Hi Kachelo yes, windows 32. thanks --- On Mon, 7/6/10, Cristobal Fresno Rodr�guez <cristobalfresno@gmail.com> wrote: From: Cristobal Fresno Rodr�guez <cristobalfresno@gmail.com> Subject: Re: [BioC] install Rgraphviz To: "Yuan Jian" <jayuan2008@yahoo.com> Cc: bioconductor@stat.math.ethz.ch Received: Monday, 7 June, 2010, 5:31 PM Hi Yuan, Do you have installed graphviz for windows? Kachelo 2010/6/5 Yuan Jian <jayuan2008@yahoo.com> Hi, � could you tell me what the problem in installation of "Rgraphviz" package? >�source("http://bioconductor.org/biocLite.R") > biocLite("Rgraphviz") > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_Australia.1252� LC_CTYPE=English_Australia.1252�� [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C��������������������� [5] LC_TIME=English_Australia.1252��� attached base packages: [1] grid����� stats���� graphics� grDevices utils���� datasets� methods�� base���� other attached packages: [1] limma_3.4.2� graph_1.26.0 loaded via a namespace (and not attached): [1] tools_2.11.1 > library(Rgraphviz) Loading required package: graph Loading required package: grid Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: � call: value[[3L]](cond) � error: unable to load shared library 'C:/PROGRA~1/R/R-211~1.1/library/Rgraphviz/libs/Rgraphviz.dll': � LoadLibrary failure:� The specified module could not be found. � > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_Australia.1252� LC_CTYPE=English_Australia.1252�� [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C��������������������� [5] LC_TIME=English_Australia.1252��� attached base packages: [1] grid����� stats���� graphics� grDevices utils���� datasets� methods�� base���� other attached packages: [1] limma_3.4.2� graph_1.26.0 loaded via a namespace (and not attached): [1] tools_2.11.1 > � � � �[[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

Thanks Kachelo, � I have just installed graphviz-2.26.3.msi. now I got error: "This application has failed to start because libcdt-4.dll was not found,.." � could you give advice? � thanks � --- On Tue, 8/6/10, Cristobal Fresno Rodr�guez <cristobalfresno@gmail.com> wrote: From: Cristobal Fresno Rodr�guez <cristobalfresno@gmail.com> Subject: Re: [BioC] install Rgraphviz To: "Yuan Jian" <jayuan2008@yahoo.com> Cc: bioconductor@stat.math.ethz.ch Received: Tuesday, 8 June, 2010, 12:34 PM Hi Yuan, What version of graphviz do you have? you can get the latest at http:/ /www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.26.3.msi Have you tried the examples (out of R)? Have you check if the dll exists? Do you have read/write permissions on�'C:/PROGRA~1/R/R-211~1.1/ library/Rgraphviz/libs/Rgraphviz.dll'? Kachelo El 7 de junio de 2010 18:20, Yuan Jian <jayuan2008@yahoo.com> escribi�: Hi Kachelo yes, windows 32. thanks --- On Mon, 7/6/10, Cristobal Fresno Rodr�guez <cristobalfresno@gmail.com> wrote: From: Cristobal Fresno Rodr�guez <cristobalfresno@gmail.com> Subject: Re: [BioC] install Rgraphviz To: "Yuan Jian" <jayuan2008@yahoo.com> Cc: bioconductor@stat.math.ethz.ch Received: Monday, 7 June, 2010, 5:31 PM Hi Yuan, Do you have installed graphviz for windows? Kachelo 2010/6/5 Yuan Jian <jayuan2008@yahoo.com> Hi, � could you tell me what the problem in installation of "Rgraphviz" package? >�source("http://bioconductor.org/biocLite.R") > biocLite("Rgraphviz") > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_Australia.1252� LC_CTYPE=English_Australia.1252�� [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C��������������������� [5] LC_TIME=English_Australia.1252��� attached base packages: [1] grid����� stats���� graphics� grDevices utils���� datasets� methods�� base���� other attached packages: [1] limma_3.4.2� graph_1.26.0 loaded via a namespace (and not attached): [1] tools_2.11.1 > library(Rgraphviz) Loading required package: graph Loading required package: grid Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: � call: value[[3L]](cond) � error: unable to load shared library 'C:/PROGRA~1/R/R-211~1.1/library/Rgraphviz/libs/Rgraphviz.dll': � LoadLibrary failure:� The specified module could not be found. � > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_Australia.1252� LC_CTYPE=English_Australia.1252�� [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C��������������������� [5] LC_TIME=English_Australia.1252��� attached base packages: [1] grid����� stats���� graphics� grDevices utils���� datasets� methods�� base���� other attached packages: [1] limma_3.4.2� graph_1.26.0 loaded via a namespace (and not attached): [1] tools_2.11.1 > � � � �[[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor � [[alternative HTML version deleted]]

On 06/08/2010 02:34 PM, Cristobal Fresno Rodr?guez wrote: > Hi Yuan, > What version of graphviz do you have? you can get the latest at > http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.26.3. msi Have This is not the recommended solution. Please instead visit http://bioconductor.org/packages/2.6/bioc/html/Rgraphviz.html and follow the directions (very carefully) in the README file of Rgraphviz. These say Using the Windows binary ------------------------ o. install Graphviz ***2.20.3.1*** Windows ***binary*** distribution from http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1. msi in a directory that we'll call $DIR. We use the following as an example: C:\Graphviz2.20 If you install it in other dir, just use your dir correspondingly. o. Add Graphviz' bin diretory to the user PATH variable, e.g., c:\Graphviz2.20\bin o. Check the configuration by starting a new DOS window and displaying the PATH environment variable, e.g., c:\> echo %PATH% o. Use biocLite('Rgraphviz') to install Rgraphviz To this I would add that you should start R and try strsplit(Sys.getenv("PATH"), ";") inspect the result of this and, when you find the component that you think is the 'graphviz bin directory mentioned above, confirm that it points to a valid location, e.g., > strsplit(Sys.getenv("PATH"), ";")$PATH[13] [1] "C:\\Program Files\\Graphviz2.20\\bin" > list.files(strsplit(Sys.getenv("PATH"), ";")$PATH[13]) [1] "acyclic.exe" "bcomps.exe" [3] "ccomps.exe" "circo.exe" [5] "comdlg32.ocx" "config" ... Martin > you tried the examples (out of R)? > Have you check if the dll exists? Do you have read/write permissions > on 'C:/PROGRA~1/R/R-211~1.1/ > library/Rgraphviz/libs/Rgraphviz.dll'? > > Kachelo > > El 7 de junio de 2010 18:20, Yuan Jian <jayuan2008 at="" yahoo.com=""> escribi?: > >> Hi Kachelo >> >> yes, windows 32. >> >> thanks >> >> >> >> --- On *Mon, 7/6/10, Cristobal Fresno Rodr?guez <cristobalfresno at="" gmail.com="">>> * wrote: >> >> >> From: Cristobal Fresno Rodr?guez <cristobalfresno at="" gmail.com=""> >> Subject: Re: [BioC] install Rgraphviz >> To: "Yuan Jian" <jayuan2008 at="" yahoo.com=""> >> Cc: bioconductor at stat.math.ethz.ch >> Received: Monday, 7 June, 2010, 5:31 PM >> >> >> Hi Yuan, >> Do you have installed graphviz for windows? >> Kachelo >> >> >> 2010/6/5 Yuan Jian <jayuan2008 at="" yahoo.com<http:="" mc="" compose?to="jayuan2008" at="" yahoo.com=""> >>> >> >>> Hi, >>> >>> could you tell me what the problem in installation of "Rgraphviz" package? >>>> source("http://bioconductor.org/biocLite.R") >>>> biocLite("Rgraphviz") >>>> sessionInfo() >>> R version 2.11.1 (2010-05-31) >>> i386-pc-mingw32 >>> locale: >>> [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 >>> [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C >>> [5] LC_TIME=English_Australia.1252 >>> attached base packages: >>> [1] grid stats graphics grDevices utils datasets methods >>> base >>> other attached packages: >>> [1] limma_3.4.2 graph_1.26.0 >>> loaded via a namespace (and not attached): >>> [1] tools_2.11.1 >>> >>>> library(Rgraphviz) >>> Loading required package: graph >>> Loading required package: grid >>> Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: >>> call: value[[3L]](cond) >>> error: unable to load shared library >>> 'C:/PROGRA~1/R/R-211~1.1/library/Rgraphviz/libs/Rgraphviz.dll': >>> LoadLibrary failure: The specified module could not be found. >>> >>>> sessionInfo() >>> R version 2.11.1 (2010-05-31) >>> i386-pc-mingw32 >>> locale: >>> [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 >>> [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C >>> [5] LC_TIME=English_Australia.1252 >>> attached base packages: >>> [1] grid stats graphics grDevices utils datasets methods >>> base >>> other attached packages: >>> [1] limma_3.4.2 graph_1.26.0 >>> loaded via a namespace (and not attached): >>> [1] tools_2.11.1 >>>> >>> >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch<http: mc="" compose?to="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 >>> >> >> >> > > [[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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793