Package: rBiopaxParser

Version: 2.23.0

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_2.23.0.tar.gz

StartedAt: 2019-04-09 03:01:30 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:06:28 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 298.3 seconds

RetCode: 0

Status:  OK

CheckDir: rBiopaxParser.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_2.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/rBiopaxParser.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.23.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
diffGraphs              126.543  0.600  33.722
intersectGraphs         125.813  0.582  33.240
uniteGraphs             123.558  0.615  32.639
calcGraphOverlap        117.679  0.543  28.766
pathway2AdjacancyMatrix  75.980  0.355  22.363
removeNodes              75.575  0.358  21.393
plotRegulatoryGraph      75.489  0.368  21.109
pathway2RegulatoryGraph  74.181  0.347  19.860
colorGraphNodes          69.251  0.321  17.612
pathway2Geneset          55.753  0.284  15.681
pathway2Graph            32.594  0.121   8.560
getXrefAnnotations       12.456  0.061   3.324
* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL rBiopaxParser
###
##############################################################################
##############################################################################


* 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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 -- Tue Apr  9 03:06:21 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 
  0.601   0.064   0.709 

name	user	system	elapsed
addBiochemicalReaction	2.388	0.007	0.453
addBiopaxInstance	0.507	0.000	0.095
addBiopaxInstances	0.992	0.004	0.155
addControl	1.507	0.012	0.185
addPathway	1.91	0.00	0.24
addPathwayComponents	0.472	0.000	0.055
addPhysicalEntity	0.19	0.00	0.03
addPhysicalEntityParticipant	0.532	0.003	0.059
addPropertiesToBiopaxInstance	0.264	0.004	0.031
biopax	0.160	0.001	0.036
calcGraphOverlap	117.679	0.543	28.766
colorGraphNodes	69.251	0.321	17.612
combineNodes	0.004	0.002	0.005
createBiopax	0.188	0.000	0.051
diffGraphs	126.543	0.600	33.722
downloadBiopaxData	0	0	0
getClassProperties	0.001	0.000	0.001
getInstanceClass	0.291	0.000	0.078
getInstanceProperty	0.309	0.000	0.075
getReferencedIDs	2.845	0.004	0.679
getReferencingIDs	1.522	0.004	0.424
getSubClasses	0.004	0.000	0.000
getSuperClasses	0	0	0
getXrefAnnotations	12.456	0.061	3.324
intersectGraphs	125.813	0.582	33.240
listComplexComponents	1.175	0.000	0.339
listInstances	1.532	0.008	0.430
listInteractionComponents	2.758	0.008	0.777
listPathwayComponents	1.498	0.004	0.349
listPathways	0.422	0.004	0.122
pathway2AdjacancyMatrix	75.980	0.355	22.363
pathway2Geneset	55.753	0.284	15.681
pathway2Graph	32.594	0.121	8.560
pathway2RegulatoryGraph	74.181	0.347	19.860
plotRegulatoryGraph	75.489	0.368	21.109
print.biopax	0.083	0.000	0.028
rBiopaxParser-package	0	0	0
readBiopax	0	0	0
removeNodes	75.575	0.358	21.393
selectInstances	0.168	0.001	0.065
splitComplex	3.347	0.008	0.846
uniteGraphs	123.558	0.615	32.639
writeBiopax	0.001	0.000	0.002