Package: topGO

Version: 2.34.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:topGO.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings topGO_2.34.0.tar.gz

StartedAt: 2019-04-16 03:10:24 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:12:32 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 128.0 seconds

RetCode: 0

Status:  OK

CheckDir: topGO.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:topGO.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings topGO_2.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/topGO.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 ... 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
topGOdata-class 6.907  0.291   7.264
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/topGO.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL topGO
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘topGO’ ...
** 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

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (topGO)

name	user	system	elapsed
GOdata	0.074	0.011	0.087
annFUN	1.047	0.090	1.170
classicCount-class	0	0	0
classicExpr-class	0.002	0.001	0.002
classicScore-class	0.003	0.000	0.004
dagFunctions	0	0	0
diagnosticMethods	0.349	0.011	0.362
elimExpr-class	0.000	0.000	0.001
elimScore-class	0	0	0
geneList	0.002	0.001	0.004
getPvalues	3.482	0.152	3.662
getSigGroups	3.565	0.124	3.718
groupGOTerms	0.329	0.002	0.331
inducedGraph	0.039	0.002	0.040
parentChild-class	0.001	0.000	0.002
printGraph-methods	0	0	0
topGOdata-class	6.907	0.291	7.264
topGOresult-class	0.048	0.003	0.052