BioC 2.1: CHECK report for ontoTools on lamb1

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/ontoTools.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-06-03 r41797)
* 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 ... WARNING
Found the following significant warnings:
  Warning: 'GDI_NCIThesaurus' looks like a pre-2.4.0 S4 object: please recreate it
  Warning: 'SGDIvocab' looks like a pre-2.4.0 S4 object: please recreate it
  Warning: 'STMA' looks like a pre-2.4.0 S4 object: please recreate it
  Warning: 'gomfAmat' looks like a pre-2.4.0 S4 object: please recreate it
See '/home/biocbuild/bbs-2.1-bioc/meat/ontoTools.Rcheck/00install.out' for details.
* 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' ... OK
* creating ontoTools-manual.tex ... OK
* checking ontoTools-manual.tex ... OK

WARNING: There was 1 warning, see
  /home/biocbuild/bbs-2.1-bioc/meat/ontoTools.Rcheck/00check.log
for details

* Installing *source* package 'ontoTools' ...
** R
** data
** inst
** preparing package for lazy loading
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
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Creating a new generic function for "grep" in "ontoTools"
** 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 ...
Warning: 'GDI_NCIThesaurus' looks like a pre-2.4.0 S4 object: please recreate it
Warning: 'SGDIvocab' looks like a pre-2.4.0 S4 object: please recreate it
Warning: 'STMA' looks like a pre-2.4.0 S4 object: please recreate it
Warning: 'gomfAmat' looks like a pre-2.4.0 S4 object: please recreate it
* DONE (ontoTools)

Package 155/238	Hostname	OS	Arch	BUILD	CHECK	BUILD BIN
ontoTools 1.13.1 Vince Carey Last Changed Date: 2007-05-11 21:56:41 -0700 Last Changed Rev: 24616	lamb1	Linux (SUSE 10.1)	x86_64	OK	[ WARNINGS ]
	wellington	Linux (SUSE 9.2)	i686	OK	WARNINGS
	churchill	Solaris 2.9	sparc	OK	WARNINGS
	lemming	Windows Server 2003 (32-bit)	x64	OK	WARNINGS	skipped

ontoTools

1.13.1

Command output