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Package 318/462HostnameOS / ArchBUILDCHECKBUILD BIN
ontoTools 1.31.0
Vince Carey
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ontoTools
Last Changed Rev: 54810 / Revision: 55359
Last Changed Date: 2011-04-13 18:14:51 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: ontoTools
Version: 1.31.0
Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings ontoTools_1.31.0.tar.gz
StartedAt: 2011-05-09 18:46:32 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 18:49:05 -0700 (Mon, 09 May 2011)
EllapsedTime: 152.1 seconds
RetCode: 0
Status:  OK  
CheckDir: ontoTools.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/ontoTools.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* 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 '1.31.0'
* 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  6.2Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.7Mb
* 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 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 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

ontoTools.Rcheck/00install.out:

* 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 new generic function for "grep" in "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)

ontoTools.Rcheck/ontoTools-Ex.timings:

nameusersystemelapsed
GDI0.470.000.47
OOC-class0.280.000.28
SGDIvocab0.010.000.01
STMA000
buildGOgraph000
depthStruct000
namedSparse-class0.000.020.03
ontology-class0.090.000.09
otkvEnv2namedSparse0.020.000.02
semsim37.00 0.2037.33
taggedHierNomenclature-class0.250.000.25
toDot-methods0.060.000.51