BioC 2.14: CHECK report for rBiopaxParser on petty

Package: rBiopaxParser

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rBiopaxParser_2.2.0.tar.gz

StartedAt: 2014-10-07 23:41:49 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:43:51 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 122.1 seconds

RetCode: 0

Status:  OK

CheckDir: rBiopaxParser.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rBiopaxParser_2.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/rBiopaxParser.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘2.2.0’
* 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 ... [5s/6s] 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 ... NOTE
addBiopaxInstance: no visible binding for global variable ‘property’
addBiopaxInstances: no visible binding for global variable ‘id’
addBiopaxInstances: no visible binding for global variable ‘property’
addPropertiesToBiopaxInstance: no visible binding for global variable
  ‘property’
createBiopax: no visible binding for global variable ‘id’
createBiopax: no visible binding for global variable ‘property’
getReferencedIDs: no visible binding for global variable
  ‘property_attr’
getReferencedIDs: no visible binding for global variable ‘property’
getReferencingIDs: no visible binding for global variable
  ‘property_attr’
getReferencingIDs: no visible binding for global variable ‘property’
internal_generateXMLfromBiopax: no visible binding for global variable
  ‘id’
internal_getBiopaxModelAsDataFrame: no visible binding for global
  variable ‘property’
internal_propertyListToDF: no visible binding for global variable
  ‘property’
internal_XMLInstance2DF: no visible binding for global variable ‘i’
internal_XMLInstance2DF: no visible binding for global variable ‘p’
listInstances: no visible binding for global variable ‘property_value’
listInstances: no visible binding for global variable ‘property’
pathway2RegulatoryGraph: no visible binding for global variable ‘id’
pathway2RegulatoryGraph: no visible binding for global variable
  ‘property’
removeProperties: no visible binding for global variable ‘property’
selectInstances: no visible binding for global variable
  ‘property_value’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [45s/46s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
calcGraphOverlap 5.840  0.046   5.992
uniteGraphs      5.699  0.024   5.759
intersectGraphs  5.626  0.022   5.681
diffGraphs       5.531  0.017   5.569
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [3s/3s]
 [4s/4s] 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-2.14-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	0.090	0.003	0.092
addBiopaxInstance	0.023	0.000	0.024
addBiopaxInstances	0.093	0.002	0.096
addControl	0.111	0.001	0.111
addPathway	0.127	0.001	0.131
addPathwayComponents	0.148	0.001	0.149
addPhysicalEntity	0.042	0.001	0.042
addPhysicalEntityParticipant	0.077	0.001	0.080
addPropertiesToBiopaxInstance	0.042	0.000	0.043
biopax	0.029	0.002	0.031
calcGraphOverlap	5.840	0.046	5.992
colorGraphNodes	3.859	0.032	3.950
combineNodes	0.008	0.001	0.009
createBiopax	0.011	0.000	0.011
diffGraphs	5.531	0.017	5.569
downloadBiopaxData	0.001	0.000	0.001
getClassProperties	0.003	0.000	0.003
getInstanceClass	0.010	0.000	0.011
getInstanceProperty	0.03	0.00	0.03
getReferencedIDs	0.060	0.001	0.062
getReferencingIDs	0.058	0.001	0.059
getSubClasses	0.003	0.000	0.002
getSuperClasses	0.002	0.000	0.002
getXrefAnnotations	0.461	0.002	0.466
intersectGraphs	5.626	0.022	5.681
listComplexComponents	0.031	0.001	0.032
listInstances	0.071	0.005	0.075
listInteractionComponents	0.042	0.002	0.044
listPathwayComponents	0.046	0.003	0.048
listPathways	0.022	0.001	0.025
pathway2AdjacancyMatrix	3.034	0.013	3.061
pathway2Geneset	0.867	0.005	0.876
pathway2RegulatoryGraph	3.355	0.014	3.393
plotRegulatoryGraph	3.435	0.013	3.478
print.biopax	0.025	0.001	0.027
rBiopaxParser-package	0.001	0.000	0.001
readBiopax	0.001	0.000	0.001
removeNodes	3.568	0.022	3.621
selectInstances	0.053	0.002	0.055
splitComplex	0.080	0.002	0.081
uniteGraphs	5.699	0.024	5.759
writeBiopax	0.003	0.001	0.004