Package: rBiopaxParser

Version: 0.99.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rBiopaxParser_0.99.10.tar.gz

StartedAt: 2013-03-25 04:17:52 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:18:53 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 60.8 seconds

RetCode: 0

Status:  OK

CheckDir: rBiopaxParser.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/rBiopaxParser.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'rBiopaxParser/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rBiopaxParser' version '0.99.10'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'rBiopaxParser' can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... OK
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [20s/20s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [1s/1s]
 [2s/2s] 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 'rBiopaxParser' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'rBiopaxParserVignette.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
* DONE (rBiopaxParser)

name	user	system	elapsed
addBiochemicalReaction	0.383	0.072	0.465
addBiopaxInstance	0.062	0.017	0.079
addBiopaxInstances	0.137	0.024	0.161
addControl	0.459	0.098	0.558
addPathway	0.539	0.116	0.659
addPathwayComponents	0.590	0.125	0.719
addPhysicalEntity	0.137	0.033	0.172
addPhysicalEntityParticipant	0.246	0.063	0.311
addPropertiesToBiopaxInstance	0.134	0.032	0.166
biopax	0.022	0.007	0.030
calcGraphOverlap	2.264	0.060	2.326
colorGraphNodes	2.083	0.046	2.128
combineNodes	0.007	0.005	0.012
createBiopax	0.007	0.004	0.011
diffGraphs	1.525	0.024	1.551
downloadBiopaxData	0.005	0.004	0.009
getClassProperties	0.015	0.004	0.019
getInstanceClass	0.013	0.006	0.018
getInstanceProperty	0.019	0.008	0.032
getReferencedIDs	0.021	0.007	0.029
getReferencingIDs	0.020	0.007	0.027
getSubClasses	0.006	0.004	0.011
getSuperClasses	0.005	0.004	0.010
getXrefAnnotations	0.055	0.008	0.066
intersectGraphs	1.435	0.024	1.460
listComplexComponents	0.015	0.005	0.020
listInstances	0.031	0.010	0.041
listInteractionComponents	0.016	0.005	0.022
listPathwayComponents	0.019	0.006	0.024
listPathways	0.013	0.006	0.019
pathway2AdjacancyMatrix	0.581	0.013	0.595
pathway2Geneset	0.149	0.011	0.161
pathway2RegulatoryGraph	1.183	0.019	1.497
plotRegulatoryGraph	0.994	0.020	1.015
print.biopax	0.017	0.005	0.025
rBiopaxParser-package	0.005	0.004	0.009
readBiopax	0.005	0.003	0.008
removeNodes	1.459	0.021	1.482
selectInstances	0.045	0.021	0.066
splitComplex	0.037	0.008	0.047
uniteGraphs	2.512	0.022	2.535
writeBiopax	0.009	0.006	0.015