Package: rBiopaxParser

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rBiopaxParser_1.0.0.tar.gz

StartedAt: 2013-05-01 09:56:34 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 09:57:40 -0700 (Wed, 01 May 2013)

EllapsedTime: 65.9 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 Patched (2013-04-08 r62531)
* 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 '1.0.0'
* 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 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 ... [23s/26s] 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
** testing if installed package can be loaded
* DONE (rBiopaxParser)

name	user	system	elapsed
addBiochemicalReaction	0.558	0.041	0.636
addBiopaxInstance	0.056	0.014	0.076
addBiopaxInstances	0.148	0.020	0.191
addControl	0.696	0.046	1.102
addPathway	0.822	0.053	1.044
addPathwayComponents	0.812	0.051	1.396
addPhysicalEntity	0.173	0.018	0.193
addPhysicalEntityParticipant	0.397	0.029	0.428
addPropertiesToBiopaxInstance	0.174	0.018	0.193
biopax	0.019	0.003	0.023
calcGraphOverlap	1.969	0.051	2.568
colorGraphNodes	2.529	0.061	2.725
combineNodes	0.007	0.004	0.014
createBiopax	0.005	0.002	0.007
diffGraphs	1.934	0.029	2.134
downloadBiopaxData	0.006	0.003	0.008
getClassProperties	0.024	0.004	0.029
getInstanceClass	0.009	0.003	0.024
getInstanceProperty	0.020	0.006	0.037
getReferencedIDs	0.026	0.004	0.031
getReferencingIDs	0.026	0.005	0.042
getSubClasses	0.007	0.002	0.009
getSuperClasses	0.008	0.003	0.010
getXrefAnnotations	0.093	0.003	0.096
intersectGraphs	1.799	0.017	1.833
listComplexComponents	0.018	0.005	0.022
listInstances	0.035	0.007	0.043
listInteractionComponents	0.018	0.004	0.021
listPathwayComponents	0.017	0.004	0.022
listPathways	0.015	0.003	0.019
pathway2AdjacancyMatrix	0.780	0.022	0.810
pathway2Geneset	0.159	0.014	0.174
pathway2RegulatoryGraph	1.231	0.024	1.270
plotRegulatoryGraph	1.350	0.026	1.393
print.biopax	0.015	0.004	0.019
rBiopaxParser-package	0.006	0.003	0.008
readBiopax	0.006	0.002	0.009
removeNodes	2.071	0.038	2.128
selectInstances	0.051	0.022	0.082
splitComplex	0.051	0.005	0.060
uniteGraphs	3.310	0.050	3.434
writeBiopax	0.008	0.004	0.011