Package: rBiopaxParser

Version: 2.26.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:rBiopaxParser.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings rBiopaxParser_2.26.0.tar.gz

StartedAt: 2020-04-15 01:36:14 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:39:55 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 220.6 seconds

RetCode: 0

Status:  OK

CheckDir: rBiopaxParser.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:rBiopaxParser.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings rBiopaxParser_2.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/rBiopaxParser.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.26.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
intersectGraphs         125.676  0.584  23.165
diffGraphs              123.080  0.668  25.182
calcGraphOverlap        121.724  0.788  25.177
uniteGraphs             121.056  0.656  22.456
colorGraphNodes          73.696  0.456  17.527
pathway2AdjacancyMatrix  73.320  0.364  12.523
removeNodes              71.312  0.428  13.573
pathway2RegulatoryGraph  68.668  0.420  13.721
plotRegulatoryGraph      68.548  0.440  13.122
pathway2Geneset          54.692  0.268   9.493
pathway2Graph            30.568  0.180   6.436
getXrefAnnotations       12.080  0.060   2.336
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/rBiopaxParser.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL rBiopaxParser
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 Apr 15 01:39:51 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 
  0.632   0.028   0.668 

name	user	system	elapsed
addBiochemicalReaction	2.596	0.004	0.618
addBiopaxInstance	0.488	0.000	0.104
addBiopaxInstances	1.020	0.016	0.260
addControl	4.204	0.004	0.813
addPathway	4.160	0.016	0.736
addPathwayComponents	4.576	0.000	0.798
addPhysicalEntity	1.092	0.008	0.200
addPhysicalEntityParticipant	2.732	0.020	0.448
addPropertiesToBiopaxInstance	1.244	0.000	0.174
biopax	0.152	0.008	0.036
calcGraphOverlap	121.724	0.788	25.177
colorGraphNodes	73.696	0.456	17.527
combineNodes	0.004	0.000	0.005
createBiopax	0.212	0.000	0.065
diffGraphs	123.080	0.668	25.182
downloadBiopaxData	0	0	0
getClassProperties	0.000	0.000	0.001
getInstanceClass	0.288	0.004	0.076
getInstanceProperty	0.256	0.000	0.051
getReferencedIDs	2.436	0.004	0.455
getReferencingIDs	1.348	0.004	0.251
getSubClasses	0	0	0
getSuperClasses	0.000	0.000	0.001
getXrefAnnotations	12.080	0.060	2.336
intersectGraphs	125.676	0.584	23.165
listComplexComponents	1.092	0.000	0.215
listInstances	1.528	0.008	0.285
listInteractionComponents	2.520	0.012	0.412
listPathwayComponents	1.444	0.012	0.234
listPathways	0.408	0.000	0.075
pathway2AdjacancyMatrix	73.320	0.364	12.523
pathway2Geneset	54.692	0.268	9.493
pathway2Graph	30.568	0.180	6.436
pathway2RegulatoryGraph	68.668	0.420	13.721
plotRegulatoryGraph	68.548	0.440	13.122
print.biopax	0.068	0.000	0.017
rBiopaxParser-package	0	0	0
readBiopax	0.004	0.000	0.000
removeNodes	71.312	0.428	13.573
selectInstances	0.188	0.004	0.045
splitComplex	3.528	0.024	0.790
uniteGraphs	121.056	0.656	22.456
writeBiopax	0.000	0.000	0.002