Multiple platform build/check report for BioC 3.15 - CHECK results for rBiopaxParser on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 20.04.5 LTS)	x86_64	4.2.1 (2022-06-23) -- "Funny-Looking Kid"	4386
palomino3	Windows Server 2022 Datacenter	x64	4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"	4138
merida1	macOS 10.14.6 Mojave	x86_64	4.2.1 (2022-06-23) -- "Funny-Looking Kid"	4205
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: rBiopaxParser

Version: 2.36.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rBiopaxParser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rBiopaxParser_2.36.0.tar.gz

StartedAt: 2022-10-19 06:45:10 -0400 (Wed, 19 Oct 2022)

EndedAt: 2022-10-19 06:46:37 -0400 (Wed, 19 Oct 2022)

EllapsedTime: 87.2 seconds

RetCode: 0

Status: OK

CheckDir: rBiopaxParser.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rBiopaxParser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rBiopaxParser_2.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/rBiopaxParser.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.36.0’
* 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’
  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’
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
* 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-3.15-bioc/meat/rBiopaxParser.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rBiopaxParser
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 -- Wed Oct 19 06:46:25 2022 
*********************************************** 
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 
  0.863   0.102   0.941

name	user	system	elapsed
addBiochemicalReaction	0.050	0.004	0.053
addBiopaxInstance	0.007	0.000	0.008
addBiopaxInstances	0.042	0.006	0.049
addControl	0.038	0.002	0.040
addPathway	0.047	0.001	0.048
addPathwayComponents	0.052	0.001	0.053
addPhysicalEntity	0.016	0.001	0.016
addPhysicalEntityParticipant	0.021	0.001	0.021
addPropertiesToBiopaxInstance	0.014	0.001	0.015
biopax	0.033	0.005	0.038
calcGraphOverlap	3.974	0.082	4.063
colorGraphNodes	2.407	0.029	2.479
combineNodes	0.006	0.002	0.007
createBiopax	0.003	0.000	0.002
diffGraphs	3.662	0.033	3.728
downloadBiopaxData	0	0	0
getClassProperties	0.001	0.000	0.002
getInstanceClass	0.009	0.002	0.011
getInstanceProperty	0.014	0.001	0.015
getReferencedIDs	0.058	0.002	0.060
getReferencingIDs	0.034	0.002	0.036
getSubClasses	0.001	0.000	0.000
getSuperClasses	0.000	0.000	0.001
getXrefAnnotations	0.266	0.003	0.270
hasProperty	0.006	0.002	0.007
intersectGraphs	3.404	0.023	3.443
isOfClass	0.005	0.001	0.006
layoutRegulatoryGraph	2.159	0.017	2.185
listComplexComponents	0.025	0.001	0.028
listInstances	0.041	0.005	0.047
listInteractionComponents	0.039	0.001	0.041
listPathwayComponents	0.032	0.003	0.036
listPathways	0.015	0.002	0.017
pathway2AdjacancyMatrix	1.999	0.013	2.029
pathway2Geneset	0.830	0.006	0.840
pathway2Graph	1.688	0.021	1.711
pathway2RegulatoryGraph	2.025	0.017	2.044
plotRegulatoryGraph	1.932	0.017	1.952
print.biopax	0.011	0.002	0.013
rBiopaxParser-package	0	0	0
readBiopax	0.005	0.002	0.007
removeInstance	0.007	0.002	0.007
removeNodes	2.113	0.027	2.151
removeProperties	0.008	0.002	0.009
selectInstances	0.036	0.004	0.039
splitComplex	0.061	0.003	0.064
transitiveClosure	1.966	0.030	2.012
transitiveReduction	1.928	0.042	1.976
uniteGraphs	3.520	0.038	3.569
writeBiopax	0.002	0.002	0.004

CHECK results for rBiopaxParser on merida1

Summary

Command output

Installation output

Tests output

Example timings