BioC 3.1: CHECK report for rBiopaxParser on petty

Package: rBiopaxParser

Version: 2.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rBiopaxParser_2.6.0.tar.gz

StartedAt: 2015-10-09 01:26:22 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:27:44 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 82.1 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 rBiopaxParser_2.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘2.6.0’
* 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/4s] 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 ... [29s/30s] 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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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	0.152	0.002	0.154
addBiopaxInstance	0.019	0.001	0.020
addBiopaxInstances	0.069	0.008	0.079
addControl	0.093	0.001	0.094
addPathway	0.094	0.002	0.095
addPathwayComponents	0.108	0.001	0.114
addPhysicalEntity	0.03	0.00	0.03
addPhysicalEntityParticipant	0.054	0.001	0.055
addPropertiesToBiopaxInstance	0.035	0.001	0.036
biopax	0.025	0.002	0.027
calcGraphOverlap	3.660	0.030	3.694
colorGraphNodes	2.366	0.030	2.397
combineNodes	0.008	0.001	0.008
createBiopax	0.009	0.000	0.009
diffGraphs	3.871	0.013	3.892
downloadBiopaxData	0.001	0.000	0.001
getClassProperties	0.003	0.001	0.003
getInstanceClass	0.009	0.001	0.009
getInstanceProperty	0.021	0.000	0.021
getReferencedIDs	0.040	0.001	0.041
getReferencingIDs	0.040	0.001	0.041
getSubClasses	0.002	0.001	0.002
getSuperClasses	0.002	0.000	0.002
getXrefAnnotations	0.331	0.003	0.334
intersectGraphs	3.586	0.009	3.600
listComplexComponents	0.025	0.001	0.026
listInstances	0.058	0.004	0.063
listInteractionComponents	0.028	0.001	0.030
listPathwayComponents	0.036	0.002	0.038
listPathways	0.016	0.001	0.016
pathway2AdjacancyMatrix	2.018	0.008	2.028
pathway2Geneset	0.560	0.004	0.565
pathway2RegulatoryGraph	2.274	0.008	2.284
plotRegulatoryGraph	2.278	0.007	2.289
print.biopax	0.021	0.002	0.023
rBiopaxParser-package	0.001	0.000	0.001
readBiopax	0.001	0.000	0.001
removeNodes	2.404	0.011	2.418
selectInstances	0.046	0.002	0.048
splitComplex	0.062	0.001	0.063
uniteGraphs	3.765	0.015	3.784
writeBiopax	0.002	0.000	0.003