BioC 2.13: CHECK report for rBiopaxParser on zin1

Package: rBiopaxParser

Version: 1.2.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings rBiopaxParser_1.2.0.tar.gz

StartedAt: 2014-04-05 03:22:43 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:23:17 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 33.2 seconds

RetCode: 0

Status:  OK

CheckDir: rBiopaxParser.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/rBiopaxParser.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.2.0’
* 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 ... [1s/1s] 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 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 ... [13s/13s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [1s/1s]
 [1s/1s] 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
  ‘/home/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	0.320	0.012	0.331
addBiopaxInstance	0.056	0.000	0.056
addBiopaxInstances	0.084	0.000	0.084
addControl	0.388	0.000	0.387
addPathway	0.416	0.012	0.432
addPathwayComponents	0.488	0.000	0.490
addPhysicalEntity	0.100	0.000	0.099
addPhysicalEntityParticipant	0.24	0.00	0.24
addPropertiesToBiopaxInstance	0.100	0.004	0.103
biopax	0.008	0.000	0.011
calcGraphOverlap	1.248	0.008	1.257
colorGraphNodes	1.452	0.016	1.468
combineNodes	0.004	0.000	0.004
createBiopax	0.000	0.000	0.003
diffGraphs	1.076	0.004	1.083
downloadBiopaxData	0.004	0.000	0.002
getClassProperties	0.008	0.000	0.011
getInstanceClass	0.004	0.000	0.004
getInstanceProperty	0.008	0.004	0.011
getReferencedIDs	0.012	0.000	0.013
getReferencingIDs	0.016	0.000	0.013
getSubClasses	0.004	0.000	0.003
getSuperClasses	0.000	0.000	0.002
getXrefAnnotations	0.044	0.000	0.044
intersectGraphs	1.044	0.000	1.051
listComplexComponents	0.008	0.000	0.010
listInstances	0.020	0.000	0.022
listInteractionComponents	0.012	0.000	0.012
listPathwayComponents	0.008	0.000	0.010
listPathways	0.008	0.000	0.009
pathway2AdjacancyMatrix	0.464	0.004	0.469
pathway2Geneset	0.092	0.004	0.096
pathway2RegulatoryGraph	0.736	0.000	0.736
plotRegulatoryGraph	0.744	0.004	0.749
print.biopax	0.012	0.000	0.009
rBiopaxParser-package	0.004	0.000	0.002
readBiopax	0.004	0.000	0.002
removeNodes	1.156	0.000	1.160
selectInstances	0.108	0.004	0.112
splitComplex	0.028	0.000	0.028
uniteGraphs	1.856	0.004	1.865
writeBiopax	0.004	0.000	0.004