Try library(Rgraphviz) before calling plot(). Martin -- Martin Morgan On Aug 27, 2012, at 9:12 AM, Kasper Daniel Hansen <kasperdanielhansen at="" gmail.com=""> wrote: > First, a warning is not the same as an error. Does a plot appear? > > Second, I cannot reproduce this on OS X, with the same package versions. > > Kasper > > On Mon, Aug 27, 2012 at 11:52 AM, narsis [guest] <guest at="" bioconductor.org=""> wrote: >> >> I have installed Rgraphvis on my computer >> (OS:Windows vista. >> I have tried to make the following graph >> >> V <- letters[1:10] >>> M <- 1:4 >>> set.seed(123) >>> V <- letters[1:10] >>> M <- 1:4 >>> g1 <- randomGraph(V, M, .2) >>> plot(g1, "neato") >> >> Then I got following error: >> There were 32 warnings (use warnings() to see them) >>> warnings() >> Warning messages: >> 1: In plot.xy(xy.coords(x, y), type = type, ...) : >> "len" is not a graphical parameter >> 2: In plot.xy(xy.coords(x, y), type = type, ...) : >> "edgemode" is not a graphical parameter >> 3: In plot.xy(xy.coords(x, y), type = type, ...) : >> "len" is not a graphical parameter >> 4: In plot.xy(xy.coords(x, y), type = type, ...) : >> "edgemode" is not a graphical parameter >> .... >> I have cheked Path variables for both R and Graphvis >> strsplit(Sys.getenv("PATH"), ";") >> [[1]] >> [1] "C:\\Program Files\\copasi.org\\COPASI 4.8.35\\bin" >> [2] "C:\\Program Files\\Common Files\\Microsoft Shared\\Windows Live" >> [3] "C:\\texmf\\miktex\\bin" >> [4] "C:\\Windows\\system32" >> [5] "C:\\Windows" >> [6] "C:\\Windows\\System32\\Wbem" >> [7] "C:\\Program Files\\Common Files\\Roxio Shared\\9.0\\DLLShared\\" >> [8] "C:\\Program Files\\Common Files\\Roxio Shared\\DLLShared\\" >> [9] "c:\\Program Files\\Microsoft SQL Server\\100\\Tools\\Binn\\" >> [10] "c:\\Program Files\\Microsoft SQL Server\\100\\DTS\\Binn\\" >> [11] "C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\" >> [12] "C:\\Program Files\\Windows Live\\Shared" >> [13] "C:\\Program Files\\QuickTime\\QTSystem\\" >> [14] "C:\\Program Files\\MATLAB\\R2010b\\runtime\\win32" >> [15] "C:\\Program Files\\MATLAB\\R2010b\\bin" >> [16] "c:\\Program Files\\Graphviz2.20\\bin" >> [17] "C:\\Program Files\\SSH Communications Security\\SSH Secure Shell" >> >> and >> list.files(strsplit(Sys.getenv("PATH"), ";")[[1]][[14]], "dll") >> [1] "mclcom7_14.dll" "mclcommain7_14.dll" "mclmcrrt7_14.dll" >> [4] "mclxlmain7_14.dll" "msvcp60.dll" "mwcommgr.dll" >> [7] "mwcomutil.dll" >> >> I do not know what is the problem , It would be appreciated if you can help me. >> Best >> Narsis >> >> -- output of sessionInfo(): >> >> R version 2.15.1 (2012-06-22) >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 >> [2] LC_CTYPE=English_United States.1252 >> [3] LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] grid stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] Rgraphviz_1.34.2 graph_1.34.0 BiocInstaller_1.4.7 >> >> loaded via a namespace (and not attached): >> [1] BiocGenerics_0.2.0 stats4_2.15.1 tools_2.15.1 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi Thanks for reply! I did not get any graph !A new  window was opened but there was nothing on it, just   white background window! Can you  get the plot with XP? Best Narsis ________________________________ From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com> To: narsis [guest] <guest@bioconductor.org> Sent: Monday, August 27, 2012 8:42 PM Subject: Re: [BioC] Rgraphviz- \"len\" is not a graphical parameter First, a warning is not the same as an error.  Does a plot appear? Second, I cannot reproduce this on OS X, with the same package versions. Kasper On Mon, Aug 27, 2012 at 11:52 AM, narsis [guest] <guest@bioconductor.org> wrote: > > I have installed  Rgraphvis on my computer > (OS:Windows vista. > I have tried to make the following graph > >  V <- letters[1:10] >> M <- 1:4 >> set.seed(123) >> V <- letters[1:10] >> M <- 1:4 >> g1 <- randomGraph(V, M, .2) >> plot(g1, "neato") > > Then I got following error: > There were 32 warnings (use warnings() to see them) >>  warnings() > Warning messages: > 1: In plot.xy(xy.coords(x, y), type = type, ...) : >  "len" is not a graphical parameter > 2: In plot.xy(xy.coords(x, y), type = type, ...) : >  "edgemode" is not a graphical parameter > 3: In plot.xy(xy.coords(x, y), type = type, ...) : >  "len" is not a graphical parameter > 4: In plot.xy(xy.coords(x, y), type = type, ...) : >  "edgemode" is not a graphical parameter > .... > I have cheked Path variables for both R and Graphvis >  strsplit(Sys.getenv("PATH"), ";") > [[1]] >  [1] "C:\\Program Files\\copasi.org\\COPASI 4.8.35\\bin" >  [2] "C:\\Program Files\\Common Files\\Microsoft Shared\\Windows Live" >  [3] "C:\\texmf\\miktex\\bin" >  [4] "C:\\Windows\\system32" >  [5] "C:\\Windows" >  [6] "C:\\Windows\\System32\\Wbem" >  [7] "C:\\Program Files\\Common Files\\Roxio Shared\\9.0\\DLLShared\\" >  [8] "C:\\Program Files\\Common Files\\Roxio Shared\\DLLShared\\" >  [9] "c:\\Program Files\\Microsoft SQL Server\\100\\Tools\\Binn\\" > [10] "c:\\Program Files\\Microsoft SQL Server\\100\\DTS\\Binn\\" > [11] "C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\" > [12] "C:\\Program Files\\Windows Live\\Shared" > [13] "C:\\Program Files\\QuickTime\\QTSystem\\" > [14] "C:\\Program Files\\MATLAB\\R2010b\\runtime\\win32" > [15] "C:\\Program Files\\MATLAB\\R2010b\\bin" > [16] "c:\\Program Files\\Graphviz2.20\\bin" > [17] "C:\\Program Files\\SSH Communications Security\\SSH Secure Shell" > > and >  list.files(strsplit(Sys.getenv("PATH"), ";")[[1]][[14]], "dll") > [1] "mclcom7_14.dll"    "mclcommain7_14.dll" "mclmcrrt7_14.dll" > [4] "mclxlmain7_14.dll"  "msvcp60.dll"        "mwcommgr.dll" > [7] "mwcomutil.dll" > > I do not know what is the problem , It would be appreciated if you can help me. > Best > Narsis > >  -- output of sessionInfo(): > > R version 2.15.1 (2012-06-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] grid      stats    graphics  grDevices utils    datasets methods > [8] base > > other attached packages: > [1] Rgraphviz_1.34.2    graph_1.34.0        BiocInstaller_1.4.7 > > loaded via a namespace (and not attached): > [1] BiocGenerics_0.2.0 stats4_2.15.1      tools_2.15.1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]