Back to Multiple platform build/check report for BioC 3.10
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

CHECK report for rBiopaxParser on merida1

This page was generated on 2020-04-15 12:38:29 -0400 (Wed, 15 Apr 2020).

Package 1373/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rBiopaxParser 2.26.0
Frank Kramer
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/rBiopaxParser
Branch: RELEASE_3_10
Last Commit: e3452ac
Last Changed Date: 2019-10-29 13:08:37 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: rBiopaxParser
Version: 2.26.0
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_2.26.0.tar.gz
StartedAt: 2020-04-15 04:58:50 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:59:57 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 67.2 seconds
RetCode: 0
Status:  OK 
CheckDir: rBiopaxParser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running 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_2.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/rBiopaxParser.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.26.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
calcGraphOverlap        16.568 12.593   4.150
intersectGraphs         16.288 12.210   3.548
diffGraphs              16.382 11.658   3.737
uniteGraphs             16.183 10.318   3.784
pathway2RegulatoryGraph  9.517  7.855   2.203
removeNodes              9.500  7.506   2.173
plotRegulatoryGraph     10.130  6.808   2.322
colorGraphNodes          9.973  6.218   2.402
pathway2AdjacancyMatrix  8.676  6.592   2.019
pathway2Graph            6.746  4.844   1.394
pathway2Geneset          3.879  3.280   1.013
* 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-3.10-bioc/meat/rBiopaxParser.Rcheck/00check.log’
for details.



Installation output

rBiopaxParser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rBiopaxParser
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)

Tests output

rBiopaxParser.Rcheck/tests/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 -- Wed Apr 15 04:59:51 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 
  0.631   0.087   0.698 

Example timings

rBiopaxParser.Rcheck/rBiopaxParser-Ex.timings

nameusersystemelapsed
addBiochemicalReaction0.1790.2500.062
addBiopaxInstance0.0500.0740.016
addBiopaxInstances0.1270.1550.041
addControl0.1660.1930.052
addPathway0.1830.2070.057
addPathwayComponents0.2390.2710.074
addPhysicalEntity0.0600.0680.019
addPhysicalEntityParticipant0.1070.1230.033
addPropertiesToBiopaxInstance0.0690.0720.021
biopax0.1250.1490.039
calcGraphOverlap16.56812.593 4.150
colorGraphNodes9.9736.2182.402
combineNodes0.0050.0010.007
createBiopax0.0080.0080.003
diffGraphs16.38211.658 3.737
downloadBiopaxData000
getClassProperties0.0020.0000.002
getInstanceClass0.0170.0170.012
getInstanceProperty0.0480.0670.015
getReferencedIDs0.1980.2500.062
getReferencingIDs0.1440.2090.046
getSubClasses0.0020.0030.001
getSuperClasses0.0020.0030.001
getXrefAnnotations1.0631.3100.302
intersectGraphs16.28812.210 3.548
listComplexComponents0.1130.1010.027
listInstances0.1840.2460.055
listInteractionComponents0.2070.2050.052
listPathwayComponents0.1760.1880.046
listPathways0.0490.0710.016
pathway2AdjacancyMatrix8.6766.5922.019
pathway2Geneset3.8793.2801.013
pathway2Graph6.7464.8441.394
pathway2RegulatoryGraph9.5177.8552.203
plotRegulatoryGraph10.130 6.808 2.322
print.biopax0.0500.0660.015
rBiopaxParser-package0.0010.0020.000
readBiopax0.0010.0020.000
removeNodes9.5007.5062.173
selectInstances0.0830.0870.029
splitComplex0.2650.3070.075
uniteGraphs16.18310.318 3.784
writeBiopax0.0020.0010.003