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CHECK report for topGO on tokay1

This page was generated on 2019-04-13 11:20:08 -0400 (Sat, 13 Apr 2019).

Package 1573/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
topGO 2.34.0
Adrian Alexa
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/topGO
Branch: RELEASE_3_8
Last Commit: 44cb5ea
Last Changed Date: 2018-10-30 11:41:43 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
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: topGO
Version: 2.34.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:topGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings topGO_2.34.0.tar.gz
StartedAt: 2019-04-13 05:58:25 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 06:02:00 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 215.2 seconds
RetCode: 0
Status:  OK  
CheckDir: topGO.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:topGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings topGO_2.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/topGO.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 'topGO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'topGO' version '2.34.0'
* 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'
 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
Examples with CPU or elapsed time > 5s
                user system elapsed
topGOdata-class 7.12   0.19    7.32
* 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/topGO.Rcheck/00check.log'
for details.



Installation output

topGO.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/topGO_2.34.0.tar.gz && rm -rf topGO.buildbin-libdir && mkdir topGO.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=topGO.buildbin-libdir topGO_2.34.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL topGO_2.34.0.zip && rm topGO_2.34.0.tar.gz topGO_2.34.0.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  428k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  428k  100  428k    0     0  6508k      0 --:--:-- --:--:-- --:--:-- 6794k

install for i386

* installing *source* package 'topGO' ...
** 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  
    classicExpr-class                       html  
    classicScore-class                      html  
    dagFunctions                            html  
    diagnosticMethods                       html  
    elimCount-class                         html  
    elimExpr-class                          html  
    elimScore-class                         html  
    geneList                                html  
    getPvalues                              html  
    getSigGroups                            html  
    groupGOTerms                            html  
    groupStats-class                        html  
    inducedGraph                            html  
    parentChild-class                       html  
    printGraph-methods                      html  
    topGO-package                           html  
    topGOdata-class                         html  
    topGOresult-class                       html  
    weightCount-class                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
In R CMD INSTALL

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_2.34.0.zip
* DONE (topGO)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'topGO' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

topGO.Rcheck/examples_i386/topGO-Ex.timings

nameusersystemelapsed
GOdata0.060.000.06
annFUN1.110.111.76
classicCount-class000
classicExpr-class000
classicScore-class000
dagFunctions000
diagnosticMethods0.410.090.50
elimExpr-class000
elimScore-class000
geneList000
getPvalues3.150.093.25
getSigGroups2.600.032.63
groupGOTerms0.250.000.25
inducedGraph0.040.000.04
parentChild-class000
printGraph-methods000
topGOdata-class4.470.164.63
topGOresult-class0.030.020.05

topGO.Rcheck/examples_x64/topGO-Ex.timings

nameusersystemelapsed
GOdata0.060.000.07
annFUN0.780.040.81
classicCount-class000
classicExpr-class000
classicScore-class000
dagFunctions000
diagnosticMethods0.350.010.36
elimExpr-class0.010.000.01
elimScore-class000
geneList000
getPvalues3.850.063.93
getSigGroups4.460.054.50
groupGOTerms0.250.000.25
inducedGraph0.030.000.03
parentChild-class000
printGraph-methods000
topGOdata-class7.120.197.32
topGOresult-class0.060.010.07