BioC 2.1: CHECK report for Category on lemming

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/Category.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-06-03 r41797)
* checking for file 'Category/DESCRIPTION' ... OK
* this is package 'Category' version '2.3.13'
* 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 ... 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
gseaperm : <anonymous>: no visible global function definition for
  'Matrix'
gseaperm: no visible binding for global variable 'x'
htmlReportFromDf: no visible global function definition for 'xtable'
makeEBcontr: no visible global function definition for 'ebPatterns'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 ... OK

installing R.css in D:/biocbld/bbs-2.1-bioc/meat/Category.Rcheck


---------- Making package Category ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  preparing package Category 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: KEGG
Loading required package: GO
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
  installing inst files
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'Category'
     Formats: text html latex example chm 
  ChrMapHyperGParams-class          text    html    latex   example chm
  ChrMapHyperGResult-class          text    html    latex   example chm
  DatPkg-class                      text    html    latex   example chm
  GOHyperGParams-class              text    html    latex           chm
  HyperGParams-class                text    html    latex           chm
  HyperGResult-accessors            text    html    latex           chm
  HyperGResult-class                text    html    latex           chm
  HyperGResultBase-class            text    html    latex           chm
  KEGGHyperGParams-class            text    html    latex           chm
  MAPAmat                           text    html    latex   example chm
  applyByCategory                   text    html    latex   example chm
  cateGOryMatrix                    text    html    latex   example chm
  categoryToEntrezBuilder           text    html    latex           chm
  cb_contingency                    text    html    latex           chm
  cb_parse_band_hsa                 text    html    latex   example chm
  chrBandInciMat                    text    html    latex   example chm
  findAMstats                       text    html    latex   example chm
  geneGoHyperGeoTest                text    html    latex           chm
  geneKeggHyperGeoTest              text    html    latex           chm
  getPathNames                      text    html    latex   example chm
  gseaperm                          text    html    latex           chm
  hyperGTest                        text    html    latex           chm
  makeChrBandGraph                  text    html    latex   example chm
  makeEBcontr                       text    html    latex   example chm
  makeValidParams                   text    html    latex           chm
  probes2MAP                        text    html    latex   example chm
  probes2Path                       text    html    latex   example chm
  ttperm                            text    html    latex   example chm
  universeBuilder                   text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.1-bioc\meat\Category.Rcheck\00_pkg_src\Category\chm\Category.chm


Compile time: 0 minutes, 0 seconds
30	Topics
216	Local links
0	Internet links
1	Graphic


Created d:\biocbld\bbs-2.1-bioc\meat\Category.Rcheck\00_pkg_src\Category\chm\Category.chm, 56,383 bytes
Compression decreased file by 86,112 bytes.
  adding MD5 sums

* DONE (Category)

Package 43/238	Hostname	OS	Arch	BUILD	CHECK	BUILD BIN
Category 2.3.13 S. Falcon Last Changed Date: 2007-06-09 10:46:21 -0700 Last Changed Rev: 25296	lamb1	Linux (SUSE 10.1)	x86_64	OK	OK
	wellington	Linux (SUSE 9.2)	i686	OK	OK
	churchill	Solaris 2.9	sparc	OK	OK
	lemming	Windows Server 2003 (32-bit)	x64	OK	[ OK ]	skipped

Category

2.3.13

Command output