Question: bioconductor and ESS
0
gravatar for Patrick Brown
14.2 years ago by
Patrick Brown30 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.
gui • 487 views
ADD COMMENTlink modified 14.2 years ago by Liaw, Andy360 • written 14.2 years ago by Patrick Brown30
Answer: bioconductor and ESS
0
gravatar for Wolfgang Huber
14.2 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k 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
ADD COMMENTlink written 14.2 years ago by Wolfgang Huber13k
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
ADD REPLYlink written 14.2 years ago by A.J. Rossini210
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
ADD REPLYlink written 14.2 years ago by Barry Rowlingson10
Answer: bioconductor and ESS
0
gravatar for Seth Falcon
14.2 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
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
ADD COMMENTlink written 14.2 years ago by Seth Falcon7.4k
Answer: bioconductor and ESS
0
gravatar for Liaw, Andy
14.2 years ago by
Liaw, Andy360
Liaw, Andy360 wrote:
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 > > >
ADD COMMENTlink written 14.2 years ago by Liaw, Andy360
> Sys.getenv("R_HOME") R_HOME "D:\\PROGRA~1\\R" same in all places
ADD REPLYlink written 14.2 years ago by Patrick Brown30
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
ADD REPLYlink written 14.2 years ago by Patrick Brown30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 397 users visited in the last hour