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-boun...@r-project.org
[mailto:bioconductor-boun...@r-project.org] On Behalf Of Shields, Rusty (IMS)
Sent: Tuesday, March 26, 2013 12:34 PM
To: bioconduc...@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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