Package: rBiopaxParser

Version: 2.24.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rBiopaxParser.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rBiopaxParser_2.24.0.tar.gz

StartedAt: 2019-10-16 04:18:21 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:23:01 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 280.5 seconds

RetCode: 0

Status:  OK

CheckDir: rBiopaxParser.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rBiopaxParser.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rBiopaxParser_2.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/rBiopaxParser.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.24.0’
* 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
uniteGraphs             127.424  0.694  35.671
calcGraphOverlap        123.500  0.641  31.989
diffGraphs              115.537  0.542  18.082
intersectGraphs         112.317  0.515  21.127
pathway2RegulatoryGraph  75.901  0.353  21.441
plotRegulatoryGraph      75.843  0.396  21.377
colorGraphNodes          75.203  0.384  20.475
removeNodes              75.014  0.398  20.279
pathway2AdjacancyMatrix  73.827  0.339  20.078
pathway2Geneset          53.923  0.246  13.295
pathway2Graph            33.149  0.183   8.955
getXrefAnnotations       10.949  0.076   1.841
addPathwayComponents      5.606  0.032   1.554
* 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-3.9-bioc/meat/rBiopaxParser.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL rBiopaxParser
###
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* installing to library ‘/home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 Oct 16 04:22:54 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 
  0.590   0.049   0.764 

name	user	system	elapsed
addBiochemicalReaction	2.861	0.032	0.810
addBiopaxInstance	0.600	0.005	0.157
addBiopaxInstances	1.024	0.006	0.272
addControl	4.243	0.024	0.999
addPathway	2.444	0.005	0.550
addPathwayComponents	5.606	0.032	1.554
addPhysicalEntity	1.317	0.000	0.330
addPhysicalEntityParticipant	1.657	0.020	0.404
addPropertiesToBiopaxInstance	1.197	0.012	0.301
biopax	0.158	0.000	0.050
calcGraphOverlap	123.500	0.641	31.989
colorGraphNodes	75.203	0.384	20.475
combineNodes	0.005	0.000	0.005
createBiopax	0.198	0.004	0.070
diffGraphs	115.537	0.542	18.082
downloadBiopaxData	0	0	0
getClassProperties	0.001	0.000	0.001
getInstanceClass	0.252	0.000	0.048
getInstanceProperty	0.273	0.000	0.049
getReferencedIDs	2.519	0.004	0.407
getReferencingIDs	1.249	0.008	0.222
getSubClasses	0	0	0
getSuperClasses	0.001	0.000	0.001
getXrefAnnotations	10.949	0.076	1.841
intersectGraphs	112.317	0.515	21.127
listComplexComponents	0.896	0.000	0.239
listInstances	1.541	0.012	0.457
listInteractionComponents	2.476	0.012	0.549
listPathwayComponents	1.211	0.017	0.272
listPathways	0.257	0.000	0.046
pathway2AdjacancyMatrix	73.827	0.339	20.078
pathway2Geneset	53.923	0.246	13.295
pathway2Graph	33.149	0.183	8.955
pathway2RegulatoryGraph	75.901	0.353	21.441
plotRegulatoryGraph	75.843	0.396	21.377
print.biopax	0.077	0.004	0.023
rBiopaxParser-package	0	0	0
readBiopax	0	0	0
removeNodes	75.014	0.398	20.279
selectInstances	0.155	0.000	0.062
splitComplex	3.502	0.036	0.940
uniteGraphs	127.424	0.694	35.671
writeBiopax	0.000	0.001	0.001