topGO 1.10.1
Adrian Alexa
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/topGO | | Last Changed Rev: 35382 / Revision: 38965 | | Last Changed Date: 2008-11-17 14:19:26 -0800 (Mon, 17 Nov 2008) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.6) / i386 | OK | [ WARNINGS ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/topGO.Rcheck'
* using R version 2.8.1 Patched (2009-03-18 r48200)
* using session charset: ASCII
* checking for file 'topGO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'topGO' version '1.10.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'topGO' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.sigGroups.weight2: no visible binding for global variable
'nodesUpSubgraph'
GOglobalTest,classicExpr: no visible global function definition for
'p.value'
GOglobalTest,classicExpr: no visible global function definition for
'globaltest'
GOtTest,classicScore: no visible global function definition for
'alternative'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
nodesInInducedGraph
Undocumented data sets:
geneList topDiffGenes
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* creating topGO-Ex.R ... OK
* checking examples ... OK
* creating topGO-manual.tex ... OK
* checking topGO-manual.tex using pdflatex ... OK
WARNING: There was 1 warning, see
/Users/biocbuild/bbs-2.3-bioc/meat/topGO.Rcheck/00check.log
for details
* Installing *source* package 'topGO' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: graph
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: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: SparseM
Package SparseM (0.79) loaded. To cite, see citation("SparseM")
Attaching package: 'SparseM'
The following object(s) are masked from package:stats :
model.response
The following object(s) are masked from package:base :
backsolve,
chol
Creating a new generic function for "print" in "topGO"
** help
>>> Building/Updating help pages for package 'topGO'
Formats: text html latex example
GOFisherTest text html latex
GOKSTest text html latex
GOdata text html latex example
GOglobalTest text html latex
annFUN text html latex example
buildGOgraph.topology text html latex
buildLevels text html latex example
classicCount-class text html latex example
classicExpr-class text html latex example
classicScore-class text html latex example
elimCount-class text html latex example
elimExpr-class text html latex example
elimScore-class text html latex example
getPvalues text html latex example
getSigGroups text html latex example
groupGOTerms text html latex example
groupStats-class text html latex example
inducedGraph text html latex example
mapGenes2GOgraph text html latex example
parentChild-class text html latex example
printGenes-methods text html latex
printGraph-methods text html latex example
reverseArch text html latex example
topGO-package text html latex
topGOdata-class text html latex example
topGOresult-class text html latex
weightCount-class text html latex example
weightScore-class text html latex
** building package indices ...
* DONE (topGO)