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NOTES: (1) a maintainance reboot of lemming prevented these builds to complete on this machine (2) these are the last builds with R 2.6.0 (2007-06-03 r41797) on lamb1 and lemming, next builds will be with R 2.6.0 (2007-06-10 r41908) configured with --enable-strict-barrier |
Package 230/238 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
topGO1.3.0Adrian AlexaLast Changed Date: 2007-04-24 11:31:42 -0700 Last Changed Rev: 24217 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | OK | |
wellington | Linux (SUSE 9.2) | i686 | OK | [ OK ] | ||
churchill | Solaris 2.9 | sparc | OK | OK | ||
lemming | Windows Server 2003 (32-bit) | x64 | OK | skipped | skipped |
Package: topGO |
Version: 1.3.0 |
Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check topGO_1.3.0.tar.gz |
RetCode: 0 |
Time: 671.4 seconds |
Status: OK |
CheckDir: topGO.Rcheck |
Warnings: 0 |
* checking for working latex ... OK * using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/topGO.Rcheck' * using R version 2.6.0 Under development (unstable) (2007-06-03 r41797) * checking for file 'topGO/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'topGO' version '1.3.0' * checking package name space information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'topGO' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking top-level 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 name space can be loaded with stated dependencies ... OK * checking for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE getPvalues: no visible global function definition for 'mt.teststat' getPvalues: no visible global function definition for 'mt.rawp2adjp' 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 : buildDrawing : <anonymous>: no visible global function definition for 'getX' GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible global function definition for 'getY' 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 : plotSigChart: no visible binding for global variable 'rootCenter' GOplot.counts: no visible global function definition for 'getDefaultAttrs' GOplot.counts: no visible global function definition for 'getEdgeWeights' GOplot.counts: no visible global function definition for 'agopen' printDOT: no visible binding for global variable '.DOT.FILE.NAME' printDOT: no visible global function definition for 'getDefaultAttrs' printDOT: no visible global function definition for 'getEdgeWeights' printDOT: no visible global function definition for 'toDot' showSigOfNodes: no visible binding for global variable 'goDAG.r2l' * checking Rd files ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking data for non-ASCII characters ... OK * creating topGO-Ex.R ... OK * checking examples ... OK * checking package vignettes in 'inst/doc' ... OK * creating topGO-manual.tex ... OK * checking topGO-manual.tex ... OK
topGO.Rcheck/00install.out:
* Installing *source* package 'topGO' ... ** R ** data ** inst ** preparing package for lazy loading Loading required package: graph Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: GO Loading required package: annotate Loading required package: AnnotationDbi Loading required package: DBI Loading required package: RSQLite Loading required package: SparseM Package SparseM (0.72) loaded. To cite, see citation("SparseM") Creating a new generic function for "print" in "topGO" ** help Note: unmatched right brace in 'buildGOgraph.topology' on or after line 21 Note: unmatched right brace in 'classicScore-class' on or after line 69 >>> Building/Updating help pages for package 'topGO' Formats: text html latex example GOFisherTest text html latex GOKSTest text html latex GOdata text html latex example annFUN.hgu text html latex example buildGOgraph.topology text html latex buildLevels text html latex example classicCount-class text html latex example classicScore-class text html latex example elimCount-class text html latex example elimScore-class text html latex example getPvalues text html latex example getSigGroups text html latex example groupGOTerms text html latex example groupStats-class text html latex example inducedGraph text html latex example mapGenes2GOgraph text html latex example printGenes-methods text html latex printGraph-methods text html latex example reverseArch text html latex example topGO-package text html latex topGOdata-class text html latex example topGOresult-class text html latex weightCount-class text html latex example weightScore-class text html latex ** building package indices ... * DONE (topGO)