Shields, Rusty (IMS)
2013-Mar-28 18:05 UTC
[R] Error in setMethod("combine"... was - Error when installing globaltest package
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.
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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Martin Morgan
2013-Mar-28 18:52 UTC
[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 ?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]: > > ________________________________ > > 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