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BioC 3.4: CHECK report for topGO on moscato1

This page was generated on 2016-09-21 03:41:57 -0700 (Wed, 21 Sep 2016).

Package 1207/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
topGO 2.25.0
Adrian Alexa
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/topGO
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: topGO
Version: 2.25.0
Command: rm -rf topGO.buildbin-libdir topGO.Rcheck && mkdir topGO.buildbin-libdir topGO.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=topGO.buildbin-libdir topGO_2.25.0.tar.gz >topGO.Rcheck\00install.out 2>&1 && cp topGO.Rcheck\00install.out topGO-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=topGO.buildbin-libdir --install="check:topGO-install.out" --force-multiarch --no-vignettes --timings topGO_2.25.0.tar.gz
StartedAt: 2016-09-20 17:42:59 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 17:45:55 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 176.7 seconds
RetCode: 0
Status:  OK  
CheckDir: topGO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf topGO.buildbin-libdir topGO.Rcheck && mkdir topGO.buildbin-libdir topGO.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=topGO.buildbin-libdir topGO_2.25.0.tar.gz >topGO.Rcheck\00install.out 2>&1 && cp topGO.Rcheck\00install.out topGO-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=topGO.buildbin-libdir --install="check:topGO-install.out" --force-multiarch --no-vignettes --timings topGO_2.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/topGO.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '2.25.0'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
topGOdata-class 5.63    0.1    5.72
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
topGOdata-class 7.48   0.18    7.66
* 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
  'D:/biocbld/bbs-3.4-bioc/meat/topGO.Rcheck/00check.log'
for details.


topGO.Rcheck/00install.out:


install for i386

* installing *source* package 'topGO' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'print' from package 'base' in package 'topGO'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

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_2.25.0.zip
* DONE (topGO)

topGO.Rcheck/examples_i386/topGO-Ex.timings:

nameusersystemelapsed
GOdata0.040.010.07
annFUN1.680.083.17
classicCount-class000
classicExpr-class000
classicScore-class000
dagFunctions000
diagnosticMethods0.270.000.27
elimExpr-class000
elimScore-class000
geneList000
getPvalues3.250.063.31
getSigGroups3.040.053.09
groupGOTerms0.360.000.36
inducedGraph0.050.000.04
parentChild-class0.010.000.02
printGraph-methods000
topGOdata-class5.630.105.72
topGOresult-class0.030.000.03

topGO.Rcheck/examples_x64/topGO-Ex.timings:

nameusersystemelapsed
GOdata0.090.010.11
annFUN1.780.131.90
classicCount-class000
classicExpr-class000
classicScore-class000
dagFunctions000
diagnosticMethods0.340.020.36
elimExpr-class000
elimScore-class000
geneList000
getPvalues3.790.063.85
getSigGroups4.190.034.21
groupGOTerms0.460.010.49
inducedGraph0.070.000.06
parentChild-class000
printGraph-methods000
topGOdata-class7.480.187.66
topGOresult-class0.030.000.04