Package: ontoTools

Version: 1.30.0

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch ontoTools_1.30.0.tar.gz

StartedAt: 2011-10-20 15:43:29 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 15:45:26 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 117.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ontoTools.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/ontoTools.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ontoTools/DESCRIPTION' ... OK
* this is package 'ontoTools' version '1.30.0'
* checking package namespace 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 ... 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 whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   ontoTools.Rnw
   ontoToolsArchiving.Rnw
   sgdiOnto.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/ontoTools.Rcheck/00check.log'
for details

* installing *source* package 'ontoTools' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "grep" in "ontoTools"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (ontoTools)

name	user	system	elapsed
GDI	0.45	0.00	0.45
OOC-class	0.31	0.00	0.35
SGDIvocab	0.02	0.00	0.01
STMA	0	0	0
buildGOgraph	0	0	0
depthStruct	0.01	0.00	0.02
namedSparse-class	0.02	0.00	0.01
ontology-class	0.08	0.00	0.08
otkvEnv2namedSparse	0.01	0.00	0.02
semsim	37.36	0.14	37.71
taggedHierNomenclature-class	0.25	0.00	0.25
toDot-methods	0.04	0.00	0.43