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: 2013-03-24 09:19:13 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 09:20:17 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 63.9 seconds

RetCode: 0

Status:  OK

CheckDir: rBiopaxParser.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/rBiopaxParser.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-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 ... [3s/3s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [25s/25s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [2s/2s]
 [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	0.594	0.040	0.636
addBiopaxInstance	0.098	0.014	0.111
addBiopaxInstances	0.142	0.020	0.162
addControl	0.764	0.047	0.820
addPathway	0.838	0.048	0.887
addPathwayComponents	0.936	0.057	1.019
addPhysicalEntity	0.217	0.023	0.241
addPhysicalEntityParticipant	0.471	0.033	0.511
addPropertiesToBiopaxInstance	0.212	0.020	0.234
biopax	0.024	0.004	0.029
calcGraphOverlap	2.280	0.057	2.370
colorGraphNodes	2.577	0.054	2.638
combineNodes	0.008	0.004	0.011
createBiopax	0.008	0.003	0.011
diffGraphs	2.015	0.036	2.065
downloadBiopaxData	0.010	0.006	0.017
getClassProperties	0.019	0.004	0.022
getInstanceClass	0.018	0.004	0.022
getInstanceProperty	0.021	0.005	0.025
getReferencedIDs	0.027	0.005	0.033
getReferencingIDs	0.030	0.007	0.038
getSubClasses	0.006	0.002	0.009
getSuperClasses	0.008	0.003	0.010
getXrefAnnotations	0.085	0.006	0.093
intersectGraphs	1.860	0.020	1.891
listComplexComponents	0.020	0.005	0.025
listInstances	0.175	0.008	0.184
listInteractionComponents	0.022	0.005	0.027
listPathwayComponents	0.019	0.005	0.023
listPathways	0.020	0.006	0.025
pathway2AdjacancyMatrix	0.792	0.020	0.826
pathway2Geneset	0.169	0.015	0.186
pathway2RegulatoryGraph	1.294	0.028	1.353
plotRegulatoryGraph	1.280	0.018	1.302
print.biopax	0.016	0.004	0.020
rBiopaxParser-package	0.007	0.003	0.009
readBiopax	0.005	0.002	0.008
removeNodes	2.114	0.039	2.161
selectInstances	0.051	0.021	0.072
splitComplex	0.048	0.005	0.052
uniteGraphs	3.542	0.048	3.640
writeBiopax	0.008	0.004	0.012