Package: ontoTools

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/2.9/Resources/bin/R CMD check --no-vignettes ontoTools_1.22.0.tar.gz

StartedAt: 2009-10-20 18:24:28 -0700 (Tue, 20 Oct 2009)

EndedAt: 2009-10-20 18:27:40 -0700 (Tue, 20 Oct 2009)

EllapsedTime: 191.7 seconds

RetCode: 0

Status: OK

CheckDir: ontoTools.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.4-bioc/meat/ontoTools.Rcheck'
* using R version 2.9.2 Patched (2009-08-24 r49419)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ontoTools/DESCRIPTION' ... OK
* this is package 'ontoTools' version '1.22.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ontoTools' 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 ... OK
* checking Rd files ... OK
* checking Rd files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* Installing *source* package ‘ontoTools’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Package SparseM (0.80) 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 

Loading required package: DBI
Creating a generic for "colSums" in package  "ontoTools"
    (the supplied definition differs from and overrides the implicit generic in package "base": Formal arguments differ: (x, na.rm, dims), (x, na.rm, dims, ...))
Creating a generic for "rowSums" in package  "ontoTools"
    (the supplied definition differs from and overrides the implicit generic in package "base": Formal arguments differ: (x, na.rm, dims), (x, na.rm, dims, ...))
Creating a new generic function for "grep" in "ontoTools"
In method for function "grep": expanding the signature to include
omitted arguments in definition: invert = "missing"
** help
*** installing help indices
 >>> Building/Updating help pages for package 'ontoTools'
     Formats: text html latex example 
Note: removing empty section \references in file 'A.csr.Rd'
  A.csr                             text    html    latex
Note: removing empty section \value in file 'GDI.Rd'
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  GDI                               text    html    latex   example
  LLGOMFcp                          text    html    latex
  OOC-class                         text    html    latex   example
Note: removing empty section \references in file 'SGDIvocab.Rd'
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  STMA                              text    html    latex   example
Note: removing empty section \details in file 'accessMat.Rd'
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  accessMat                         text    html    latex
  buildGOgraph                      text    html    latex   example
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  compoundGraph-class               text    html    latex
  depthStruct                       text    html    latex   example
  gomfAmat                          text    html    latex
Note: removing empty section \source in file 'litOnto.Rd'
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  litOnto                           text    html    latex
  namedSparse-class                 text    html    latex   example
  ontology-class                    text    html    latex   example
Note: removing empty section \references in file 'ooMapLL2GOMFdemo.Rd'
  ooMapLL2GOMFdemo                  text    html    latex
  otkvEnv2namedSparse               text    html    latex   example
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  rootedDAG-class                   text    html    latex
  semsim                            text    html    latex   example
Note: removing empty section \references in file 'taggedHierNomenclature-class.Rd'
  taggedHierNomenclature-class      text    html    latex   example
  toDot-methods                     text    html    latex   example
** building package indices ...
* DONE (ontoTools)