Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2021-10-15 15:06:49 -0400 (Fri, 15 Oct 2021).

CHECK results for rBiopaxParser on machv2

To the developers/maintainers of the rBiopaxParser package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rBiopaxParser.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1509/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rBiopaxParser 2.32.0  (landing page)
Frank Kramer
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/rBiopaxParser
git_branch: RELEASE_3_13
git_last_commit: ed5cf40
git_last_commit_date: 2021-05-19 11:57:28 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: rBiopaxParser
Version: 2.32.0
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_2.32.0.tar.gz
StartedAt: 2021-10-14 22:52:42 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 22:53:52 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 70.1 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_2.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/rBiopaxParser.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.32.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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’
  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’
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
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 -- Thu Oct 14 22:53:42 2021 
*********************************************** 
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 
  0.730   0.094   0.802 

Example timings

rBiopaxParser.Rcheck/rBiopaxParser-Ex.timings

nameusersystemelapsed
addBiochemicalReaction0.0310.0020.033
addBiopaxInstance0.0050.0000.005
addBiopaxInstances0.0260.0030.030
addControl0.0210.0010.022
addPathway0.0240.0010.026
addPathwayComponents0.0330.0010.035
addPhysicalEntity0.0080.0000.009
addPhysicalEntityParticipant0.0210.0010.023
addPropertiesToBiopaxInstance0.0190.0010.021
biopax0.0220.0050.028
calcGraphOverlap3.1110.0823.199
colorGraphNodes1.7440.0261.772
combineNodes0.0030.0010.004
createBiopax0.0010.0000.001
diffGraphs2.5060.0302.538
downloadBiopaxData0.0000.0000.001
getClassProperties0.0010.0000.002
getInstanceClass0.0090.0020.010
getInstanceProperty0.0120.0020.013
getReferencedIDs0.0370.0020.039
getReferencingIDs0.0320.0020.034
getSubClasses0.0000.0000.001
getSuperClasses0.0000.0000.001
getXrefAnnotations0.1810.0030.185
hasProperty0.0030.0010.005
intersectGraphs2.4870.0212.512
isOfClass0.0040.0010.005
layoutRegulatoryGraph1.4460.0141.478
listComplexComponents0.0250.0030.029
listInstances0.0360.0090.047
listInteractionComponents0.0260.0010.028
listPathwayComponents0.0240.0040.027
listPathways0.0130.0010.015
pathway2AdjacancyMatrix1.2180.0201.238
pathway2Geneset0.5880.0080.597
pathway2Graph1.0290.0191.058
pathway2RegulatoryGraph1.8210.0161.865
plotRegulatoryGraph1.5110.0161.531
print.biopax0.0110.0040.015
rBiopaxParser-package000
readBiopax0.0030.0010.005
removeInstance0.0060.0010.007
removeNodes1.6550.0161.672
removeProperties0.0070.0020.009
selectInstances0.0200.0060.026
splitComplex0.0480.0030.051
transitiveClosure1.4160.0191.437
transitiveReduction1.3920.0221.416
uniteGraphs2.8090.0402.851
writeBiopax0.0020.0010.003