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@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/contr ib/globaltest_5.8.1.tar.gz' >> Content type 'application/x-gzip' length 956376 bytes (933 Kb) >> opened URL >> ================================================== >> downloaded 933 Kb >> >> * installing *source* package ?globaltest? ... >> ** R >> ** data >> ** inst >> ** preparing package for lazy loading >> Warning in .simpleDuplicateClass(def, prev) : >> A specification for class ?data.frameOrNULL? >> Creating a generic function for ?sort? from package ?base? in package ?globaltest? >> Creating a generic function for ?model.matrix? from package ?stats? in package ?globaltest? >> Creating a generic function for ?coefficients? from package ?stats? in package ?globaltest? >> Creating a generic function for ?fitted.values? from package ?stats? in package ?globaltest? >> Creating a generic function for ?residuals? from package ?stats? in package ?globaltest? >> Error in setMethod("combine", signature(x = "gt.result", y = "gt.result"), : >> no existing definition for function ?combine? >> Error : unable to load R code in package ?globaltest? >> ERROR: lazy loading failed for package ?globaltest? >> * removing ?/usr/local/R-2.14.0/lib64/R/library/globaltest? >> >> The downloaded packages are in >> ?/tmp/RtmpdCwjNB/downloaded_packages? >> Updating HTML index of packages in '.Library' >> Making packages.html ... done >> Old packages: 'caret' >> Update all/some/none? 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