BioC 3.2: CHECK report for rBiopaxParser on linux1.bioconductor.org

Package: rBiopaxParser

Version: 2.8.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings rBiopaxParser_2.8.0.tar.gz

StartedAt: 2015-10-27 07:13:59 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:14:44 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 45.1 seconds

RetCode: 0

Status:  OK

CheckDir: rBiopaxParser.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings rBiopaxParser_2.8.0.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 ‘2.8.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/20s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [1s/1s]
 [1s/1s] 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	0.115	0.000	0.114
addBiopaxInstance	0.013	0.000	0.013
addBiopaxInstances	0.044	0.000	0.043
addControl	0.054	0.000	0.054
addPathway	0.061	0.000	0.060
addPathwayComponents	0.066	0.000	0.065
addPhysicalEntity	0.020	0.000	0.019
addPhysicalEntityParticipant	0.035	0.000	0.035
addPropertiesToBiopaxInstance	0.018	0.004	0.022
biopax	0.011	0.004	0.015
calcGraphOverlap	2.618	0.020	2.653
colorGraphNodes	1.773	0.019	1.797
combineNodes	0.003	0.000	0.003
createBiopax	0.004	0.000	0.004
diffGraphs	2.295	0.000	2.315
downloadBiopaxData	0	0	0
getClassProperties	0.002	0.000	0.002
getInstanceClass	0.007	0.000	0.007
getInstanceProperty	0.015	0.000	0.015
getReferencedIDs	0.036	0.000	0.035
getReferencingIDs	0.029	0.000	0.028
getSubClasses	0.001	0.000	0.001
getSuperClasses	0.001	0.000	0.001
getXrefAnnotations	0.195	0.000	0.197
intersectGraphs	2.399	0.000	2.403
listComplexComponents	0.021	0.000	0.021
listInstances	0.028	0.004	0.032
listInteractionComponents	0.014	0.004	0.018
listPathwayComponents	0.018	0.004	0.023
listPathways	0.013	0.000	0.013
pathway2AdjacancyMatrix	1.184	0.004	1.193
pathway2Geneset	0.376	0.000	0.377
pathway2RegulatoryGraph	1.592	0.004	1.611
plotRegulatoryGraph	1.311	0.000	1.313
print.biopax	0.014	0.000	0.013
rBiopaxParser-package	0.001	0.000	0.000
readBiopax	0.000	0.000	0.001
removeNodes	1.665	0.008	1.689
selectInstances	0.028	0.000	0.028
splitComplex	0.040	0.000	0.041
uniteGraphs	2.620	0.004	2.627
writeBiopax	0.001	0.000	0.001