[BioC] FW: XPS crahses R session

[cstrato]

Dear Guido,

Since Bioconductor has compiled the Windows version of xps using root 
5.22.00 you need to install the binary of this version, as mentioned in 
"System Requirements". You can download this version from: 
http://root.cern.ch/root/Version522.html
I would suggest to install version: root_v5.22.00.win32.vc90.msi

Please see also my introductory comments for Windows users:
https://www.stat.math.ethz.ch/pipermail/bioconductor/2008-December/025452.html 


Please let me know if this solved your problem.

Best regards
Christian

P.S.: Although the BioC mailing list is currently down I assume that it 
will contain your question, thus I cc to the list.

Hooiveld, Guido wrote:
>  
> Hi,
> Since the BioC mailing list seems not to work properly (i haven't 
> received any BioC mails the last days), I am sending you this email 
> directly.
>  
> Regards,
> Guido
>
> ------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>
> email:      guido.hooiveld at wur.nl
>
>  
>
> ------------------------------------------------------------------------
> *From:* Hooiveld, Guido
> *Sent:* 17 August 2009 17:50
> *To:* bioconductor at stat.math.ethz.ch
> *Subject:* XPS crahses R session
>
> Dear Christian,
>  
> I am new to XPS and i would like to use it to analyse Mouse Gene ST 
> arrays (MoGene ST arrays). However, XPS crashes my R session when 
> trying to create a ROOT scheme file fore these arrays, and i don't 
> know what may go wrong. Hopefully you can advise. :)
>  
> Thanks,
> Guido
>  
>  
> What did i do?
> - I am using a windows machine (WinXP-SP3, 4GB memory)
> - I installed ROOT v5.24.00 (1st) and XPS (2nd). PS: is there a way to 
> check whether ROOT installed properly?
> - Then i downloaded the 'library' files', MoGene-1_0-st-v1.r4.pgf and 
> MoGene-1_0-st-v1.r4.clf, and put them in a directory 
> (D:\XPS\Affy\libraryfiles)
> - Next i downloaded the latest annotation files from Affymetrix 
> (MoGene-1_0-st-v1.na29.mm9.transcript.csv and 
> MoGene-1_0-st-v1.na29.mm9.probeset.csv), and repaired them according 
> to your instructions here: 
> http://article.gmane.org/gmane.science.biology.informatics.conductor/24587. 
> The annotation files are in the dir D:\XPS\Affy\Annotation.
> - I also created a dir to save the ROOT scheme 
> file (D:\XPS\CRAN\Workspaces\Schemes).
>  
> When running XPS to create the scheme file R crashes...
>  
> My lines of code:
> library(xps)
> libdir <- "d:/XPS/Affy/libraryfiles"
> anndir <- "d:/XPS/Affy/Annotation"
> scmdir <- "d:/XPS/CRAN/Workspaces/Schemes"
> Below it crashes (line is from your previous referred post on the 
> mailing list):
>  
> scheme.mogene10stv1r4.na29 <-
> import.exon.scheme("Scheme_MoGene10stv1r4_na29",filedir=scmdir,
> paste(libdir,"MoGene-1_0-st-v1.r4.clf",sep="/"),
> paste(libdir,"MoGene-1_0-st-v1.r4.pgf",sep="/"),
> paste(anndir,"MoGene-1_0-st-v1.na29.mm9.probeset.fixed.csv",sep="/"),
> paste(anndir,"MoGene-1_0-st-v1.na29.mm9.transcript.fixed.csv",sep="/"))
>  
> Error message:
> Rgui.exe - Application error. The instruction at "0x002288931" 
> references memory at "0x8d5056fc". The memory could not be "read".
>  
>
> > sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-pc-mingw32
>  
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United 
> Kingdom.1252;LC_MONETARY=English_United 
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>  
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base    
>  
> other attached packages:
> [1] xps_1.4.8
> >
>  
>  
>  
>
> ------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>
> email:      guido.hooiveld at wur.nl
>
>