BioC 3.3: CHECK report for rBiopaxParser on linux2.bioconductor.org

Package: rBiopaxParser

Version: 2.9.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings rBiopaxParser_2.9.0.tar.gz

StartedAt: 2015-10-27 07:13:21 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:14:05 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 44.1 seconds

RetCode: 0

Status:  OK

CheckDir: rBiopaxParser.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings rBiopaxParser_2.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/rBiopaxParser.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘2.9.0’
* 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’
Undefined global functions or variables:
  addEdge edgeWeights i id nodes p property property_attr
  property_value removeNode
* 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 ... [17s/17s] 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-3.3-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	0.105	0.001	0.105
addBiopaxInstance	0.007	0.001	0.010
addBiopaxInstances	0.038	0.004	0.041
addControl	0.048	0.000	0.048
addPathway	0.054	0.001	0.057
addPathwayComponents	0.06	0.00	0.06
addPhysicalEntity	0.016	0.004	0.019
addPhysicalEntityParticipant	0.033	0.000	0.033
addPropertiesToBiopaxInstance	0.019	0.000	0.018
biopax	0.014	0.000	0.014
calcGraphOverlap	2.452	0.019	2.472
colorGraphNodes	1.759	0.016	1.776
combineNodes	0.005	0.000	0.005
createBiopax	0.005	0.000	0.005
diffGraphs	2.361	0.000	2.361
downloadBiopaxData	0.001	0.000	0.001
getClassProperties	0.002	0.000	0.002
getInstanceClass	0.007	0.000	0.007
getInstanceProperty	0.015	0.000	0.015
getReferencedIDs	0.027	0.000	0.027
getReferencingIDs	0.024	0.004	0.028
getSubClasses	0.001	0.000	0.001
getSuperClasses	0.001	0.000	0.002
getXrefAnnotations	0.132	0.000	0.132
intersectGraphs	1.879	0.000	1.879
listComplexComponents	0.008	0.003	0.012
listInstances	0.018	0.000	0.018
listInteractionComponents	0.013	0.000	0.012
listPathwayComponents	0.013	0.000	0.012
listPathways	0.007	0.000	0.007
pathway2AdjacancyMatrix	1.017	0.000	1.016
pathway2Geneset	0.359	0.000	0.360
pathway2RegulatoryGraph	1.095	0.004	1.099
plotRegulatoryGraph	0.959	0.000	0.960
print.biopax	0.008	0.000	0.008
rBiopaxParser-package	0	0	0
readBiopax	0	0	0
removeNodes	1.552	0.000	1.556
selectInstances	0.029	0.000	0.028
splitComplex	0.04	0.00	0.04
uniteGraphs	2.62	0.00	2.62
writeBiopax	0.000	0.004	0.002