Package: ontoTools

Version: 1.12.0

Command: E:\biocbld\bbs-2.0-bioc\R\bin\R.exe CMD check ontoTools_1.12.0.tar.gz

RetCode: 0

Time: 2284.3 seconds

Status: OK

CheckDir: ontoTools.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.0-bioc/meat/ontoTools.Rcheck'
* using R version 2.5.0 (2007-04-23)
* checking for file 'ontoTools/DESCRIPTION' ... OK
* this is package 'ontoTools' version '1.12.0'
* 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 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 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
* checking data for non-ASCII characters ... OK
* creating ontoTools-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating ontoTools-manual.tex ... OK
* checking ontoTools-manual.tex ... OK

installing R.css in E:/biocbld/bbs-2.0-bioc/meat/ontoTools.Rcheck


---------- Making package ontoTools ------------
  adding build stamp to DESCRIPTION
  installing R files
  save image
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: SparseM
Package SparseM (0.72) loaded.  To cite, see citation("SparseM")
Loading required package: GO
Loading required package: annotate
[1] "rootedDAG"
[1] "root"
[1] "root"
[1] "DAG"
[1] "DAG"
[1] "getMatrix"
[1] "getMatrix"
[1] "compoundGraph"
[1] "grList"
[1] "grList"
[1] "between"
[1] "between"
[1] "toDot"
[1] "toDot"
[1] "toDot"
[1] "toDot"
[1] "toDot"
[1] "toDot"
[1] "toDot"
[1] "toDot"
[1] "toDot"
[1] "toDot"
[1] "toDot"
[1] "toDot"
[1] "adjMat"
[1] "adjMat"
[1] TRUE
[1] "namedSparse"
[1] "dimnames"
[1] "rowinds"
[1] "colinds"
[1] "mat"
[1] "mat"
[1] "["
[1] "rowinds"
[1] "colinds"
[1] "dimnames<-"
[1] "mat"
[1] "mat"
[1] "nrow"
[1] "nrow"
[1] "ncol"
[1] "ncol"
[1] "dimnames"
[1] "as.matrix"
[1] "colSums"
[1] "rowSums"
[1] "colSums"
[1] "rowSums"
[1] "Arith"
[1] "%*%"
[1] "+"
[1] "maxval"
[1] "maxval"
[1] "show"
[1] "t"
[1] "ontology"
[1] "name"
[1] "name"
[1] "OVersion"
[1] "OVersion"
[1] "rDAG"
[1] "rDAG"
[1] "show"
[1] "accessMat"
[1] "accessMat"
[1] "OOC"
[1] "ontology"
[1] "ontology"
[1] "OOmap"
[1] "OOmap"
[1] "show"
[1] "coverageMat"
[1] "coverageMat"
[1] "provStruct"
[1] "show"
[1] "nomenclature"
[1] "taggedHierNomenclature"
[1] "show"
[1] "GDIontology"
[1] "show"
[1] "parents"
[1] "parents"
[1] "children"
[1] "children"
Creating a new generic function for "grep" in "ontoTools"
[1] "grep"
[1] "getTerms"
[1] "getTerms"
[1] "annotationResource"
[1] "symMapping"
[1] "typedSymMapping"
[1] "show"
[1] "GDIplatform"
[1] "show"
[1] "getDefs"
[1] "getDefs"
[1] "GDILabel"
[1] "exptArchive"
[1] "show"
[1] "exptSample"
[1] "show"
[1] "annoSource"
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'ontoTools'
     Formats: text html latex example chm 
  A.csr                             text    html    latex           chm
  GDI                               text    html    latex   example chm
  LLGOMFcp                          text    html    latex           chm
  OOC-class                         text    html    latex   example chm
  SGDIvocab                         text    html    latex   example chm
  STMA                              text    html    latex   example chm
  accessMat                         text    html    latex   example chm
  buildGOgraph                      text    html    latex   example chm
  compoundGraph-class               text    html    latex   example chm
  depthStruct                       text    html    latex   example chm
  gomfAmat                          text    html    latex           chm
  litOnto                           text    html    latex           chm
  namedSparse-class                 text    html    latex   example chm
  ontology-class                    text    html    latex   example chm
  ooMapLL2GOMFdemo                  text    html    latex           chm
  otkvEnv2namedSparse               text    html    latex   example chm
  rootedDAG-class                   text    html    latex   example chm
  semsim                            text    html    latex   example chm
  taggedHierNomenclature-class      text    html    latex   example chm
  toDot-methods                     text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.0-bioc\meat\ontoTools.Rcheck\00_pkg_src\ontoTools\chm\ontoTools.chm


Compile time: 0 minutes, 0 seconds
21	Topics
179	Local links
0	Internet links
1	Graphic


Created e:\biocbld\bbs-2.0-bioc\meat\ontoTools.Rcheck\00_pkg_src\ontoTools\chm\ontoTools.chm, 43,844 bytes
Compression decreased file by 62,093 bytes.
  adding MD5 sums

* DONE (ontoTools)