[BioC] Upgrading Bioconductor using BiocUpgrade

[Dan Tenenbaum]

Hi Lavinia,

On Tue, Oct 23, 2012 at 2:14 PM, Lavinia Gordon
<lavinia.gordon at mcri.edu.au> wrote:
> 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.
>

It looks like older versions of R-2.15 did not have the
globalVariables() function.

We just pushed a new version of BiocInstaller (1.8.3) for Bioc 2.11
that checks to make sure this function exists before calling it.

Start a fresh R session and try the upgrade instructions again.
Thanks,
Dan


>
>
>> 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/>
>
>
>
>
> ______________________________________________________________________
> This email has been scanned by the Symantec Email Security.cloud service.
> For more information please visit http://www.symanteccloud.com
> ______________________________________________________________________
>         [[alternative HTML version deleted]]
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor