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Question: BiocUpgrade to 3.1 fails on R 3.2.0
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gravatar for ori.staszewski
2.5 years ago by
Germany
ori.staszewski0 wrote:

Hi,

 

I am trying to update my current Bioconductor installation to 3.1 - however using BiocUpgrade this fails citing an incorrect R version, how would I get around this?


R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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  Natural language support but running in an English locale

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> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.4), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.4), R version 3.2.0.
> biocLite("BiocUpgrade")
Error: Bioconductor version 3.0 cannot be upgraded with R version 3.1.0
>

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.16.4

loaded via a namespace (and not attached):
[1] tools_3.2.0
>

 

ADD COMMENTlink written 2.5 years ago by ori.staszewski0

Start R with R --vanilla and then

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

You should end up with Bioconductor 3.1.

ADD REPLYlink written 2.5 years ago by Dan Tenenbaum ♦♦ 8.2k
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