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

Shields, Rusty (IMS) ShieldsR at imsweb.com
Thu Mar 28 21:00:24 CET 2013 

Correcting the version of Biobase seems to have fixed it, and after that it doesn't appear that anything else is of the wrong version - based on the code that you provided below.

globaltest now installs successfully through BiocLite.

As for how the wrong version of Biobase was installed, I have to take the blame for that.  Rather than following the instructions on the bioconductor website to install using BiocLite, I made the mistake of downloading the package source manually and installing via 'R CMD INSTALL ...'.  I believe I used the biocLite method to install all of the other packages.  It has been a very educational few days.

Thanks again.

-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
Sent: Thursday, March 28, 2013 3:26 PM
To: Shields, Rusty (IMS)
Cc: bioconductor at r-project.org
Subject: Re: [BioC] [R] Error in setMethod("combine"... was - Error when installing globaltest package

On 03/28/2013 12:07 PM, Shields, Rusty (IMS) wrote:
> 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

yes, this is the version of Biobase from the current version of R /
Bioconductor, whereas you're using a relatively old R / Biocondcutor (R 2.14,
Bioc 2.9, from the 'Previous versions' box at http://bioconductor.org/help/)
where Biobase is at version 2.14. This doesn't bode well, as other packages are
also likely at incorrect versions.

The easiest solution is to upgrade to a recent R, and start again with
biocLite('globaltest').

You could also try biocLite("Biobase") to get the correct version, then
biocLite("globaltest"), but if other packages are also installed incorrectly...

Something like

   source("http://bioconductor.org/biocLite.R")
   avail = available.packages(contriburl=contrib.url(biocinstallRepos()))
   inst = installed.packages(priority="NA")
   idx = rownames(avail) %in% rownames(inst)
   vers = avail[idx, "Version"]
   vers[vers < inst[names(vers), "Version"]]

will give you the too-new packages that need to be re-installed.

It's hard to know how your system got to its current state; one candidate is
that .libPaths() includes a path shared by several versions of R. but using
biocLite() to install packages should help avoiding that in the future.

Martin

> 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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