[BioC] [R] Error in setMethod("combine"... was - Error when installing globaltest package

Shields, Rusty (IMS) ShieldsR at imsweb.com
Thu Mar 28 20:07:19 CET 2013 

Thanks Martin,

No apologies necessary, just happy to have some help.

Here's the info on Biobase:

> packageDescription("Biobase")
Package: Biobase
Title: Biobase: Base functions for Bioconductor
Version: 2.18.0
Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon
Description: Functions that are needed by many other packages or which
        replace R functions.
Suggests: tools, tkWidgets, ALL
Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), utils
Imports: methods, BiocGenerics
Maintainer: Bioconductor Package Maintainer
        <maintainer at bioconductor.org>
License: Artistic-2.0
Collate: tools.R strings.R environment.R vignettes.R packages.R
        AllGenerics.R VersionsClass.R VersionedClasses.R
        methods-VersionsNull.R methods-VersionedClass.R DataClasses.R
        methods-aggregator.R methods-container.R methods-MIAxE.R
        methods-MIAME.R methods-AssayData.R
        methods-AnnotatedDataFrame.R methods-eSet.R
        methods-ExpressionSet.R methods-MultiSet.R methods-SnpSet.R
        methods-NChannelSet.R anyMissing.R rowOp-methods.R
        updateObjectTo.R methods-ScalarObject.R zzz.R
LazyLoad: yes
biocViews: Infrastructure, Bioinformatics
Packaged: 2012-10-02 02:41:50 UTC; biocbuild
Built: R 2.14.0; x86_64-unknown-linux-gnu; 2013-03-22 15:01:20 UTC;
        unix

-- File: /usr/local/R-2.14.0/lib64/R/library/Biobase/Meta/package.rds

-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
Sent: Thursday, March 28, 2013 2:52 PM
To: Shields, Rusty (IMS)
Cc: r-help at r-project.org
Subject: Re: [R] Error in setMethod("combine"... was - Error when installing globaltest package

On 3/28/2013 11:05 AM, Shields, Rusty (IMS) wrote:
> Hi All,
>
> I posted this on the bioconductor list and didn't get a response there, so I'm hoping someone here can help.
>
> I don't know a heck of a lot about R, so I apologize if this seems like a trivial issue.  This error comes up when trying to install the bioconductor globaltest package.
>

Sorry that you didn't get a response on the Bioc mailing list; I'd actually
suggest returning to the original thread there and I'll see that it gets answered.

My guess is that you have a version of Biobase that is too new compared to the
version (2.14.0) expected in the version of Bioconductor you are using. What
does packageDescription("Biobase") say?

Martin




> Any clues?
>
> Thanks!
> Rusty
>
> -----Original Message-----
> From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Shields, Rusty (IMS)
> Sent: Tuesday, March 26, 2013 12:34 PM
> To: bioconductor at r-project.org
> Subject: [BioC] Error when installing globaltest package
>
> Hi all,
>
> I've run into a problem when attempting to install the globaltest package from Bioconductor.  I'm using R 2.14.0 on 64bit SLES 11.  Let me know what other information you might need about my system to troubleshoot this.
>
> Using the method described for this installation on the Bioconductor website:
>
>      source("http://bioconductor.org/biocLite.R")
>      biocLite("globaltest")
>
> I get and the following result, which I can't find an reference to on the list archives:
>
>> biocLite("globaltest")
> BioC_mirror: 'http://www.bioconductor.org'
> Using R version 2.14, BiocInstaller version 1.2.1.
> Installing package(s) 'globaltest'
> trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/globaltest_5.8.1.tar.gz'
> Content type 'application/x-gzip' length 956376 bytes (933 Kb)
> opened URL
> ==================================================
> downloaded 933 Kb
>
> * installing *source* package âglobaltestâ ...
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> Warning in .simpleDuplicateClass(def, prev) :
>    A specification for class âdata.frameOrNULLâ
>                                                Creating a generic function for âsortâ from package âbaseâ in package âglobaltestâ
> Creating a generic function for âmodel.matrixâ from package âstatsâ in package âglobaltestâ
> Creating a generic function for âcoefficientsâ from package âstatsâ in package âglobaltestâ
> Creating a generic function for âfitted.valuesâ from package âstatsâ in package âglobaltestâ
> Creating a generic function for âresidualsâ from package âstatsâ in package âglobaltestâ
> Error in setMethod("combine", signature(x = "gt.result", y = "gt.result"),  :
>    no existing definition for function âcombineâ
> Error : unable to load R code in package âglobaltestâ
> ERROR: lazy loading failed for package âglobaltestâ
> * removing â/usr/local/R-2.14.0/lib64/R/library/globaltestâ
>
> The downloaded packages are in
>          â/tmp/RtmpdCwjNB/downloaded_packagesâ
> Updating HTML index of packages in '.Library'
> Making packages.html  ... done
> Old packages: 'caret'
> Update all/some/none? [a/s/n]:
>
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--
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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