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CHECK report for rBiopaxParser on tokay1

This page was generated on 2019-04-13 11:22:38 -0400 (Sat, 13 Apr 2019).

Package 1255/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rBiopaxParser 2.22.0
Frank Kramer
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/rBiopaxParser
Branch: RELEASE_3_8
Last Commit: 789779b
Last Changed Date: 2018-10-30 11:41:50 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 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: 2.22.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rBiopaxParser.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings rBiopaxParser_2.22.0.tar.gz
StartedAt: 2019-04-13 04:53:05 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:55:27 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 141.6 seconds
RetCode: 0
Status:  OK  
CheckDir: rBiopaxParser.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rBiopaxParser.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings rBiopaxParser_2.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/rBiopaxParser.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rBiopaxParser/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rBiopaxParser' version '2.22.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/rBiopaxParser.Rcheck/00check.log'
for details.



Installation output

rBiopaxParser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/rBiopaxParser_2.22.0.tar.gz && rm -rf rBiopaxParser.buildbin-libdir && mkdir rBiopaxParser.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rBiopaxParser.buildbin-libdir rBiopaxParser_2.22.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL rBiopaxParser_2.22.0.zip && rm rBiopaxParser_2.22.0.tar.gz rBiopaxParser_2.22.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  334k  100  334k    0     0  8892k      0 --:--:-- --:--:-- --:--:-- 9544k

install for i386

* installing *source* package 'rBiopaxParser' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rBiopaxParser'
    finding HTML links ... done
    CLASS_INHERITANCE_BP2                   html  
    CLASS_INHERITANCE_BP3                   html  
    CLASS_PROPERTIES_BP2                    html  
    CLASS_PROPERTIES_BP3                    html  
    DATABASE_BIOPAX                         html  
    addBiochemicalReaction                  html  
    addBiopaxInstance                       html  
    addBiopaxInstances                      html  
    addControl                              html  
    addPathway                              html  
    addPathwayComponents                    html  
    addPhysicalEntity                       html  
    addPhysicalEntityParticipant            html  
    addPropertiesToBiopaxInstance           html  
    addhash                                 html  
    addns                                   html  
    biopax                                  html  
    calcGraphOverlap                        html  
    checkValidity                           html  
    colorGraphNodes                         html  
    combineNodes                            html  
    createBiopax                            html  
    diffGraphs                              html  
    downloadBiopaxData                      html  
    generateNewUniqueID                     html  
    getClassProperties                      html  
    getInstanceClass                        html  
    getInstanceProperty                     html  
    getNeighborhood                         html  
    getParticipants                         html  
    getReferencedIDs                        html  
    getReferencingIDs                       html  
    getSubClasses                           html  
    getSuperClasses                         html  
    getXrefAnnotations                      html  
    hasProperty                             html  
    internal_NrOfXMLNodes                   html  
    internal_XMLInstance2DF                 html  
    internal_checkArguments                 html  
    internal_generateXMLfromBiopax          html  
    internal_getBiopaxModelAsDataFrame      html  
    internal_propertyListToDF               html  
    internal_resolvePhysicalEntityParticipant
                                            html  
    intersectGraphs                         html  
    isOfClass                               html  
    isOfNamespace                           html  
    isURL                                   html  
    layoutRegulatoryGraph                   html  
    listComplexComponents                   html  
    listInstances                           html  
    listInteractionComponents               html  
    listPathwayComponents                   html  
    listPathways                            html  
    mergePathways                           html  
    pathway2AdjacancyMatrix                 html  
    pathway2Geneset                         html  
    pathway2Graph                           html  
    pathway2RegulatoryGraph                 html  
    plotRegulatoryGraph                     html  
    print.biopax                            html  
    rBiopaxParser-package                   html  
    readBiopax                              html  
    removeDisconnectedParts                 html  
    removeInstance                          html  
    removeNodes                             html  
    removeProperties                        html  
    selectInstances                         html  
    splitComplex                            html  
    striphash                               html  
    stripns                                 html  
    transitiveClosure                       html  
    transitiveReduction                     html  
    unfactorize                             html  
    uniteGraphs                             html  
    writeBiopax                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'rBiopaxParser' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rBiopaxParser' as rBiopaxParser_2.22.0.zip
* DONE (rBiopaxParser)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'rBiopaxParser' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

rBiopaxParser.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 -- Sat Apr 13 04:55:21 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 
   0.45    0.04    0.51 

rBiopaxParser.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 -- Sat Apr 13 04:55:22 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 
   0.45    0.07    0.51 

Example timings

rBiopaxParser.Rcheck/examples_i386/rBiopaxParser-Ex.timings

nameusersystemelapsed
addBiochemicalReaction0.080.010.05
addBiopaxInstance000
addBiopaxInstances0.020.020.03
addControl0.030.010.04
addPathway0.050.020.04
addPathwayComponents0.060.010.06
addPhysicalEntity000
addPhysicalEntityParticipant0.020.000.02
addPropertiesToBiopaxInstance0.010.000.02
biopax0.020.000.01
calcGraphOverlap2.930.472.73
colorGraphNodes1.720.281.59
combineNodes000
createBiopax000
diffGraphs2.490.542.54
downloadBiopaxData000
getClassProperties000
getInstanceClass0.010.000.02
getInstanceProperty0.020.000.01
getReferencedIDs0.050.000.05
getReferencingIDs0.030.000.03
getSubClasses000
getSuperClasses000
getXrefAnnotations0.280.010.22
intersectGraphs2.550.532.38
listComplexComponents0.000.020.02
listInstances0.030.000.03
listInteractionComponents0.030.000.03
listPathwayComponents0.020.010.03
listPathways0.010.000.02
pathway2AdjacancyMatrix1.690.251.39
pathway2Geneset0.940.140.79
pathway2Graph0.870.070.83
pathway2RegulatoryGraph1.580.221.41
plotRegulatoryGraph1.530.261.44
print.biopax000
rBiopaxParser-package000
readBiopax000
removeNodes1.550.221.49
selectInstances0.000.020.01
splitComplex0.030.040.06
uniteGraphs2.830.422.49
writeBiopax000

rBiopaxParser.Rcheck/examples_x64/rBiopaxParser-Ex.timings

nameusersystemelapsed
addBiochemicalReaction0.050.000.05
addBiopaxInstance000
addBiopaxInstances0.010.030.03
addControl0.030.010.05
addPathway0.030.000.03
addPathwayComponents0.050.020.06
addPhysicalEntity000
addPhysicalEntityParticipant0.030.000.04
addPropertiesToBiopaxInstance0.020.000.01
biopax0.000.010.02
calcGraphOverlap3.750.473.50
colorGraphNodes1.870.321.92
combineNodes000
createBiopax0.020.000.01
diffGraphs3.080.562.93
downloadBiopaxData000
getClassProperties000
getInstanceClass000
getInstanceProperty000
getReferencedIDs0.040.020.06
getReferencingIDs0.030.000.04
getSubClasses000
getSuperClasses000
getXrefAnnotations0.250.050.28
intersectGraphs2.790.502.70
listComplexComponents0.030.030.03
listInstances0.030.000.03
listInteractionComponents0.050.000.05
listPathwayComponents0.030.000.03
listPathways000
pathway2AdjacancyMatrix1.340.311.44
pathway2Geneset0.770.220.78
pathway2Graph1.000.160.92
pathway2RegulatoryGraph1.540.251.53
plotRegulatoryGraph1.600.351.55
print.biopax0.010.000.01
rBiopaxParser-package000
readBiopax000
removeNodes1.530.211.54
selectInstances000
splitComplex0.040.030.04
uniteGraphs2.560.552.47
writeBiopax000