[BioC] Loading the PGSEA package.

[Dykema, Karl]

Marcus,
 
Ruuid is only need for creating GSEAbase geneSetCollection objects so it shouldn't have been in the "Depends:" field in the first place! I moved it to "Suggests:" and committed my changes to the development version. Look for version 1.11.1 to show up here:
 
http://bioconductor.org/packages/devel/bioc/html/PGSEA.html
 
Thanks for your interest!

 
-------------------------------------------
Karl Dykema
Computational Biologist
Van Andel Research Institute
333 Bostwick Ave NE
Grand Rapids, MI 49503


 
------ Forwarded Message
From: Patrick Aboyoun <paboyoun at fhcrc.org>
Date: Thu, 22 Jan 2009 14:12:30 -0500
To: Marcus Gry <marcus.gry at genpat.uu.se>
Cc: <bioconductor at stat.math.ethz.ch>
Conversation: [BioC] Loading the PGSEA package.
Subject: Re: [BioC] Loading the PGSEA package.

Marcus,
The Ruuid package requires the glib (3rd party) library installed on
your machine. A popular way to get glib for Mac OS X users of R is to
install the full GTK+ framework provided by Simon Urbanek at

http://r.research.att.com

The particular file of interest is

http://r.research.att.com/gtk2-framework.dmg


Patrick



Marcus Gry wrote:
> Hello mailinglist!
>
> I have a problem loading the PGSEA package using R 2.8.0 on Mac OS X 
> 10.5.6.
>
>  > library(PGSEA)
> Loading required package: AnnotationDbi
> Loading required package: Biobase
> Loading required package: tools
>
> Welcome to Bioconductor
>
>    Vignettes contain introductory material. To view, type
>    'openVignette()'. To cite Bioconductor, see
>    'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: Ruuid
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>    unable to load shared library '/Library/Frameworks/R.framework/
> Resources/library/Ruuid/libs/i386/Ruuid.so':
>    dlopen(/Library/Frameworks/R.framework/Resources/library/Ruuid/libs/
> i386/Ruuid.so, 6): Library not loaded: /usr/local/lib/
> libglib-2.0.0.dylib
>    Referenced from: /Library/Frameworks/R.framework/Resources/library/
> Ruuid/libs/i386/Ruuid.so
>    Reason: image not found
> Error: package 'Ruuid' could not be loaded
>  > sessionInfo()
> R version 2.8.0 (2008-10-20)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  
> methods   base
>
> other attached packages:
> [1] AnnotationDbi_1.4.2 Biobase_2.2.1
>
> loaded via a namespace (and not attached):
> [1] DBI_0.2-4     RSQLite_0.7-1
>
>
> I would really appreciate some help in this matter.
>
> Best regards
>
> /Marcus
>       [[alternative HTML version deleted]]
>
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