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This page was generated on 2021-07-21 15:05:40 -0400 (Wed, 21 Jul 2021).

CHECK results for topGO on tokay2

To the developers/maintainers of the topGO package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/topGO.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 1937/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
topGO 2.44.0  (landing page)
Adrian Alexa
Snapshot Date: 2021-07-20 04:50:13 -0400 (Tue, 20 Jul 2021)
URL: https://git.bioconductor.org/packages/topGO
Branch: RELEASE_3_13
Last Commit: d907c12
Last Changed Date: 2021-05-19 11:38:47 -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: topGO
Version: 2.44.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:topGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings topGO_2.44.0.tar.gz
StartedAt: 2021-07-21 07:38:01 -0400 (Wed, 21 Jul 2021)
EndedAt: 2021-07-21 07:41:10 -0400 (Wed, 21 Jul 2021)
EllapsedTime: 189.0 seconds
RetCode: 0
Status:   OK  
CheckDir: topGO.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:topGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings topGO_2.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/topGO.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'topGO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'topGO' version '2.44.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'graph', 'Biobase', 'GO.db', 'AnnotationDbi',
  'SparseM'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'topGO' 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:
  'Rgraphviz' 'multtest'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing object imported by a ':::' call: 'globaltest:::globaltest'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GOplot: no visible global function definition for 'getDefaultAttrs'
GOplot: no visible global function definition for 'agopen'
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for 'getNodeCenter'
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for 'pieGlyph'
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for 'getX'
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for 'getY'
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for 'getNodeLW'
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for 'drawTxtLabel'
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
  global function definition for 'txtLabel'
GOplot.counts : plotSigChart: no visible global function definition for
  'AgNode'
GOplot.counts : plotSigChart : <anonymous>: no visible global function
  definition for 'name'
GOplot.counts : plotSigChart : <anonymous>: no visible global function
  definition for 'getNodeCenter'
GOplot.counts : plotSigChart: no visible global function definition for
  'getNodeXY'
GOplot.counts : plotSigChart: no visible global function definition for
  'getY'
GOplot.counts: no visible global function definition for
  'getDefaultAttrs'
GOplot.counts: no visible global function definition for 'agopen'
getPvalues: no visible global function definition for 'mt.teststat'
getPvalues: no visible global function definition for 'mt.rawp2adjp'
printDOT: no visible global function definition for 'getDefaultAttrs'
printDOT: no visible global function definition for 'toDot'
GOSumTest,classicScore: no visible binding for global variable
  '.PERMSUM.MAT'
GOSumTest,classicScore: no visible binding for global variable
  '.PERMSUM.LOOKUP'
initialize,classicExpr: no visible global function definition for
  'error'
scoresInTerm,topGOdata-missing: no visible global function definition
  for 'scoreInNode'
Undefined global functions or variables:
  .PERMSUM.LOOKUP .PERMSUM.MAT AgNode agopen drawTxtLabel error
  getDefaultAttrs getNodeCenter getNodeLW getNodeXY getX getY
  mt.rawp2adjp mt.teststat name pieGlyph scoreInNode toDot txtLabel
* 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 ... OK
* 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 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-3.13-bioc/meat/topGO.Rcheck/00check.log'
for details.



Installation output

topGO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/topGO_2.44.0.tar.gz && rm -rf topGO.buildbin-libdir && mkdir topGO.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=topGO.buildbin-libdir topGO_2.44.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL topGO_2.44.0.zip && rm topGO_2.44.0.tar.gz topGO_2.44.0.zip
###
##############################################################################
##############################################################################


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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  424k  100  424k    0     0  1571k      0 --:--:-- --:--:-- --:--:-- 1577k

install for i386

* installing *source* package 'topGO' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'topGO'
    finding HTML links ... done
    GOTests                                 html  
    GOdata                                  html  
    annFUN                                  html  
    classicCount-class                      html  
REDIRECT:topic	 sigMembers<- -> classicCount-class.html [ FAIL ]
REDIRECT:topic	 sigMembers<-,classicCount-method -> classicCount-class.html [ FAIL ]
    classicExpr-class                       html  
REDIRECT:topic	 pType<- -> classicExpr-class.html [ FAIL ]
REDIRECT:topic	 allMembers<-,classicExpr-method -> classicExpr-class.html [ FAIL ]
REDIRECT:topic	 pType<-,classicExpr-method -> classicExpr-class.html [ FAIL ]
    classicScore-class                      html  
REDIRECT:topic	 score<- -> classicScore-class.html [ FAIL ]
REDIRECT:topic	 score<-,classicScore-method -> classicScore-class.html [ FAIL ]
    dagFunctions                            html  
    diagnosticMethods                       html  
    elimCount-class                         html  
REDIRECT:topic	 cutOff<- -> elimCount-class.html [ FAIL ]
REDIRECT:topic	 cutOff<-,elimCount-method -> elimCount-class.html [ FAIL ]
REDIRECT:topic	 elim<- -> elimCount-class.html [ FAIL ]
REDIRECT:topic	 elim<-,elimCount-method -> elimCount-class.html [ FAIL ]
REDIRECT:topic	 elim<-,weight01Count-method -> elimCount-class.html [ FAIL ]
REDIRECT:topic	 depth<- -> elimCount-class.html [ FAIL ]
REDIRECT:topic	 depth<-,leaCount-method -> elimCount-class.html [ FAIL ]
REDIRECT:topic	 sigMembers<-,elimCount-method -> elimCount-class.html [ FAIL ]
    elimExpr-class                          html  
REDIRECT:topic	 depth<-,leaExpr-method -> elimExpr-class.html [ FAIL ]
REDIRECT:topic	 cutOff<-,elimExpr-method -> elimExpr-class.html [ FAIL ]
REDIRECT:topic	 elim<-,weight01Expr-method -> elimExpr-class.html [ FAIL ]
    elimScore-class                         html  
REDIRECT:topic	 cutOff<-,elimScore-method -> elimScore-class.html [ FAIL ]
REDIRECT:topic	 elim<-,elimScore-method -> elimScore-class.html [ FAIL ]
REDIRECT:topic	 depth<-,leaScore-method -> elimScore-class.html [ FAIL ]
REDIRECT:topic	 score<-,elimScore-method -> elimScore-class.html [ FAIL ]
REDIRECT:topic	 elim<-,weight01Score-method -> elimScore-class.html [ FAIL ]
    geneList                                html  
    getPvalues                              html  
    getSigGroups                            html  
    groupGOTerms                            html  
    groupStats-class                        html  
REDIRECT:topic	 allMembers<- -> groupStats-class.html [ FAIL ]
REDIRECT:topic	 members<- -> groupStats-class.html [ FAIL ]
REDIRECT:topic	 Name<- -> groupStats-class.html [ FAIL ]
REDIRECT:topic	 allMembers<-,groupStats-method -> groupStats-class.html [ FAIL ]
REDIRECT:topic	 members<-,groupStats-method -> groupStats-class.html [ FAIL ]
REDIRECT:topic	 Name<-,groupStats-method -> groupStats-class.html [ FAIL ]
    inducedGraph                            html  
    parentChild-class                       html  
REDIRECT:topic	 allMembers<-,parentChild-method -> parentChild-class.html [ FAIL ]
REDIRECT:topic	 sigMembers<-,parentChild-method -> parentChild-class.html [ FAIL ]
REDIRECT:topic	 allMembers<-,pC-method -> parentChild-class.html [ FAIL ]
REDIRECT:topic	 sigMembers<-,pC-method -> parentChild-class.html [ FAIL ]
    printGraph-methods                      html  
    topGO-package                           html  
    topGOdata-class                         html  
REDIRECT:topic	 description<- -> topGOdata-class.html [ FAIL ]
REDIRECT:topic	 feasible<- -> topGOdata-class.html [ FAIL ]
REDIRECT:topic	 geneSelectionFun<- -> topGOdata-class.html [ FAIL ]
REDIRECT:topic	 graph<- -> topGOdata-class.html [ FAIL ]
REDIRECT:topic	 ontology<- -> topGOdata-class.html [ FAIL ]
REDIRECT:topic	 updateTerm<- -> topGOdata-class.html [ FAIL ]
REDIRECT:topic	 description<-,topGOdata,ANY-method -> topGOdata-class.html [ FAIL ]
REDIRECT:topic	 feasible<-,topGOdata-method -> topGOdata-class.html [ FAIL ]
REDIRECT:topic	 geneSelectionFun<-,topGOdata-method -> topGOdata-class.html [ FAIL ]
REDIRECT:topic	 graph<-,topGOdata-method -> topGOdata-class.html [ FAIL ]
REDIRECT:topic	 ontology<-,topGOdata-method -> topGOdata-class.html [ FAIL ]
REDIRECT:topic	 updateTerm<-,topGOdata,character-method -> topGOdata-class.html [ FAIL ]
    topGOresult-class                       html  
REDIRECT:topic	 description<-,topGOresult,ANY-method -> topGOresult-class.html [ FAIL ]
REDIRECT:topic	 score<-,topGOresult-method -> topGOresult-class.html [ FAIL ]
REDIRECT:topic	 testName<- -> topGOresult-class.html [ FAIL ]
REDIRECT:topic	 testName<-,topGOresult-method -> topGOresult-class.html [ FAIL ]
REDIRECT:topic	 algorithm<- -> topGOresult-class.html [ FAIL ]
REDIRECT:topic	 algorithm<-,topGOresult-method -> topGOresult-class.html [ FAIL ]
REDIRECT:topic	 geneData<- -> topGOresult-class.html [ FAIL ]
REDIRECT:topic	 geneData<-,topGOresult-method -> topGOresult-class.html [ FAIL ]
    weightCount-class                       html  
REDIRECT:topic	 sigRatio<- -> weightCount-class.html [ FAIL ]
REDIRECT:topic	 Weights<- -> weightCount-class.html [ FAIL ]
REDIRECT:topic	 Weights<-,weightCount-method -> weightCount-class.html [ FAIL ]
REDIRECT:topic	 sigRatio<-,weightCount-method -> weightCount-class.html [ FAIL ]
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'topGO' ...
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'topGO' as topGO_2.44.0.zip
* DONE (topGO)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'topGO' successfully unpacked and MD5 sums checked

Tests output


Example timings

topGO.Rcheck/examples_i386/topGO-Ex.timings

nameusersystemelapsed
GOdata0.030.000.04
annFUN1.220.091.57
classicCount-class000
classicExpr-class000
classicScore-class000
dagFunctions000
diagnosticMethods0.290.020.30
elimExpr-class000
elimScore-class000
geneList000
getPvalues3.770.234.00
getSigGroups2.290.092.39
groupGOTerms0.220.000.22
inducedGraph0.030.000.03
parentChild-class000
printGraph-methods000
topGOdata-class4.330.224.66
topGOresult-class0.030.000.04

topGO.Rcheck/examples_x64/topGO-Ex.timings

nameusersystemelapsed
GOdata0.050.000.04
annFUN1.000.081.08
classicCount-class000
classicExpr-class0.020.000.01
classicScore-class000
dagFunctions000
diagnosticMethods0.310.000.32
elimExpr-class000
elimScore-class000
geneList000
getPvalues4.130.074.20
getSigGroups2.530.042.56
groupGOTerms0.250.000.25
inducedGraph0.030.000.03
parentChild-class000
printGraph-methods000
topGOdata-class4.400.144.55
topGOresult-class0.080.000.08