Package: globaltest

Version: 4.7.3

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD build globaltest

RetCode: 1

Time: 179.9 seconds

Status: ERROR

PackageFile: None

* checking for file 'globaltest/DESCRIPTION' ... OK
* preparing 'globaltest':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* Installing *source* package 'globaltest' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: multtest
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: survival
Loading required package: splines
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: annotate
New generic for "combine" does not agree with implicit generic from package "Biobase"; a new generic will be assigned with package "globaltest"
Creating a new generic function for "fitted.values" in "globaltest"
Creating a new generic function for "residuals" in "globaltest"
** help
 >>> Building/Updating help pages for package 'globaltest'
     Formats: text html latex example 
  GOstructure                       text    html    latex
  annotation.vandeVijver            text    html    latex
  checkerboard                      text    html    latex   example
  geneplot                          text    html    latex   example
  globaltest                        text    html    latex   example
  gostructure.vandeVijver           text    html    latex
  gt.barplot-class                  text    html    latex
  gt.result-class                   text    html    latex
  gtGO                              text    html    latex   example
  mlogit                            text    html    latex   example
  multtest                          text    html    latex   example
  permutations                      text    html    latex   example
  regressionplot                    text    html    latex   example
  sampleplot                        text    html    latex   example
  sampling                          text    html    latex   example
  vandeVijver                       text    html    latex
** building package indices ...
* DONE (globaltest)
* creating vignettes ... ERROR
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: multtest
Loading required package: survival
Loading required package: splines
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: annotate
Loading required package: GO
Loading required package: graph
Loading required package: GO.db

Attaching package: 'GO.db'


	The following object(s) are masked from package:GO :

	 GOBPANCESTOR,
	 GOBPCHILDREN,
	 GOBPOFFSPRING,
	 GOBPPARENTS,
	 GOCCANCESTOR,
	 GOCCCHILDREN,
	 GOCCOFFSPRING,
	 GOCCPARENTS,
	 GOMAPCOUNTS,
	 GOMFANCESTOR,
	 GOMFCHILDREN,
	 GOMFOFFSPRING,
	 GOMFPARENTS,
	 GOOBSOLETE,
	 GOSYNONYM,
	 GOTERM 

Loading required package: RBGL
Loading required package: Category
Loading required package: genefilter

Attaching package: 'Rgraphviz'


	The following object(s) are masked from package:annotate :

	 toFile 


Error: processing vignette 'GlobalTest.Rnw' failed with diagnostics:
 chunk 33 (label=visualizeGO) 
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "Term", for signature "character"
In addition: Warning message:
Multiple methods lists found for 'combine' 
Execution halted