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Package 352/514HostnameOS / ArchBUILDCHECKBUILD BIN
ontoTools 1.32.0
Vince Carey
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/ontoTools
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: ontoTools
Version: 1.32.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings ontoTools_1.32.0.tar.gz
StartedAt: 2012-03-24 01:47:52 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 01:51:20 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 207.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ontoTools.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/ontoTools.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ontoTools/DESCRIPTION’ ... OK
* this is package ‘ontoTools’ version ‘1.32.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘ontoTools’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.7Mb
* 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 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 ... NOTE
File ‘ontoTools/R/zzz.R’:
  .onLoad calls:
    require("Biobase")

Package startup functions should not change the search path.
See section ‘Good practice’ in ?.onAttach.

* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                        old_size new_size compress
  GDI_NCIThesaurus.rda     1.8Mb    1.1Mb       xz
  GOMF1.15.rda             103Kb     40Kb       xz
  LL2GOMFcp.1.15.rda        52Kb     13Kb       xz
  LL2GOMFooMap.1.15.rda    137Kb     67Kb       xz
  LL2GOMFooc1.15.rda       242Kb    107Kb       xz
  LLGOMFcp.rda              20Kb      6Kb       xz
  go1.15DAG.rda            103Kb     40Kb       xz
  goMFamat.1.15.rda         85Kb     27Kb       xz
  goMFgraph.1.15.rda       103Kb     40Kb       xz
  goMFgraphDemo.rda         45Kb     13Kb       xz
  gomfAmat.rda              62Kb     20Kb       xz
  ooMapLL2GOMFdemo.rda     378Kb    124Kb       xz
* 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
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class “connection” in package ‘IRanges’ seems equivalent to one from package ‘graph’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class “file” in package ‘IRanges’ seems equivalent to one from package ‘graph’ and is not turning on duplicate class definitions for this class
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)

ontoTools.Rcheck/ontoTools-Ex.timings:

nameusersystemelapsed
GDI0.4880.0080.496
OOC-class0.1640.0080.173
SGDIvocab0.0080.0000.008
STMA0.0040.0000.005
buildGOgraph000
depthStruct0.0200.0000.023
namedSparse-class0.0160.0000.018
ontology-class0.0640.0000.066
otkvEnv2namedSparse0.2880.0000.312
semsim36.654 0.20437.621
taggedHierNomenclature-class0.2080.0040.212
toDot-methods0.0480.0040.259