Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-02-04 11:05:16 -0500 (Sat, 04 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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 nebbiolo1


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 2051/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
topGO 2.51.0  (landing page)
Adrian Alexa
Snapshot Date: 2023-02-03 14:00:22 -0500 (Fri, 03 Feb 2023)
git_url: https://git.bioconductor.org/packages/topGO
git_branch: master
git_last_commit: 074dd0d
git_last_commit_date: 2022-11-01 11:03:20 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    NA  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: topGO
Version: 2.51.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:topGO.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings topGO_2.51.0.tar.gz
StartedAt: 2023-02-04 00:31:37 -0500 (Sat, 04 Feb 2023)
EndedAt: 2023-02-04 00:37:39 -0500 (Sat, 04 Feb 2023)
EllapsedTime: 361.5 seconds
RetCode: 0
Status:   OK  
CheckDir: topGO.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:topGO.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings topGO_2.51.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/topGO.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘topGO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘topGO’ version ‘2.51.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘topGO.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/topGO.Rcheck/00check.log’
for details.



Installation output

topGO.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL topGO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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
GOdata0.0310.0040.035
annFUN1.1570.0721.234
classicCount-class0.0010.0000.000
classicExpr-class0.0020.0000.002
classicScore-class0.0020.0000.003
dagFunctions000
diagnosticMethods0.2250.0080.233
elimExpr-class0.0010.0000.001
elimScore-class000
geneList0.0020.0000.002
getPvalues3.0770.2163.294
getSigGroups2.5740.0802.654
groupGOTerms0.2950.0000.295
inducedGraph0.0320.0000.032
parentChild-class0.0010.0000.001
printGraph-methods000
topGOdata-class4.0600.1964.256
topGOresult-class0.0220.0030.024