[BioC] Upgrading Bioconductor using BiocUpgrade

[Lavinia Gordon]

Thanks Dan, works perfectly, greatly appreciate your prompt response.

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


-----Original Message-----
From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] 
Sent: Wednesday, 24 October 2012 8:44 AM
To: Lavinia Gordon
Cc: bioconductor at r-project.org
Subject: Re: [BioC] Upgrading Bioconductor using BiocUpgrade

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/>
>
>
>
>
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