Back to Multiple platform build/check report for BioC 3.10 |
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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
############################################################################## ############################################################################## ### ### Running command: ### ### 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 ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 428k 100 428k 0 0 10.3M 0 --:--:-- --:--:-- --:--:-- 11.3M 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
topGO.Rcheck/examples_i386/topGO-Ex.timings
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topGO.Rcheck/examples_x64/topGO-Ex.timings
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