Category 2.5.10
Robert Gentleman
| Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Category | | Last Changed Rev: 30915 / Revision: 30951 | | Last Changed Date: 2008-04-08 08:58:50 -0700 (Tue, 08 Apr 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | WARNINGS | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | WARNINGS | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.1) / i386 | OK | [ WARNINGS ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.2-bioc/meat/Category.Rcheck'
* using R version 2.7.0 beta (2008-04-07 r45159)
* using session charset: ASCII
* checking for file 'Category/DESCRIPTION' ... OK
* this is package 'Category' version '2.5.10'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Category' can be installed ... WARNING
Found the following significant warnings:
missing link(s): LinearMResult-class LinearMParams-class
See '/Users/biocbuild/bbs-2.2-bioc/meat/Category.Rcheck/00install.out' for details.
* 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 ... OK
* checking Rd files ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object 'linearMTest.Rd':
LinearMResult-class LinearMParams-class
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
ChrMapLinearMParams ChrMapLinearMResult LinearMParams LinearMResult
LinearMResultBase
Undocumented S4 methods:
generic 'annotation' and siglist 'LinearMParams'
generic 'annotation' and siglist 'LinearMResultBase'
generic 'annotation<-' and siglist 'LinearMParams,character'
generic 'categoryName' and siglist 'LinearMParams'
generic 'chrGraph' and siglist 'ChrMapLinearMResult'
generic 'condGeneIdUniverse' and siglist 'LinearMResultBase'
generic 'condGeneIdUniverse' and siglist 'ChrMapLinearMResult'
generic 'conditional' and siglist 'LinearMParams'
generic 'conditional' and siglist 'ChrMapLinearMParams'
generic 'conditional' and siglist 'LinearMResultBase'
generic 'conditional<-' and siglist 'ChrMapLinearMParams,logical'
generic 'description' and siglist 'LinearMResultBase'
generic 'geneIdUniverse' and siglist 'LinearMResult'
generic 'geneIdUniverse' and siglist 'ChrMapLinearMResult'
generic 'geneIds' and siglist 'LinearMParams'
generic 'geneIds' and siglist 'LinearMResultBase'
generic 'geneIds<-' and siglist 'LinearMParams'
generic 'geneIdsByCategory' and siglist 'LinearMResultBase'
generic 'geneMappedCount' and siglist 'LinearMResultBase'
generic 'isConditional' and siglist 'LinearMResultBase'
generic 'isConditional' and siglist 'ChrMapLinearMResult'
generic 'pvalueCutoff' and siglist 'LinearMParams'
generic 'pvalueCutoff' and siglist 'LinearMResultBase'
generic 'pvalueCutoff<-' and siglist 'LinearMParams'
generic 'pvalues' and siglist 'LinearMResult'
generic 'pvalues' and siglist 'ChrMapLinearMResult'
generic 'show' and siglist 'LinearMResultBase'
generic 'show' and siglist 'LinearMParams'
generic 'sigCategories' and siglist 'LinearMResultBase'
generic 'summary' and siglist 'LinearMResultBase'
generic 'testDirection' and siglist 'LinearMParams'
generic 'testDirection' and siglist 'LinearMResultBase'
generic 'testDirection<-' and siglist 'LinearMParams'
generic 'testName' and siglist 'LinearMResultBase'
generic 'universeCounts' and siglist 'LinearMResultBase'
generic 'universeGeneIds' and siglist 'LinearMParams'
generic 'universeMappedCount' and siglist 'LinearMResultBase'
All user-level objects in a package (including S4 classes and methods)
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
* creating Category-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating Category-manual.tex ... OK
* checking Category-manual.tex using pdflatex ... OK
WARNING: There were 3 warnings, see
/Users/biocbuild/bbs-2.2-bioc/meat/Category.Rcheck/00check.log
for details
* Installing *source* package 'Category' ...
** R
** inst
** preparing package for lazy loading
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: graph
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
** help
Note: removing empty section \details
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: ignoring empty \keyword entries
Note: removing empty section \examples
>>> Building/Updating help pages for package 'Category'
Formats: text html latex example
ChrBandTree-class text html latex example
ChrMapHyperGParams-class text html latex example
ChrMapHyperGResult-class text html latex example
DatPkg-class text html latex example
GOHyperGParams-class text html latex
HyperGParams-class text html latex
HyperGResult-accessors text html latex example
HyperGResult-class text html latex
HyperGResultBase-class text html latex
KEGGHyperGParams-class text html latex
MAPAmat text html latex example
NewChrBandTree text html latex
applyByCategory text html latex example
cateGOryMatrix text html latex example
categoryToEntrezBuilder text html latex
cb_contingency text html latex
cb_parse_band_Hs text html latex example
cb_parse_band_Mm text html latex example
cb_test text html latex
exampleLevels text html latex
findAMstats text html latex example
geneGoHyperGeoTest text html latex
geneKeggHyperGeoTest text html latex
getPathNames text html latex example
gseattperm text html latex example
hyperGTest text html latex
linearMTest text html latex
missing link(s): LinearMResult-class LinearMParams-class
local_test_factory text html latex
makeChrBandGraph text html latex example
makeEBcontr text html latex example
makeValidParams text html latex
probes2MAP text html latex example
probes2Path text html latex example
tree_visitor text html latex
ttperm text html latex example
universeBuilder text html latex
** building package indices ...
* DONE (Category)