Package: ontoTools

Version: 1.31.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ontoTools_1.31.0.tar.gz

StartedAt: 2011-06-22 04:27:54 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 04:30:43 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 168.9 seconds

RetCode: 0

Status:  OK

CheckDir: ontoTools.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/ontoTools.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ontoTools/DESCRIPTION’ ... OK
* this is package ‘ontoTools’ version ‘1.31.0’
* 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 installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.6Mb
* 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... NOTE
prepare_Rd: A.csr.Rd:20-22: Dropping empty section \references
prepare_Rd: GDI.Rd:32-33: Dropping empty section \value
prepare_Rd: GDI.Rd:34: Dropping empty section \references
prepare_Rd: SGDIvocab.Rd:37: Dropping empty section \references
prepare_Rd: STMA.Rd:8-9: Dropping empty section \details
prepare_Rd: STMA.Rd:10-11: Dropping empty section \value
prepare_Rd: STMA.Rd:12: Dropping empty section \references
prepare_Rd: accessMat.Rd:21-22: Dropping empty section \details
prepare_Rd: accessMat.Rd:32-33: Dropping empty section \examples
prepare_Rd: compoundGraph-class.Rd:41-42: Dropping empty section \examples
prepare_Rd: litOnto.Rd:42-44: Dropping empty section \source
prepare_Rd: litOnto.Rd:45-47: Dropping empty section \references
prepare_Rd: ooMapLL2GOMFdemo.Rd:31-33: Dropping empty section \references
prepare_Rd: rootedDAG-class.Rd:44-45: Dropping empty section \examples
prepare_Rd: taggedHierNomenclature-class.Rd:47: Dropping empty section \references
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... 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
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Package SparseM (0.89) loaded.
	   To cite, see citation("SparseM")


Attaching package: ‘SparseM’

The following object(s) are masked from ‘package:base’:

    backsolve

Loading required package: DBI

Creating a generic function for "grep" from package "base" in package “ontoTools”
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘ontoTools.Rnw’ 
   ‘ontoToolsArchiving.Rnw’ 
   ‘sgdiOnto.Rnw’ 
** testing if installed package can be loaded

* DONE (ontoTools)

name	user	system	elapsed
GDI	0.503	0.020	0.581
OOC-class	0.388	0.009	0.399
SGDIvocab	0.011	0.001	0.012
STMA	0.008	0.001	0.009
buildGOgraph	0.001	0.000	0.000
depthStruct	0.012	0.002	0.013
namedSparse-class	0.027	0.001	0.028
ontology-class	0.097	0.001	0.099
otkvEnv2namedSparse	0.035	0.001	0.035
semsim	49.342	2.380	52.362
taggedHierNomenclature-class	0.324	0.010	0.340
toDot-methods	0.067	0.014	0.310