[BioC] Error during installation packages

[James W. MacDonald]

Hi Elodie,

On 1/30/2014 7:44 AM, Elodie Chapeaublanc wrote:
>
> Dear list,
>
> I try to install BrainArray EntrezGene version 12.1 packages (build
> genome version hg18) for U95av2 on U133Plus2 affymetrix arrays, but I
> have got two errors.
>
> I have got the lastest version of R and Bioconductor :
>
> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
> [5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
> [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] BiocInstaller_1.12.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4
> [4] DBI_0.2-7 AnnotationDbi_1.24.0 Biobase_2.22.0
> [7] BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.20.6 stats4_3.0.2 tools_3.0.2
>
>
> When I try to install R CMD INSTALL hgu95av2hsentrezg.db_12.1.0.tar.gz,
> I have got error message :
>
> * installing to library
> ‘/home/echapeaublanc/R/x86_64-pc-linux-gnu-library/3.0’
> * installing *source* package ‘hgu95av2hsentrezg.db’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> Error : .onLoad failed in loadNamespace() for 'hgu95av2hsentrezg.db',
> details:
> call: checkDBSCHEMA(dbconn, schema)
> error: invalid DB schema version (found 2.0, expected 2.1)
> Erreur : le chargement a échoué
> Exécution arrêtée
> ERROR: loading failed
> * removing
> ‘/home/echapeaublanc/R/x86_64-pc-linux-gnu-library/3.0/hgu95av2hsentrezg.db’ 
>
>
>
> For the cdf pacakges : R CMD INSTALL hgu95av2hsentrezgcdf_12.1.0.tar.gz
> * installing to library
> ‘/home/echapeaublanc/R/x86_64-pc-linux-gnu-library/3.0’
> * installing *source* package ‘hgu95av2hsentrezgcdf’ ...
> ERROR: a 'NAMESPACE' file is required
> * removing
> ‘/home/echapeaublanc/R/x86_64-pc-linux-gnu-library/3.0/hgu95av2hsentrezgcdf’ 
>
>
> How can I use the old BrainArray packages ?

By installing the correct version of R. On the page where you downloaded 
the cdf it says:

*Version 12 (Data Sources 
<http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12.1.0/version.html>)*
On Dec 2, 2009, version 12.0.0 is upgraded to 12.1.0 in order to be 
compatible with R 2.10 and Bioc 2.5

So you need R-2.10, after which you can simply use biocLite() to install.

Best,

Jim


>
> Thanks
>
> Elodie
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099