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 'E:/biocbld/bbs-2.3-bioc/meat/topGO.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* 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 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
E:/biocbld/bbs-2.3-bioc/meat/topGO.Rcheck/00check.log
for details
installing R.css in E:/biocbld/bbs-2.3-bioc/meat/topGO.Rcheck
---------- Making package topGO ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
installing R files
installing inst files
installing data files
preparing package topGO 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
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"
installing man source files
installing indices
not zipping data
installing help
>>> Building/Updating help pages for package 'topGO'
Formats: text html latex example chm
GOFisherTest text html latex chm
GOKSTest text html latex chm
GOdata text html latex example chm
GOglobalTest text html latex chm
annFUN text html latex example chm
buildGOgraph.topology text html latex chm
buildLevels text html latex example chm
classicCount-class text html latex example chm
classicExpr-class text html latex example chm
classicScore-class text html latex example chm
elimCount-class text html latex example chm
elimExpr-class text html latex example chm
elimScore-class text html latex example chm
getPvalues text html latex example chm
getSigGroups text html latex example chm
groupGOTerms text html latex example chm
groupStats-class text html latex example chm
inducedGraph text html latex example chm
mapGenes2GOgraph text html latex example chm
parentChild-class text html latex example chm
printGenes-methods text html latex chm
printGraph-methods text html latex example chm
reverseArch text html latex example chm
topGO-package text html latex chm
topGOdata-class text html latex example chm
topGOresult-class text html latex chm
weightCount-class text html latex example chm
weightScore-class text html latex chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.3-bioc\meat\topGO.Rcheck\00_pkg_src\topGO\chm\topGO.chm
Compile time: 0 minutes, 3 seconds
29 Topics
420 Local links
0 Internet links
1 Graphic
Created e:\biocbld\bbs-2.3-bioc\meat\topGO.Rcheck\00_pkg_src\topGO\chm\topGO.chm, 48,476 bytes
Compression decreased file by 137,901 bytes.
adding MD5 sums
* DONE (topGO)