BioC 3.2: CHECK report for rBiopaxParser on zin1

Package: rBiopaxParser

Version: 2.7.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings rBiopaxParser_2.7.0.tar.gz

StartedAt: 2015-08-24 03:00:26 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:01:07 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 41.2 seconds

RetCode: 0

Status:  OK

CheckDir: rBiopaxParser.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings rBiopaxParser_2.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/rBiopaxParser.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘2.7.0’
* 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 ... [2s/2s] 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’ ‘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’
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’
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 ... [15s/15s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [1s/1s]
 [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
  ‘/home/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	0.034	0.003	0.037
addBiopaxInstance	0.018	0.001	0.018
addBiopaxInstances	0.056	0.000	0.057
addControl	0.043	0.000	0.042
addPathway	0.044	0.000	0.045
addPathwayComponents	0.048	0.003	0.049
addPhysicalEntity	0.014	0.001	0.015
addPhysicalEntityParticipant	0.028	0.000	0.027
addPropertiesToBiopaxInstance	0.015	0.000	0.015
biopax	0.007	0.004	0.012
calcGraphOverlap	2.064	0.008	2.076
colorGraphNodes	1.264	0.008	1.287
combineNodes	0.004	0.000	0.004
createBiopax	0.004	0.000	0.004
diffGraphs	1.849	0.012	1.860
downloadBiopaxData	0	0	0
getClassProperties	0.002	0.000	0.001
getInstanceClass	0.004	0.000	0.005
getInstanceProperty	0.013	0.000	0.012
getReferencedIDs	0.015	0.004	0.020
getReferencingIDs	0.019	0.000	0.019
getSubClasses	0.001	0.000	0.001
getSuperClasses	0.001	0.000	0.001
getXrefAnnotations	0.154	0.000	0.155
intersectGraphs	1.809	0.004	1.819
listComplexComponents	0.015	0.000	0.015
listInstances	0.028	0.000	0.028
listInteractionComponents	0.017	0.000	0.017
listPathwayComponents	0.017	0.000	0.017
listPathways	0.012	0.000	0.012
pathway2AdjacancyMatrix	0.978	0.008	0.986
pathway2Geneset	0.291	0.004	0.298
pathway2RegulatoryGraph	1.167	0.000	1.170
plotRegulatoryGraph	1.180	0.004	1.253
print.biopax	0.011	0.000	0.013
rBiopaxParser-package	0	0	0
readBiopax	0.001	0.000	0.001
removeNodes	1.231	0.004	1.320
selectInstances	0.02	0.00	0.02
splitComplex	0.029	0.000	0.030
uniteGraphs	1.898	0.000	1.939
writeBiopax	0.002	0.000	0.002