Package: rBiopaxParser

Version: 2.27.0

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_2.27.0.tar.gz

StartedAt: 2020-01-16 07:58:26 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:59:58 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 91.2 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_2.27.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/rBiopaxParser.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘2.27.0’
* 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 (user + system) or elapsed time > 5s
                          user system elapsed
calcGraphOverlap        19.279 11.362   5.016
diffGraphs              17.657 10.383   4.670
intersectGraphs         17.026  9.073   4.684
uniteGraphs             16.184  8.212   4.684
colorGraphNodes         11.374  7.125   2.842
plotRegulatoryGraph     11.496  5.075   2.722
pathway2RegulatoryGraph  9.959  5.419   2.802
pathway2AdjacancyMatrix  9.701  5.328   2.575
removeNodes              9.656  5.289   2.780
pathway2Graph            6.788  3.291   1.691
pathway2Geneset          3.983  2.767   1.314
* 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-3.11-bioc/meat/rBiopaxParser.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rBiopaxParser
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘rBiopaxParser’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rBiopaxParser)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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 -- Thu Jan 16 07:59:48 2020 
*********************************************** 
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 
  0.950   0.197   1.097 

name	user	system	elapsed
addBiochemicalReaction	0.198	0.140	0.074
addBiopaxInstance	0.040	0.030	0.012
addBiopaxInstances	0.154	0.124	0.053
addControl	0.162	0.107	0.068
addPathway	0.189	0.114	0.081
addPathwayComponents	0.242	0.164	0.104
addPhysicalEntity	0.051	0.027	0.027
addPhysicalEntityParticipant	0.103	0.063	0.043
addPropertiesToBiopaxInstance	0.063	0.039	0.026
biopax	0.120	0.085	0.052
calcGraphOverlap	19.279	11.362	5.016
colorGraphNodes	11.374	7.125	2.842
combineNodes	0.005	0.002	0.007
createBiopax	0.010	0.006	0.004
diffGraphs	17.657	10.383	4.670
downloadBiopaxData	0.000	0.000	0.001
getClassProperties	0.002	0.000	0.002
getInstanceClass	0.023	0.012	0.014
getInstanceProperty	0.052	0.036	0.019
getReferencedIDs	0.203	0.148	0.144
getReferencingIDs	0.158	0.129	0.049
getSubClasses	0.003	0.002	0.001
getSuperClasses	0.003	0.002	0.000
getXrefAnnotations	1.412	1.124	0.381
intersectGraphs	17.026	9.073	4.684
listComplexComponents	0.541	0.003	0.062
listInstances	1.044	0.009	0.096
listInteractionComponents	0.251	0.119	0.062
listPathwayComponents	0.163	0.121	0.053
listPathways	0.051	0.037	0.017
pathway2AdjacancyMatrix	9.701	5.328	2.575
pathway2Geneset	3.983	2.767	1.314
pathway2Graph	6.788	3.291	1.691
pathway2RegulatoryGraph	9.959	5.419	2.802
plotRegulatoryGraph	11.496	5.075	2.722
print.biopax	0.035	0.021	0.021
rBiopaxParser-package	0.001	0.002	0.000
readBiopax	0.002	0.002	0.001
removeNodes	9.656	5.289	2.780
selectInstances	0.086	0.059	0.037
splitComplex	0.280	0.189	0.094
uniteGraphs	16.184	8.212	4.684
writeBiopax	0.002	0.001	0.003