Package: rBiopaxParser

Version: 2.23.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rBiopaxParser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rBiopaxParser_2.23.0.tar.gz

StartedAt: 2019-04-09 03:11:17 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:12:22 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 65.8 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 --install=check:rBiopaxParser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rBiopaxParser_2.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/rBiopaxParser.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.23.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
calcGraphOverlap        16.475 12.399   4.071
diffGraphs              16.163 12.254   3.781
uniteGraphs             15.998 10.884   3.772
intersectGraphs         15.946 10.475   3.569
colorGraphNodes          9.955  7.522   2.375
removeNodes              9.903  7.210   2.236
pathway2AdjacancyMatrix  9.296  7.601   2.010
pathway2RegulatoryGraph  9.639  6.300   2.268
plotRegulatoryGraph      8.950  5.754   2.188
pathway2Graph            6.413  4.801   1.418
pathway2Geneset          4.754  3.541   1.020
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/rBiopaxParser.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rBiopaxParser
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘rBiopaxParser’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rBiopaxParser)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("rBiopaxParser")


RUNIT TEST PROTOCOL -- Tue Apr  9 03:12:15 2019 
*********************************************** 
Number of test functions: 12 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
rBiopaxParser RUnit Tests - 12 test functions, 0 errors, 0 failures
Number of test functions: 12 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  0.591   0.084   0.655 

name	user	system	elapsed
addBiochemicalReaction	0.229	0.187	0.062
addBiopaxInstance	0.060	0.053	0.017
addBiopaxInstances	0.166	0.143	0.050
addControl	0.202	0.109	0.095
addPathway	0.256	0.196	0.066
addPathwayComponents	0.321	0.277	0.078
addPhysicalEntity	0.078	0.072	0.019
addPhysicalEntityParticipant	0.162	0.133	0.038
addPropertiesToBiopaxInstance	0.088	0.085	0.022
biopax	0.151	0.176	0.040
calcGraphOverlap	16.475	12.399	4.071
colorGraphNodes	9.955	7.522	2.375
combineNodes	0.005	0.001	0.006
createBiopax	0.009	0.008	0.003
diffGraphs	16.163	12.254	3.781
downloadBiopaxData	0.000	0.000	0.001
getClassProperties	0.002	0.001	0.002
getInstanceClass	0.018	0.007	0.013
getInstanceProperty	0.056	0.047	0.016
getReferencedIDs	0.263	0.237	0.064
getReferencingIDs	0.171	0.163	0.042
getSubClasses	0.003	0.005	0.000
getSuperClasses	0.004	0.004	0.001
getXrefAnnotations	1.282	1.070	0.300
intersectGraphs	15.946	10.475	3.569
listComplexComponents	0.139	0.089	0.029
listInstances	0.223	0.209	0.055
listInteractionComponents	0.240	0.140	0.048
listPathwayComponents	0.199	0.159	0.045
listPathways	0.072	0.054	0.016
pathway2AdjacancyMatrix	9.296	7.601	2.010
pathway2Geneset	4.754	3.541	1.020
pathway2Graph	6.413	4.801	1.418
pathway2RegulatoryGraph	9.639	6.300	2.268
plotRegulatoryGraph	8.950	5.754	2.188
print.biopax	0.112	0.075	0.023
rBiopaxParser-package	0.002	0.001	0.000
readBiopax	0.001	0.001	0.000
removeNodes	9.903	7.210	2.236
selectInstances	0.085	0.072	0.027
splitComplex	0.311	0.255	0.072
uniteGraphs	15.998	10.884	3.772
writeBiopax	0.001	0.001	0.002