Question: Error in parse() loading affylmGUI
0
gravatar for Paul Boutros
15.5 years ago by
Paul Boutros330
Paul Boutros330 wrote:
Hello, I'm just trying out affylmGUI, and I'm running into a few problems. I'm using: WinXP SP1 R1.9.0 affylmGUI 1.1.0 limma 1.6.14 When I load the library and start the interface I get an error-box popping up saying: Error in parse(file,n,text,prompt): parse error And nothing suspicous appears in the console: > library(affylmgui); Loading required package: limma Loading required package: affy Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: tcltk Warning message: Package 'affylmgui' not found. Using case-insensitive match 'affylmGUI' . Future versions of R will require exact matches. ActiveTcl was found in the Windows Registry (for LOCAL_MACHINE), installed in E:\tcl This directory will be added to the Tcl search path to enable affylmGUI to find the Tktable and BWidget extensions. To begin, type affylmGUI() or use the pull-down menu. Searching for user-defined affylmGUI commands in C:/PROGRA~1/R/rw1090/library/affylmGUI/etc ... Any suggestions? Paul
affylmgui • 579 views
ADD COMMENTlink modified 15.5 years ago by James Wettenhall1000 • written 15.5 years ago by Paul Boutros330
Answer: Error in parse() loading affylmGUI
0
gravatar for James Wettenhall
15.5 years ago by
James Wettenhall1000 wrote:
Hi Paul, I'm running R 1.9.0, limma 1.6.14 and affylmGUI 1.1.0 without problems on Windows 2000/NT. Can I suggest reinstalling limma and affylmGUI with: install.packages("limma",contriburl="http://bioinf.wehi.edu.au/limma") install.packages("affylmGUI",contriburl="http://bioinf.wehi.edu.au/aff ylmGUI") after checking that .libPaths() is set appropriately. Maybe you got a corrupt download last time. > When I load the library and start the interface I get an error-box popping up > saying: > Error in parse(file,n,text,prompt): parse error Do you have any files in the etc/ subdirectory of affylmGUI with extension .R ? affylmGUI sources these .R files automatcially when it starts so that they can be used as custom menu items. Please use the correct capitalization: library(affylmGUI) instead of library(affylmgui) Hope this helps, James > > And nothing suspicous appears in the console: > > library(affylmgui); > Loading required package: limma > Loading required package: affy > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > Loading required package: tcltk > Warning message: > Package 'affylmgui' not found. > Using case-insensitive match 'affylmGUI' . > Future versions of R will require exact matches. > > ActiveTcl was found in the Windows Registry (for LOCAL_MACHINE), installed in > E:\tcl > This directory will be added to the Tcl search path to enable affylmGUI > to find the Tktable and BWidget extensions. > > To begin, type affylmGUI() or use the pull-down menu. > > Searching for user-defined affylmGUI commands in > C:/PROGRA~1/R/rw1090/library/affylmGUI/etc ... > > Any suggestions? > Paul > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
ADD COMMENTlink written 15.5 years ago by James Wettenhall1000
Thanks James, reinstalling fixed it. It's curious, though, because I had the problem both on my initial install and after I upgraded to the newest version at WEHI. Paul > -----Original Message----- > From: James Wettenhall [mailto:wettenhall@wehi.edu.au] > Sent: Monday, June 21, 2004 10:29 PM > To: paul.boutros@utoronto.ca > Cc: BioConductor Mailing List > Subject: Re: [BioC] Error in parse() loading affylmGUI > > > Hi Paul, > > I'm running R 1.9.0, limma 1.6.14 and affylmGUI 1.1.0 without > problems on Windows 2000/NT. Can I suggest reinstalling limma > and affylmGUI with: > install.packages("limma",contriburl="http://bioinf.wehi.edu.au/limma") > install.packages("affylmGUI",contriburl="http://bioinf.wehi.edu.au > /affylmGUI") > > after checking that .libPaths() is set appropriately. > > Maybe you got a corrupt download last time. > > > When I load the library and start the interface I get an > error-box popping up > > saying: > > Error in parse(file,n,text,prompt): parse error > > Do you have any files in the etc/ subdirectory of affylmGUI with > extension .R ? affylmGUI sources these .R files automatcially > when it starts so that they can be used as custom menu items. > > Please use the correct capitalization: > library(affylmGUI) > > instead of library(affylmgui) > > Hope this helps, > James > > > > > > And nothing suspicous appears in the console: > > > library(affylmgui); > > Loading required package: limma > > Loading required package: affy > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, > > simply type: openVignette() > > For details on reading vignettes, see > > the openVignette help page. > > Loading required package: tcltk > > Warning message: > > Package 'affylmgui' not found. > > Using case-insensitive match 'affylmGUI' . > > Future versions of R will require exact matches. > > > > ActiveTcl was found in the Windows Registry (for > LOCAL_MACHINE), installed in > > E:\tcl > > This directory will be added to the Tcl search path to enable affylmGUI > > to find the Tktable and BWidget extensions. > > > > To begin, type affylmGUI() or use the pull-down menu. > > > > Searching for user-defined affylmGUI commands in > > C:/PROGRA~1/R/rw1090/library/affylmGUI/etc ... > > > > Any suggestions? > > Paul > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > >
ADD REPLYlink written 15.5 years ago by Paul Boutros330
Hi Paul and other affylmGUI and limmaGUI users, I think I've finally tracked down the real reason for the parse() error. In limmaGUI and affylmGUI 1.1.0, each GUI package introduced a new feature to display recently opened/saved files in a recent-files list in the File Menu. Unfortunately I forgot to test what would happen if you had spaces or "special characters" in your filenames/directory paths. This should be fixed now (in limmaGUI_1.1.3 and affylmGUI_1.1.1) available from: http://bioinf.wehi.edu.au/limmaGUI/ http://bioinf.wehi.edu.au/affylmGUI/ Hopefully the fix should appear on BioC devel within a day or two. Best regards, James
ADD REPLYlink written 15.5 years ago by James Wettenhall1000
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