BioC 3.3: CHECK report for rBiopaxParser on morelia

Package: rBiopaxParser

Version: 2.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rBiopaxParser_2.9.0.tar.gz

StartedAt: 2015-10-22 10:12:33 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 10:13:16 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 43.1 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_2.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/rBiopaxParser.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.9.0’
* 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 ... [1s/1s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] 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
  ‘/Users/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	0.050	0.001	0.051
addBiopaxInstance	0.028	0.000	0.028
addBiopaxInstances	0.025	0.003	0.029
addControl	0.038	0.000	0.038
addPathway	0.038	0.001	0.039
addPathwayComponents	0.043	0.001	0.044
addPhysicalEntity	0.015	0.000	0.015
addPhysicalEntityParticipant	0.023	0.000	0.024
addPropertiesToBiopaxInstance	0.013	0.000	0.013
biopax	0.009	0.001	0.010
calcGraphOverlap	1.704	0.015	1.719
colorGraphNodes	1.088	0.013	1.101
combineNodes	0.003	0.000	0.003
createBiopax	0.003	0.000	0.003
diffGraphs	1.541	0.007	1.549
downloadBiopaxData	0.000	0.000	0.001
getClassProperties	0.001	0.000	0.001
getInstanceClass	0.004	0.001	0.004
getInstanceProperty	0.008	0.000	0.009
getReferencedIDs	0.016	0.001	0.017
getReferencingIDs	0.016	0.000	0.016
getSubClasses	0.000	0.000	0.001
getSuperClasses	0.001	0.000	0.000
getXrefAnnotations	0.128	0.000	0.128
intersectGraphs	1.526	0.005	1.532
listComplexComponents	0.011	0.000	0.010
listInstances	0.026	0.002	0.028
listInteractionComponents	0.014	0.000	0.015
listPathwayComponents	0.013	0.001	0.014
listPathways	0.01	0.00	0.01
pathway2AdjacancyMatrix	0.865	0.004	0.869
pathway2Geneset	0.228	0.001	0.229
pathway2RegulatoryGraph	0.957	0.004	0.961
plotRegulatoryGraph	0.970	0.003	0.974
print.biopax	0.008	0.001	0.009
rBiopaxParser-package	0.001	0.000	0.000
readBiopax	0.001	0.000	0.001
removeNodes	1.077	0.006	1.083
selectInstances	0.018	0.001	0.019
splitComplex	0.025	0.001	0.026
uniteGraphs	1.760	0.012	1.772
writeBiopax	0.002	0.000	0.021