Package: ontoTools

Version: 1.13.1

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check ontoTools_1.13.1.tar.gz

RetCode: None

Time: 2400.8 seconds

Status: TIMEOUT

CheckDir: ontoTools.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/loc/biocbuild/bbs-2.1-bioc/meat/ontoTools.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-04-17 r41210)
* checking for file 'ontoTools/DESCRIPTION' ... OK
* this is package 'ontoTools' version '1.13.1'
* 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 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' ...

* Installing *source* package 'ontoTools' ...
** R
** data
** inst
** save image
Loading required package: graph
Loading required package: SparseM
Package SparseM (0.72) loaded.  To cite, see citation("SparseM")
Loading required package: GO
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: 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"
** help
 >>> Building/Updating help pages for package 'ontoTools'
     Formats: text html latex example 
  A.csr                             text    html    latex
  GDI                               text    html    latex   example
  LLGOMFcp                          text    html    latex
  OOC-class                         text    html    latex   example
  SGDIvocab                         text    html    latex   example
  STMA                              text    html    latex   example
  accessMat                         text    html    latex   example
  buildGOgraph                      text    html    latex   example
  compoundGraph-class               text    html    latex   example
  depthStruct                       text    html    latex   example
  gomfAmat                          text    html    latex
  litOnto                           text    html    latex
  namedSparse-class                 text    html    latex   example
  ontology-class                    text    html    latex   example
  ooMapLL2GOMFdemo                  text    html    latex
  otkvEnv2namedSparse               text    html    latex   example
  rootedDAG-class                   text    html    latex   example
  semsim                            text    html    latex   example
  taggedHierNomenclature-class      text    html    latex   example
  toDot-methods                     text    html    latex   example
** building package indices ...
* DONE (ontoTools)