bioconductor and ESS
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@patrick-brown-1136
Last seen 7.9 years ago
Hello. bioconductor behaves strangely when I run R through emacs using ESS. I'm using R 2.0.1 with windows XP. using the R gui I get > temp=new("phenoData") > validObject(temp) [1] TRUE but in emacs I get > temp=new("phenoData") > validObject(temp) Error in validityMethod(object) : No slot of name "phenoLabels" for this object of class "phenoData" so I'll use the R gui from now on, but I just wanted to point this out.
GUI GUI • 833 views
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@wolfgang-huber-3550
Last seen 5 days ago
EMBL European Molecular Biology Laborat…
Hi Patrick, are you sure that you are actually using the same versions of R when you call Rgui versus ESS? Perhaps your emacs accesses an old version of R that is still lying around somewhere on your computer. Bw Wolfgang Patrick Brown wrote: > Hello. bioconductor behaves strangely when I run R through emacs using > ESS. I'm using R 2.0.1 with windows XP. > using the R gui I get > > > temp=new("phenoData") > > validObject(temp) > [1] TRUE > > but in emacs I get > > > temp=new("phenoData") > > validObject(temp) > Error in validityMethod(object) : No slot of name "phenoLabels" for this > object of class "phenoData" > > so I'll use the R gui from now on, but I just wanted to point this out. ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber
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I really think Wolfgang is correct -- that particular command shouldn't be doing anything to change results within or without of Emacs. Please verify versions of the programs (do you have multiple R's on your laptop?) best, -tony On Wed, 09 Mar 2005 15:10:53 +0000, Wolfgang Huber <huber@ebi.ac.uk> wrote: > Hi Patrick, > > are you sure that you are actually using the same versions of R when you > call Rgui versus ESS? Perhaps your emacs accesses an old version of R > that is still lying around somewhere on your computer. > > Bw > Wolfgang > > > Patrick Brown wrote: > > Hello. bioconductor behaves strangely when I run R through emacs using > > ESS. I'm using R 2.0.1 with windows XP. > > using the R gui I get > > > > > temp=new("phenoData") > > > validObject(temp) > > [1] TRUE > > > > but in emacs I get > > > > > temp=new("phenoData") > > > validObject(temp) > > Error in validityMethod(object) : No slot of name "phenoLabels" for this > > object of class "phenoData" > > > > so I'll use the R gui from now on, but I just wanted to point this out. > > ------------------------------------- > Wolfgang Huber > European Bioinformatics Institute > European Molecular Biology Laboratory > Cambridge CB10 1SD > England > Phone: +44 1223 494642 > Fax: +44 1223 494486 > Http: www.ebi.ac.uk/huber > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- best, -tony "Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes" (AJR, 4Jan05). A.J. Rossini blindglobe@gmail.com
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A.J. Rossini wrote: > I really think Wolfgang is correct -- that particular command > shouldn't be doing anything to change results within or without of > Emacs. >>are you sure that you are actually using the same versions of R when you >>call Rgui versus ESS? Perhaps your emacs accesses an old version of R >>that is still lying around somewhere on your computer. Its the same binary, Patrick has it in D:\program files\R\bin\Rterm.exe - if we run that from the DOS command prompt it works, when launched from ESS (and I checked the ESS setup, and it does run that .exe file) it has the problem. The problem can be seen by: library(Biobase) getClassDef(class(new("phenoData")))@validity which gives this in ESS: function (object) { dm <- dim(object@pData) if (dm[2] != length(object@phenoLabels)) return(FALSE) return(TRUE) } <environment: 00a50680=""> - and then object@phenoLabels fails, since these objects dont have those slots. The validity method from Rterm or Rgui checks the correct slot. I suspect there must be an old version of some bioconductor packages around somewhere, but I dont know why ESS is using them. .libPaths() is identical in all environments. Cant give any more specifics now, since Patrick has gone off to watch mountaineer Chris Bonington become our new Chancellor... Baz
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 7.9 years ago
Hi Patrick, Patrick Brown <p.e.brown@lancaster.ac.uk> writes: > Hello. bioconductor behaves strangely when I run R through emacs > using ESS. I'm using R 2.0.1 with windows XP. That seems odd. Have you verified that ESS is using the same version of R and the same package library as Rgui? It might be useful to compare the output of these two functions: R.Version() sessionInfo() + seth
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Liaw, Andy ▴ 360
@liaw-andy-125
Last seen 7.9 years ago
One way to check what Wolfgang & Tony said is to look at the output of: Sys.getenv("R_HOME") Andy > From: Patrick Brown > > Hello. bioconductor behaves strangely when I run R through > emacs using > ESS. I'm using R 2.0.1 with windows XP. > > using the R gui I get > > > temp=new("phenoData") > > validObject(temp) > [1] TRUE > > but in emacs I get > > > temp=new("phenoData") > > validObject(temp) > Error in validityMethod(object) : No slot of name > "phenoLabels" for this > object of class "phenoData" > > so I'll use the R gui from now on, but I just wanted to point > this out. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > >
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> Sys.getenv("R_HOME") R_HOME "D:\\PROGRA~1\\R" same in all places
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problem solved. The ESS R was loading an old version of Biobase, which was in the recycle bin. emptied the recycle bin and it works fine. I'd guessed, rightly, that my version of biobase was out of sync with the other packages, and for some reason wasn't updating when I updated everything else. So I deleted it and re-installed. strangely ESS followed the old one to the recycle bin. Patrick
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