BioC 3.2: CHECK report for rBiopaxParser on perceval

Package: rBiopaxParser

Version: 2.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rBiopaxParser_2.7.0.tar.gz

StartedAt: 2015-08-24 04:19:50 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 04:20:54 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 64.4 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 rBiopaxParser_2.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/rBiopaxParser.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘2.7.0’
* 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 ‘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 ... NOTE
'library' or 'require' calls in package code:
  ‘graph’ ‘nem’ ‘RBGL’ ‘RCurl’ ‘Rgraphviz’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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’
layoutRegulatoryGraph: no visible global function definition for
  ‘nodes’
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’
plotRegulatoryGraph: no visible global function definition for ‘nodes’
removeNodes: no visible global function definition for ‘edgeWeights’
removeNodes: no visible global function definition for ‘removeNode’
removeNodes: no visible global function definition for ‘addEdge’
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 ... [21s/21s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [2s/2s]
 [3s/3s] 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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.046	0.002	0.047
addBiopaxInstance	0.012	0.000	0.011
addBiopaxInstances	0.082	0.001	0.082
addControl	0.053	0.007	0.060
addPathway	0.055	0.001	0.056
addPathwayComponents	0.062	0.001	0.062
addPhysicalEntity	0.018	0.000	0.019
addPhysicalEntityParticipant	0.035	0.001	0.036
addPropertiesToBiopaxInstance	0.019	0.001	0.020
biopax	0.015	0.002	0.017
calcGraphOverlap	2.756	0.039	2.799
colorGraphNodes	1.718	0.025	1.749
combineNodes	0.005	0.001	0.005
createBiopax	0.006	0.001	0.006
diffGraphs	2.474	0.014	2.493
downloadBiopaxData	0.001	0.000	0.001
getClassProperties	0.003	0.000	0.002
getInstanceClass	0.007	0.001	0.008
getInstanceProperty	0.021	0.001	0.022
getReferencedIDs	0.026	0.001	0.027
getReferencingIDs	0.027	0.000	0.027
getSubClasses	0.002	0.000	0.001
getSuperClasses	0.001	0.000	0.001
getXrefAnnotations	0.206	0.001	0.207
intersectGraphs	2.433	0.010	2.445
listComplexComponents	0.015	0.001	0.016
listInstances	0.037	0.004	0.040
listInteractionComponents	0.022	0.001	0.022
listPathwayComponents	0.023	0.002	0.025
listPathways	0.015	0.001	0.016
pathway2AdjacancyMatrix	1.364	0.009	1.374
pathway2Geneset	0.362	0.002	0.365
pathway2RegulatoryGraph	1.544	0.008	1.552
plotRegulatoryGraph	1.601	0.026	1.628
print.biopax	0.015	0.001	0.016
rBiopaxParser-package	0.001	0.000	0.001
readBiopax	0.001	0.000	0.000
removeNodes	1.518	0.016	1.540
selectInstances	0.033	0.002	0.036
splitComplex	0.044	0.003	0.047
uniteGraphs	2.563	0.020	2.588
writeBiopax	0.002	0.001	0.003