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Question: upgrade to Bioconductor version 3.2 (under R version 3.2.2)
2
gravatar for Jeff Zheng
2.0 years ago by
Jeff Zheng20
United States
Jeff Zheng20 wrote:

Dear All,

I installed R version 3.2.2 on our server, and tried to install Bioconductor version 3.2. However, no matter what I do, I always got the following error: 

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help
BiocInstaller version 3.0 is too old for R version 3.2.2;
  remove.packages("BiocInstaller") then
  source("http://bioconductor.org/biocLite.R")
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
​> biocLite("BiocUpgrade")
Error: Bioconductor version 3.0 cannot be upgraded with R version 3.1.0

As you can see, my R version is clearly 3.2.2. However, when I run biocLite("BiocUpgrade"), it suggested my R version is  3.1.0. So, how can I upgrade my Bioconductor to version 3.2?  I would greatly appreciate all your kind help!  Jeff

ADD COMMENTlink modified 2.0 years ago by Martin Morgan ♦♦ 21k • written 2.0 years ago by Jeff Zheng20
3
gravatar for Martin Morgan
2.0 years ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:

There is one or more copies of an old version of the BiocInstaller package in your .libPaths(). Follow the advice in the promote and remove it / them (repeatedly say remove.packages("BiocInstaller") until R says that there is no package to remove). Restart R, verify that there is no BiocInstaller package, and run the command source("http://bioconductor.org/biocLite.R").

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by Martin Morgan ♦♦ 21k
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