BioC 2.12: CHECK report for rBiopaxParser on petty

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: 2013-10-08 23:36:41 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:37:51 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 69.3 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 3.0.1 (2013-05-16)
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [27s/27s] 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	0.573	0.017	0.591
addBiopaxInstance	0.098	0.009	0.107
addBiopaxInstances	0.144	0.011	0.156
addControl	0.730	0.010	0.747
addPathway	0.829	0.011	0.859
addPathwayComponents	0.920	0.013	0.947
addPhysicalEntity	0.182	0.008	0.190
addPhysicalEntityParticipant	0.447	0.009	0.473
addPropertiesToBiopaxInstance	0.211	0.010	0.221
biopax	0.023	0.003	0.027
calcGraphOverlap	2.586	0.054	2.656
colorGraphNodes	3.082	0.051	3.165
combineNodes	0.008	0.003	0.009
createBiopax	0.007	0.000	0.007
diffGraphs	2.256	0.029	2.307
downloadBiopaxData	0.006	0.001	0.006
getClassProperties	0.022	0.001	0.023
getInstanceClass	0.012	0.002	0.014
getInstanceProperty	0.028	0.002	0.030
getReferencedIDs	0.031	0.002	0.034
getReferencingIDs	0.033	0.002	0.037
getSubClasses	0.010	0.001	0.013
getSuperClasses	0.008	0.001	0.010
getXrefAnnotations	0.101	0.001	0.107
intersectGraphs	1.969	0.026	2.005
listComplexComponents	0.013	0.001	0.014
listInstances	0.036	0.004	0.039
listInteractionComponents	0.029	0.004	0.033
listPathwayComponents	0.023	0.002	0.026
listPathways	0.020	0.001	0.022
pathway2AdjacancyMatrix	0.958	0.021	0.981
pathway2Geneset	0.169	0.008	0.177
pathway2RegulatoryGraph	1.433	0.019	1.453
plotRegulatoryGraph	1.454	0.018	1.475
print.biopax	0.018	0.002	0.020
rBiopaxParser-package	0.004	0.001	0.006
readBiopax	0.007	0.002	0.010
removeNodes	2.478	0.032	2.529
selectInstances	0.063	0.017	0.088
splitComplex	0.056	0.003	0.068
uniteGraphs	4.051	0.040	4.118
writeBiopax	0.014	0.002	0.016