BioC 3.5: CHECK report for rBiopaxParser on malbec2

Package: rBiopaxParser

Version: 2.16.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings rBiopaxParser_2.16.0.tar.gz

StartedAt: 2017-10-18 01:50:14 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:50:53 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 39.1 seconds

RetCode: 0

Status:  OK

CheckDir: rBiopaxParser.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings rBiopaxParser_2.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/rBiopaxParser.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-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 ‘2.16.0’
* 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 ... 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:
  ‘RBGL’ ‘RCurl’ ‘Rgraphviz’ ‘graph’ ‘igraph’ ‘nem’
  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’
colorGraphNodes: no visible global function definition for ‘hcl’
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_XMLInstance2DF: no visible binding for global variable ‘i’
internal_XMLInstance2DF: no visible binding for global variable ‘p’
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’
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’
pathway2AdjacancyMatrix: no visible global function definition for ‘as’
pathway2Graph: no visible global function definition for ‘new’
pathway2Graph: no visible global function definition for ‘getClassDef’
pathway2Graph: no visible binding for global variable ‘id’
pathway2Graph: no visible binding for global variable ‘property’
pathway2RegulatoryGraph: no visible global function definition for
  ‘new’
pathway2RegulatoryGraph: no visible global function definition for
  ‘getClassDef’
pathway2RegulatoryGraph: no visible binding for global variable ‘id’
pathway2RegulatoryGraph: no visible binding for global variable
  ‘property’
plotRegulatoryGraph: no visible global function definition for ‘nodes’
removeDisconnectedParts: no visible global function definition for
  ‘removeNode’
removeNodes: no visible global function definition for ‘edgeWeights’
removeNodes: no visible global function definition for ‘na.omit’
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’
transitiveReduction: no visible global function definition for ‘as’
Undefined global functions or variables:
  addEdge as edgeWeights getClassDef hcl i id na.omit new nodes p
  property property_attr property_value removeNode
Consider adding
  importFrom("grDevices", "hcl")
  importFrom("methods", "as", "getClassDef", "new")
  importFrom("stats", "na.omit")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... NOTE
  Note: found 1 marked UTF-8 string
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-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	0.264	0.004	0.214
addBiopaxInstance	0.052	0.000	0.051
addBiopaxInstances	0.096	0.000	0.093
addControl	0.140	0.004	0.055
addPathway	0.132	0.000	0.065
addPathwayComponents	0.136	0.000	0.076
addPhysicalEntity	0.032	0.000	0.013
addPhysicalEntityParticipant	0.056	0.000	0.023
addPropertiesToBiopaxInstance	0.048	0.000	0.039
biopax	0.172	0.000	0.175
calcGraphOverlap	1.900	0.012	1.893
colorGraphNodes	1.016	0.004	1.006
combineNodes	0.000	0.000	0.003
createBiopax	0.000	0.000	0.002
diffGraphs	1.812	0.012	1.788
downloadBiopaxData	0	0	0
getClassProperties	0.004	0.000	0.001
getInstanceClass	0.004	0.000	0.003
getInstanceProperty	0.008	0.000	0.008
getReferencedIDs	0.016	0.000	0.014
getReferencingIDs	0.052	0.000	0.054
getSubClasses	0	0	0
getSuperClasses	0.000	0.000	0.001
getXrefAnnotations	0.148	0.000	0.151
intersectGraphs	1.336	0.016	1.318
listComplexComponents	0.016	0.000	0.013
listInstances	0.032	0.000	0.030
listInteractionComponents	0.016	0.000	0.018
listPathwayComponents	0.020	0.000	0.022
listPathways	0.012	0.000	0.012
pathway2AdjacancyMatrix	0.692	0.004	0.685
pathway2Geneset	0.192	0.004	0.196
pathway2Graph	1.192	0.004	1.164
pathway2RegulatoryGraph	0.780	0.000	0.761
plotRegulatoryGraph	0.788	0.000	0.773
print.biopax	0.008	0.000	0.008
rBiopaxParser-package	0	0	0
readBiopax	0.004	0.000	0.000
removeNodes	0.876	0.000	0.860
selectInstances	0.012	0.000	0.015
splitComplex	0.020	0.000	0.021
uniteGraphs	1.396	0.004	1.368
writeBiopax	0.000	0.000	0.002