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 ?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? [a/s/n]:
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