BioC 2.12: CHECK report for rBiopaxParser on george2

Package: rBiopaxParser

Version: 1.0.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings rBiopaxParser_1.0.0.tar.gz

StartedAt: 2013-10-09 04:23:00 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:24:01 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 60.5 seconds

RetCode: 0

Status:  OK

CheckDir: rBiopaxParser.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/rBiopaxParser.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.0.0’
* 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 ... [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 installed files from ‘inst/doc’ ... OK
* checking examples ... [27s/28s] 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	0.704	0.032	0.786
addBiopaxInstance	0.116	0.008	0.134
addBiopaxInstances	0.196	0.000	0.196
addControl	0.924	0.000	1.256
addPathway	0.972	0.000	1.025
addPathwayComponents	0.952	0.024	0.980
addPhysicalEntity	0.244	0.000	0.242
addPhysicalEntityParticipant	0.552	0.000	0.554
addPropertiesToBiopaxInstance	0.236	0.000	0.243
biopax	0.024	0.000	0.024
calcGraphOverlap	2.228	0.020	2.403
colorGraphNodes	2.992	0.032	3.040
combineNodes	0.016	0.000	0.016
createBiopax	0.008	0.000	0.006
diffGraphs	2.052	0.020	2.266
downloadBiopaxData	0.008	0.000	0.006
getClassProperties	0.020	0.000	0.022
getInstanceClass	0.012	0.000	0.012
getInstanceProperty	0.032	0.000	0.029
getReferencedIDs	0.024	0.004	0.029
getReferencingIDs	0.040	0.000	0.037
getSubClasses	0.004	0.004	0.010
getSuperClasses	0.008	0.000	0.011
getXrefAnnotations	0.088	0.000	0.087
intersectGraphs	2.000	0.008	2.151
listComplexComponents	0.024	0.000	0.020
listInstances	0.044	0.000	0.045
listInteractionComponents	0.024	0.000	0.022
listPathwayComponents	0.028	0.000	0.028
listPathways	0.020	0.000	0.022
pathway2AdjacancyMatrix	0.853	0.008	0.964
pathway2Geneset	0.148	0.000	0.159
pathway2RegulatoryGraph	1.400	0.000	1.416
plotRegulatoryGraph	1.532	0.008	1.540
print.biopax	0.020	0.004	0.024
rBiopaxParser-package	0.008	0.000	0.009
readBiopax	0.012	0.000	0.011
removeNodes	2.760	0.004	2.763
selectInstances	0.056	0.020	0.079
splitComplex	0.064	0.000	0.063
uniteGraphs	3.884	0.008	3.891
writeBiopax	0.008	0.004	0.013