Package: GSEABase

Version: 1.0.1

Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check GSEABase_1.0.1.tar.gz

RetCode: 0

Time: 107.6 seconds

Status: WARNINGS

CheckDir: GSEABase.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.1-bioc/meat/GSEABase.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'GSEABase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSEABase' version '1.0.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GSEABase' 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 ... WARNING
Error in paste(normalizePath(file.path(libname, pkgname, "libs")), file.path(Sys.getenv("R_HOME"),  : 
  could not find function "normalizePath"
Error: .onLoad failed in 'loadNamespace' for 'XML'
Execution halted

A namespace must be able to be loaded with just the base namespace loaded:
otherwise if the namespace gets loaded by a saved object, the session will
be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating GSEABase-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating GSEABase-manual.tex ... OK
* checking GSEABase-manual.tex ... OK

WARNING: There was 1 warning, see
  E:/biocbld/bbs-2.1-bioc/meat/GSEABase.Rcheck/00check.log
for details

installing R.css in E:/biocbld/bbs-2.1-bioc/meat/GSEABase.Rcheck


---------- Making package GSEABase ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  installing inst files
  preparing package GSEABase 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: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'GSEABase'
     Formats: text html latex example chm 
  CollectionType-class              text    html    latex   example chm
  CollectionType-constructors       text    html    latex   example chm
  GSEABase-package                  text    html    latex   example chm
  GeneColorSet-class                text    html    latex   example chm
  GeneColorSet-methods              text    html    latex           chm
  GeneIdentifierType-class          text    html    latex   example chm
  GeneIdentifierType-constructors   text    html    latex   example chm
  GeneSet-class                     text    html    latex   example chm
  GeneSet-methods                   text    html    latex   example chm
  GeneSetCollection-class           text    html    latex   example chm
  GeneSetCollection-methods         text    html    latex   example chm
  details-methods                   text    html    latex           chm
  getBroadSets                      text    html    latex   example chm
  incidence-methods                 text    html    latex   example chm
  mapIdentifiers-methods            text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.1-bioc\meat\GSEABase.Rcheck\00_pkg_src\GSEABase\chm\GSEABase.chm


Compile time: 0 minutes, 0 seconds
16	Topics
300	Local links
1	Internet link
1	Graphic


Created e:\biocbld\bbs-2.1-bioc\meat\GSEABase.Rcheck\00_pkg_src\GSEABase\chm\GSEABase.chm, 54,129 bytes
Compression decreased file by 113,381 bytes.
  adding MD5 sums

* DONE (GSEABase)