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]]

Hi Marcus, On Thu, Jan 22, 2009 at 10:48 AM, Marcus Gry <marcus.gry at="" genpat.uu.se=""> wrote: > Hello mailinglist! > > I have a problem loading the PGSEA package using R 2.8.0 on Mac OS X > 10.5.6. 2.8.1 is the current release so it might be a good time to update. (more below) > > > 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 It looks like you do not have Ruuid installed properly. library(Ruuid) at the R command prompt? I suspect it fails, and then you can start by reinstalling it. best wishes Robert > > 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

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@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/li bs/ > 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ------ End of Forwarded Message This email message, including any attachments, is for th...{{dropped:6}}