[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]:
>>
>> ________________________________
>>
>> Information in this e-mail may be confidential. It is intended only for the addressee(s) identified above. If you are not the addressee(s), or an employee or agent of the addressee(s), please note that any dissemination, distribution, or copying of this communication is strictly prohibited. If you have received this e-mail in error, please notify the sender of the error.
>>
>> [[alternative HTML version deleted]]
>>
>>
>> ________________________________
>>
>> Information in this e-mail may be confidential. It is intended only for the addressee(s) identified above. If you are not the addressee(s), or an employee or agent of the addressee(s), please note that any dissemination, distribution, or copying of this communication is strictly prohibited. If you have received this e-mail in error, please notify the sender of the error.
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
> --
> Dr. Martin Morgan, PhD
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> ________________________________
>
> Information in this e-mail may be confidential. It is intended only for the addressee(s) identified above. If you are not the addressee(s), or an employee or agent of the addressee(s), please note that any dissemination, distribution, or copying of this communication is strictly prohibited. If you have received this e-mail in error, please notify the sender of the error.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
________________________________
Information in this e-mail may be confidential. It is intended only for the addressee(s) identified above. If you are not the addressee(s), or an employee or agent of the addressee(s), please note that any dissemination, distribution, or copying of this communication is strictly prohibited. If you have received this e-mail in error, please notify the sender of the error.
More information about the Bioconductor
mailing list