| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:08:53 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
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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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1980/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| topGO 2.47.0 (landing page) Adrian Alexa
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: topGO |
| Version: 2.47.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:topGO.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings topGO_2.47.0.tar.gz |
| StartedAt: 2022-03-17 20:30:03 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:32:05 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 122.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: topGO.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:topGO.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings topGO_2.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/topGO.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'topGO/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'topGO' version '2.47.0' * 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 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See 'D:/biocbuild/bbs-3.15-bioc/meat/topGO.Rcheck/00check.log' for details.
topGO.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL topGO
###
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* installing to library 'D:/biocbuild/bbs-3.15-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
converting help for package 'topGO'
finding HTML links ... done
GOTests html
GOdata html
annFUN html
classicCount-class html
classicExpr-class html
classicScore-class html
dagFunctions html
diagnosticMethods html
elimCount-class html
elimExpr-class html
elimScore-class html
geneList html
getPvalues html
getSigGroups html
groupGOTerms html
groupStats-class html
inducedGraph html
parentChild-class html
printGraph-methods html
topGO-package html
topGOdata-class html
topGOresult-class html
weightCount-class html
** 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)
Making 'packages.html' ... done
topGO.Rcheck/topGO-Ex.timings
| name | user | system | elapsed | |
| GOdata | 0.03 | 0.00 | 0.03 | |
| annFUN | 0.58 | 0.09 | 0.67 | |
| classicCount-class | 0 | 0 | 0 | |
| classicExpr-class | 0 | 0 | 0 | |
| classicScore-class | 0 | 0 | 0 | |
| dagFunctions | 0 | 0 | 0 | |
| diagnosticMethods | 0.51 | 0.00 | 0.51 | |
| elimExpr-class | 0 | 0 | 0 | |
| elimScore-class | 0 | 0 | 0 | |
| geneList | 0 | 0 | 0 | |
| getPvalues | 2.27 | 0.11 | 2.38 | |
| getSigGroups | 1.76 | 0.06 | 1.82 | |
| groupGOTerms | 0.17 | 0.00 | 0.17 | |
| inducedGraph | 0.02 | 0.00 | 0.02 | |
| parentChild-class | 0 | 0 | 0 | |
| printGraph-methods | 0 | 0 | 0 | |
| topGOdata-class | 3.08 | 0.16 | 3.24 | |
| topGOresult-class | 0.02 | 0.01 | 0.03 | |