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) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:23:52 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (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 | ||||
|
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. |
| Package 2027/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| topGO 2.48.0 (landing page) Adrian Alexa
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| 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 |
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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.
topGO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
topGO.Rcheck/topGO-Ex.timings
| name | user | system | elapsed | |
| GOdata | 0.065 | 0.006 | 0.071 | |
| annFUN | 1.606 | 0.081 | 1.710 | |
| classicCount-class | 0 | 0 | 0 | |
| classicExpr-class | 0.002 | 0.001 | 0.002 | |
| classicScore-class | 0.004 | 0.000 | 0.004 | |
| dagFunctions | 0 | 0 | 0 | |
| diagnosticMethods | 0.887 | 0.012 | 0.901 | |
| elimExpr-class | 0.001 | 0.000 | 0.002 | |
| elimScore-class | 0 | 0 | 0 | |
| geneList | 0.004 | 0.003 | 0.007 | |
| getPvalues | 5.312 | 0.173 | 5.499 | |
| getSigGroups | 5.007 | 0.116 | 5.127 | |
| groupGOTerms | 0.439 | 0.002 | 0.442 | |
| inducedGraph | 0.066 | 0.003 | 0.070 | |
| parentChild-class | 0.001 | 0.001 | 0.002 | |
| printGraph-methods | 0 | 0 | 0 | |
| topGOdata-class | 8.187 | 0.365 | 8.566 | |
| topGOresult-class | 0.043 | 0.004 | 0.046 | |