Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:20:25 -0400 (Wed, 15 Apr 2020).
Package 1235/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
pcaGoPromoter 1.30.0 Morten Hansen
| 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: pcaGoPromoter |
Version: 1.30.0 |
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcaGoPromoter.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings pcaGoPromoter_1.30.0.tar.gz |
StartedAt: 2020-04-15 05:23:10 -0400 (Wed, 15 Apr 2020) |
EndedAt: 2020-04-15 05:29:17 -0400 (Wed, 15 Apr 2020) |
EllapsedTime: 366.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pcaGoPromoter.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcaGoPromoter.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings pcaGoPromoter_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/pcaGoPromoter.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 'pcaGoPromoter/DESCRIPTION' ... OK * this is package 'pcaGoPromoter' version '1.30.0' * checking package namespace information ... OK * checking package dependencies ... OK * 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 'pcaGoPromoter' 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: 'GO.db' 'Rgraphviz' 'parallel' 'pcaGoPromoter.Hs.hg19' 'pcaGoPromoter.Mm.mm9' 'pcaGoPromoter.Rn.rn4' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: getRankedProbeIds.pca plot.GOtree plot.pca print.GOtree print.pca See section 'Registering S3 methods' in the 'Writing R Extensions' manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE dropVarNull: no visible global function definition for 'var' dropVarNull: no visible global function definition for 'na.omit' getMatricesWithHits: no visible global function definition for 'fisher.test' getMatricesWithHits: no visible global function definition for 'p.adjust' getSigGOTermsOnce: no visible global function definition for 'fisher.test' getSigGOTermsOnce : <anonymous>: no visible global function definition for 'binom.test' getSigGOTermsOnce: no visible global function definition for 'p.adjust' leaveOutFindPvalues : <anonymous>: no visible global function definition for 'median' makeGOtreeRgraphviz: no visible global function definition for 'new' makeGOtreeRgraphviz: no visible global function definition for 'rgb' makeGOtreeRgraphviz: no visible global function definition for 'addNode' makeGOtreeRgraphviz: no visible global function definition for 'addEdge' makeGOtreeRgraphviz: no visible global function definition for 'nodes' makeGOtreeRgraphviz: no visible global function definition for 'nodeRenderInfo<-' makeGOtreeRgraphviz: no visible global function definition for 'edgeRenderInfo<-' makeGOtreeRgraphviz: no visible global function definition for 'parRenderInfo<-' makeGOtreeRgraphviz: no visible global function definition for 'par' makeGOtreeRgraphviz: no visible global function definition for 'renderGraph' makeGOtreeRgraphviz: no visible global function definition for 'layoutGraph' makeGOtreeRgraphviz: no visible global function definition for 'legend' newSearchGOtreeForTerms: no visible binding for global variable 'GOBPANCESTOR' pca: no visible global function definition for 'annotation' pca: no visible global function definition for 'exprs' pca: no visible global function definition for 'var' pca: no visible global function definition for 'na.omit' pca: no visible global function definition for 'prcomp' pcaInfoPlot: no visible global function definition for 'plot' plot.pca: no visible global function definition for 'par' plot.pca: no visible global function definition for 'layout' plot.pca: no visible global function definition for 'var' plot.pca: no visible global function definition for 'plot' plot.pca: no visible global function definition for 'polygon' plot.pca: no visible global function definition for 'lines' plot.pca: no visible global function definition for 'points' plot.pca: no visible global function definition for 'abline' plot.pca: no visible global function definition for 'box' plot.pca: no visible global function definition for 'text' plot.pca: no visible global function definition for 'plot.new' plot.pca: no visible global function definition for 'legend' primo: no visible global function definition for 'data' primoData.getPromoters: no visible global function definition for 'readFASTA' primoHits: no visible global function definition for 'data' printAnnText: no visible global function definition for 'mtext' printAnnotation: no visible global function definition for 'mtext' Undefined global functions or variables: GOBPANCESTOR abline addEdge addNode annotation binom.test box data edgeRenderInfo<- exprs fisher.test layout layoutGraph legend lines median mtext na.omit new nodeRenderInfo<- nodes p.adjust par parRenderInfo<- plot plot.new points polygon prcomp readFASTA renderGraph rgb text var Consider adding importFrom("grDevices", "rgb") importFrom("graphics", "abline", "box", "layout", "legend", "lines", "mtext", "par", "plot", "plot.new", "points", "polygon", "text") importFrom("methods", "new") importFrom("stats", "binom.test", "fisher.test", "median", "na.omit", "p.adjust", "prcomp", "var") importFrom("utils", "data") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed GOtree 72.40 10.43 82.97 primo 21.36 1.81 34.53 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed GOtree 76.66 2.34 79.01 primo 26.04 0.71 26.78 * 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/pcaGoPromoter.Rcheck/00check.log' for details.
pcaGoPromoter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/pcaGoPromoter_1.30.0.tar.gz && rm -rf pcaGoPromoter.buildbin-libdir && mkdir pcaGoPromoter.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pcaGoPromoter.buildbin-libdir pcaGoPromoter_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL pcaGoPromoter_1.30.0.zip && rm pcaGoPromoter_1.30.0.tar.gz pcaGoPromoter_1.30.0.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 135k 100 135k 0 0 3177k 0 --:--:-- --:--:-- --:--:-- 3467k install for i386 * installing *source* package 'pcaGoPromoter' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'pcaGoPromoter' finding HTML links ... done GOtree html pca html pcaGoPromoter-package html primo html primoData html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'pcaGoPromoter' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'pcaGoPromoter' as pcaGoPromoter_1.30.0.zip * DONE (pcaGoPromoter) * installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library' package 'pcaGoPromoter' successfully unpacked and MD5 sums checked
pcaGoPromoter.Rcheck/examples_i386/pcaGoPromoter-Ex.timings
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pcaGoPromoter.Rcheck/examples_x64/pcaGoPromoter-Ex.timings
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