BioC 2.13: CHECK report for rBiopaxParser on perceval

Package: rBiopaxParser

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rBiopaxParser_1.2.0.tar.gz

StartedAt: 2014-04-05 03:43:12 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:44:09 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 57.6 seconds

RetCode: 0

Status:  OK

CheckDir: rBiopaxParser.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/rBiopaxParser.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rBiopaxParser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rBiopaxParser’ version ‘1.2.0’
* 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 ... [2s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘rBiopaxParserVignette.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [21s/21s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/rBiopaxParser.Rcheck/00check.log’
for details.

* 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	0.545	0.017	0.587
addBiopaxInstance	0.093	0.009	0.102
addBiopaxInstances	0.139	0.013	0.151
addControl	0.730	0.012	0.751
addPathway	0.740	0.010	0.756
addPathwayComponents	0.855	0.012	0.874
addPhysicalEntity	0.197	0.010	0.207
addPhysicalEntityParticipant	0.477	0.014	0.497
addPropertiesToBiopaxInstance	0.179	0.010	0.199
biopax	0.020	0.002	0.022
calcGraphOverlap	1.827	0.047	1.983
colorGraphNodes	2.306	0.055	2.419
combineNodes	0.007	0.003	0.009
createBiopax	0.006	0.001	0.007
diffGraphs	1.691	0.022	1.740
downloadBiopaxData	0.005	0.002	0.007
getClassProperties	0.027	0.002	0.030
getInstanceClass	0.010	0.003	0.012
getInstanceProperty	0.022	0.003	0.026
getReferencedIDs	0.025	0.004	0.030
getReferencingIDs	0.024	0.004	0.029
getSubClasses	0.009	0.003	0.012
getSuperClasses	0.009	0.001	0.011
getXrefAnnotations	0.079	0.002	0.081
intersectGraphs	1.661	0.016	1.690
listComplexComponents	0.016	0.005	0.022
listInstances	0.044	0.008	0.052
listInteractionComponents	0.020	0.003	0.023
listPathwayComponents	0.019	0.003	0.022
listPathways	0.018	0.004	0.022
pathway2AdjacancyMatrix	0.625	0.016	0.644
pathway2Geneset	0.119	0.007	0.125
pathway2RegulatoryGraph	1.050	0.018	1.083
plotRegulatoryGraph	1.091	0.017	1.119
print.biopax	0.029	0.004	0.034
rBiopaxParser-package	0.004	0.002	0.006
readBiopax	0.004	0.001	0.006
removeNodes	1.835	0.031	1.929
selectInstances	0.100	0.018	0.117
splitComplex	0.034	0.005	0.039
uniteGraphs	2.772	0.043	2.871
writeBiopax	0.008	0.003	0.010