Adrian Alexa
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/topGO |
| Branch: RELEASE_3_11 |
| Last Commit: 03af5a8 |
| Last Changed Date: 2020-04-27 14:14:44 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:59:48 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE topGO PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1816/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| topGO 2.40.0 Adrian Alexa
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: topGO |
| Version: 2.40.0 |
| 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_2.40.0.tar.gz |
| StartedAt: 2020-10-17 05:59:56 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:02:50 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 173.7 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_2.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/topGO.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.40.0’
* 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 8.179 0.503 8.688
* 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-3.11-bioc/meat/topGO.Rcheck/00check.log’
for details.
topGO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL topGO ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)
topGO.Rcheck/topGO-Ex.timings
| name | user | system | elapsed | |
| GOdata | 0.062 | 0.011 | 0.074 | |
| annFUN | 1.304 | 0.103 | 1.481 | |
| classicCount-class | 0.000 | 0.000 | 0.001 | |
| classicExpr-class | 0.003 | 0.001 | 0.003 | |
| classicScore-class | 0.004 | 0.001 | 0.004 | |
| dagFunctions | 0.001 | 0.000 | 0.000 | |
| diagnosticMethods | 0.417 | 0.014 | 0.433 | |
| elimExpr-class | 0.001 | 0.000 | 0.002 | |
| elimScore-class | 0.000 | 0.000 | 0.001 | |
| geneList | 0.004 | 0.003 | 0.007 | |
| getPvalues | 4.382 | 0.122 | 4.509 | |
| getSigGroups | 4.534 | 0.146 | 4.685 | |
| groupGOTerms | 0.429 | 0.001 | 0.430 | |
| inducedGraph | 0.065 | 0.003 | 0.068 | |
| parentChild-class | 0.002 | 0.001 | 0.003 | |
| printGraph-methods | 0 | 0 | 0 | |
| topGOdata-class | 8.179 | 0.503 | 8.688 | |
| topGOresult-class | 0.053 | 0.006 | 0.059 | |