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Package 329/479HostnameOS / ArchBUILDCHECKBUILD BIN
ontoTools 1.31.0
Vince Carey
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ontoTools
Last Changed Rev: 54810 / Revision: 56603
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 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

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: 2011-07-07 04:47:27 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 04:51:06 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 219.0 seconds
RetCode: 0
Status:  OK 
CheckDir: ontoTools.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/ontoTools.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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   3.2Mb
    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 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or 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     39Kb       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    125Kb       xz
* 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

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 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
GDI0.5160.0220.552
OOC-class0.3820.0070.411
SGDIvocab0.0090.0010.011
STMA0.0060.0010.006
buildGOgraph000
depthStruct0.0110.0010.012
namedSparse-class0.0270.0020.030
ontology-class0.1020.0020.107
otkvEnv2namedSparse0.0330.0010.033
semsim52.252 2.52455.603
taggedHierNomenclature-class0.4110.0160.430
toDot-methods0.0720.0130.209