository (no internet connection?)' while tryinghttp://bioconductor.org/packages/2.13/bioc

biocLite("genefilter") 

Error: 'no packages in repository (no internet connection?)' while tryinghttp://bioconductor.org/packages/2.13/bioc

?rowttests

No documentation for ‘rowttests’ in specified packages and libraries: you could try ‘??rowttests’

CONCLUSION: Clearly Bioconductor libraries are not being installed confirmed by the fact that the function rowtests is not found. Any suggestions? Thanks

 

 

 

 

 

 

ADD REPLYlink written 2.6 years ago by james.brophy0
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