Question: Error in loading bioconductor packages in Rterm and ESS+XEmacs modes
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gravatar for Dr Mushtaq Ahmed
16.5 years ago by
Dr Mushtaq Ahmed20 wrote:
I am using the latest Bioconductor developement version on Windows. The command library(affy) works fine from the R GUI. But I am not able to import any packages (e.g. affy) when I use the ESS+XEmacs or simply Rterm shell mode. I get the following error: I think that it may be due to some extra work the package upload routine tries to do like adding "Vignettes" menu to the GUI and fails to do so in the Rterm mode. What is the workaround? Thanks in advance, mushtaq ----------error start----------------------- > library(affy) ************* affy: development version ************* ************* IMPORTANT: you need the latest versions of the required packages too. ************* Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Creating a new generic function for "summary" in package reposTools Synching your local package management information ... Attaching package `reposTools': The following object(s) are masked from package:base : summary Error in paste(menus[1:(length(menus) - counter)], sep = "", collapse = "/") : only 0's may mix with negative subscripts Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Error in paste(menus[1:(length(menus) - counter)], sep = "", collapse = "/") : only 0's may mix with negative subscripts Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses) : Class "AffyBatch" extends an undefined class ("exprSet" Error in library(affy) : .First.lib failed > --------error end---------------- [[alternate HTML version deleted]]
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ADD COMMENTlink modified 16.5 years ago by Jeff Gentry3.9k • written 16.5 years ago by Dr Mushtaq Ahmed20
Answer: Error in loading bioconductor packages in Rterm and ESS+XEmacs modes
0
gravatar for Jeff Gentry
16.5 years ago by
Jeff Gentry3.9k
Jeff Gentry3.9k wrote:
> I am using the latest Bioconductor developement version on Windows. > The command library(affy) works fine from the R GUI. > But I am not able to import any packages (e.g. affy) when I use the > ESS+XEmacs or simply Rterm shell mode. I get the following error: > I think that it may be due to some extra work the package upload > routine tries to do like adding "Vignettes" menu to the GUI and fails to > do so in the Rterm mode. It appears that the package widgetTools (which is called by affy) tries to check if it is under GUI mode or not before adding a Vignette tab to the GUI menubar. However, the current check that it is using is if(interactive), which is still TRUE even in Rterm. We're looking at finding a mechanism to detect if it is inded Rgui instead of Rterm ... -J
ADD COMMENTlink written 16.5 years ago by Jeff Gentry3.9k
>>>>> "JeffG" == Jeff Gentry <jgentry@jimmy.harvard.edu> >>>>> on Tue, 15 Apr 2003 10:53:06 -0400 (EDT) writes: >> I am using the latest Bioconductor developement version >> on Windows. The command library(affy) works fine from >> the R GUI. But I am not able to import any packages >> (e.g. affy) when I use the ESS+XEmacs or simply Rterm >> shell mode. I get the following error: I think that it >> may be due to some extra work the package upload routine >> tries to do like adding "Vignettes" menu to the GUI and >> fails to do so in the Rterm mode. JeffG> It appears that the package widgetTools (which is JeffG> called by affy) tries to check if it is under GUI JeffG> mode or not before adding a Vignette tab to the GUI JeffG> menubar. However, the current check that it is using JeffG> is if(interactive), which is still TRUE even in JeffG> Rterm. We're looking at finding a mechanism to JeffG> detect if it is inded Rgui instead of Rterm ... That's not hard: .Platform $ GUI is "Rgui" or "RTerm", respectively. I'm not perfectly sure this will stay exactly the same, since it's not documented and the capitalization seems not logical ("Term" vs "gui") to me. R-core, shouldn't we document some of the possible values here, the two windows ones being of particular importance? Martin Maechler <maechler@stat.math.ethz.ch> http://stat.ethz.ch/~maechler/ Seminar fuer Statistik, ETH-Zentrum LEO C16 Leonhardstr. 27 ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND phone: x-41-1-632-3408 fax: ...-1228 <><
ADD REPLYlink written 16.5 years ago by Martin Maechler330
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