Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:23:52 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for topGO on merida1


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? 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 2027/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
topGO 2.48.0  (landing page)
Adrian Alexa
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/topGO
git_branch: RELEASE_3_15
git_last_commit: a47f007
git_last_commit_date: 2022-04-26 10:59:24 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: topGO
Version: 2.48.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:topGO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings topGO_2.48.0.tar.gz
StartedAt: 2022-10-19 09:01:04 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 09:04:58 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 234.2 seconds
RetCode: 0
Status:   OK  
CheckDir: topGO.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:topGO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings topGO_2.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/topGO.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.48.0’
* 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 (user + system) or elapsed time > 5s
                 user system elapsed
topGOdata-class 8.187  0.365   8.566
getPvalues      5.312  0.173   5.499
getSigGroups    5.007  0.116   5.127
* 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-3.15-bioc/meat/topGO.Rcheck/00check.log’
for details.



Installation output

topGO.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL topGO
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘topGO’ ...
** 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

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
* DONE (topGO)

Tests output


Example timings

topGO.Rcheck/topGO-Ex.timings

nameusersystemelapsed
GOdata0.0650.0060.071
annFUN1.6060.0811.710
classicCount-class000
classicExpr-class0.0020.0010.002
classicScore-class0.0040.0000.004
dagFunctions000
diagnosticMethods0.8870.0120.901
elimExpr-class0.0010.0000.002
elimScore-class000
geneList0.0040.0030.007
getPvalues5.3120.1735.499
getSigGroups5.0070.1165.127
groupGOTerms0.4390.0020.442
inducedGraph0.0660.0030.070
parentChild-class0.0010.0010.002
printGraph-methods000
topGOdata-class8.1870.3658.566
topGOresult-class0.0430.0040.046