Adrian Alexa
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/topGO |
| Branch: RELEASE_3_10 |
| Last Commit: cbe8856 |
| Last Changed Date: 2019-12-09 20:36:39 -0400 (Mon, 09 Dec 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:17:56 -0400 (Wed, 15 Apr 2020).
| Package 1738/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| topGO 2.38.1 Adrian Alexa
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: topGO |
| Version: 2.38.1 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:topGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings topGO_2.38.1.tar.gz |
| StartedAt: 2020-04-15 07:08:00 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 07:10:53 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 172.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: topGO.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:topGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings topGO_2.38.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/topGO.Rcheck' * using R version 3.6.3 (2020-02-29) * 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 '2.38.1' * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.10-bioc/meat/topGO.Rcheck/00check.log' for details.
topGO.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/topGO_2.38.1.tar.gz && rm -rf topGO.buildbin-libdir && mkdir topGO.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=topGO.buildbin-libdir topGO_2.38.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL topGO_2.38.1.zip && rm topGO_2.38.1.tar.gz topGO_2.38.1.zip
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install for i386
* 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
install for x64
* installing *source* package 'topGO' ...
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'topGO' as topGO_2.38.1.zip
* DONE (topGO)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'topGO' successfully unpacked and MD5 sums checked
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topGO.Rcheck/examples_i386/topGO-Ex.timings
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topGO.Rcheck/examples_x64/topGO-Ex.timings
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