Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 |
Package 2152/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
topGO 2.59.0 (landing page) Adrian Alexa
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the topGO package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: topGO |
Version: 2.59.0 |
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_2.59.0.tar.gz |
StartedAt: 2024-12-23 21:49:27 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 21:50:20 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 53.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: topGO.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_2.59.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/topGO.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘topGO/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘topGO’ version ‘2.59.0’ * checking package namespace information ... OK * checking package dependencies ... INFO 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 code 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 whether startup messages can be suppressed ... NOTE groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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-3.21-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/4.5-arm64/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 | 0.015 | 0.002 | 0.016 | |
annFUN | 0.383 | 0.022 | 0.408 | |
classicCount-class | 0 | 0 | 0 | |
classicExpr-class | 0.001 | 0.000 | 0.000 | |
classicScore-class | 0.001 | 0.000 | 0.001 | |
dagFunctions | 0 | 0 | 0 | |
diagnosticMethods | 0.086 | 0.004 | 0.090 | |
elimExpr-class | 0 | 0 | 0 | |
elimScore-class | 0 | 0 | 0 | |
geneList | 0.001 | 0.001 | 0.002 | |
getPvalues | 1.684 | 0.031 | 1.718 | |
getSigGroups | 0.744 | 0.034 | 0.790 | |
groupGOTerms | 0.080 | 0.000 | 0.079 | |
inducedGraph | 0.013 | 0.001 | 0.014 | |
parentChild-class | 0.001 | 0.000 | 0.000 | |
printGraph-methods | 0.000 | 0.000 | 0.001 | |
topGOdata-class | 1.653 | 0.132 | 1.788 | |
topGOresult-class | 0.009 | 0.001 | 0.011 | |