Dear all,

I am trying to upgrade Bioconductor from 2.10 to 2.11 on a machine running R.2.15.0.  Unfortunately this fails, unable to find function 'globalVariables'.  Any advice greatly appreciated.

 

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

BiocInstaller version 1.4.9, ?biocLite for help

A newer version of Bioconductor is available for this version of R,

  ?BiocUpgrade for help

>    biocLite("BiocUpgrade")

Upgrade all packages to Bioconductor version 2.11? [y/n]: y

trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/BiocInstaller_1.8.2.tar.gz'

Content type 'application/x-gzip' length 12006 bytes (11 Kb)

opened URL

==================================================

downloaded 11 Kb

 

* installing *source* package āBiocInstallerā ...

** R

** inst

** preparing package for lazy loading

Error in eval(expr, envir, enclos) : 

  could not find function "globalVariables"

Error : unable to load R code in package āBiocInstallerā

ERROR: lazy loading failed for package āBiocInstallerā

* removing ā/usr/local/lib64/R/library/BiocInstallerā

* restoring previous ā/usr/local/lib64/R/library/BiocInstallerā

 

The downloaded source packages are in

        ā/tmp/RtmpnPmRq7/downloaded_packagesā

Updating HTML index of packages in '.Library'

Making packages.html  ... done

BiocInstaller version 1.4.9, ?biocLite for help

A newer version of Bioconductor is available for this version of R,

  ?BiocUpgrade for help

'BiocInstaller' changed to version 1.4.9

BioC_mirror: http://bioconductor.org

Using R version 2.15, BiocInstaller version 1.4.9.

> sessionInfo()

R version 2.15.0 (2012-03-30)

Platform: x86_64-unknown-linux-gnu (64-bit)

 

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=C                 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_1.4.9

 

loaded via a namespace (and not attached):

[1] tools_2.15.0

 

 

Lavinia Gordon

Senior Research Officer

Quantitative Sciences Core, Bioinformatics

 

Murdoch Childrens Research Institute

The Royal Children's Hospital

Flemington Road Parkville Victoria 3052 Australia 

T 03 8341 6221

www.mcri.edu.au <http://www.mcri.edu.au/> 

 


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