Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:19:50 -0400 (Thu, 12 Apr 2018).
Package 32/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
AgiMicroRna 2.28.0 Pedro Lopez-Romero
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | ![]() |
Package: AgiMicroRna |
Version: 2.28.0 |
Command: rm -rf AgiMicroRna.buildbin-libdir AgiMicroRna.Rcheck && mkdir AgiMicroRna.buildbin-libdir AgiMicroRna.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AgiMicroRna.buildbin-libdir AgiMicroRna_2.28.0.tar.gz >AgiMicroRna.Rcheck\00install.out 2>&1 && cp AgiMicroRna.Rcheck\00install.out AgiMicroRna-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=AgiMicroRna.buildbin-libdir --install="check:AgiMicroRna-install.out" --force-multiarch --no-vignettes --timings AgiMicroRna_2.28.0.tar.gz |
StartedAt: 2018-04-11 22:08:54 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 22:17:08 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 494.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: AgiMicroRna.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf AgiMicroRna.buildbin-libdir AgiMicroRna.Rcheck && mkdir AgiMicroRna.buildbin-libdir AgiMicroRna.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AgiMicroRna.buildbin-libdir AgiMicroRna_2.28.0.tar.gz >AgiMicroRna.Rcheck\00install.out 2>&1 && cp AgiMicroRna.Rcheck\00install.out AgiMicroRna-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=AgiMicroRna.buildbin-libdir --install="check:AgiMicroRna-install.out" --force-multiarch --no-vignettes --timings AgiMicroRna_2.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/AgiMicroRna.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'AgiMicroRna/DESCRIPTION' ... OK * this is package 'AgiMicroRna' version '2.28.0' * 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 'AgiMicroRna' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Package listed in more than one of Depends, Imports, Suggests, Enhances: 'Biobase' A package should be listed in only one of these fields. * 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 ... NOTE Warning: no function found corresponding to methods exports from 'AgiMicroRna' for: 'show' A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. ** checking whether the namespace can be unloaded cleanly ... OK ** checking loading without being on the library search path ... 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 ... NOTE Warning: no function found corresponding to methods exports from 'AgiMicroRna' for: 'show' A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. ** checking whether the namespace can be unloaded cleanly ... OK ** checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls to packages already attached by Depends: 'affy' 'affycoretools' 'preprocessCore' Please remove these calls from your code. 'library' or 'require' calls in package code: 'codelink' 'gdata' 'geneplotter' 'gplots' 'gtools' 'marray' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: 'affy' 'affycoretools' 'limma' 'methods' 'preprocessCore' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function call to a different package: .Call("rma_c_complete_copy", ..., PACKAGE = "affy") See chapter 'System and foreign language interfaces' in the 'Writing R Extensions' manual. * checking R code for possible problems ... NOTE DEG.print.info: no visible global function definition for 'is' DEG.print.info: no visible global function definition for 'exprs' HeatMapMicroRna: no visible binding for global variable 'var' HeatMapMicroRna: no visible global function definition for 'rainbow' HeatMapMicroRna: no visible global function definition for 'maPalette' HeatMapMicroRna: no visible global function definition for 'heatmap.2' HeatMapMicroRna: no visible global function definition for 'title' MA.plot.miRNA: no visible global function definition for 'dev.new' MA.plot.miRNA: no visible global function definition for 'plot' MA.plot.miRNA: no visible global function definition for 'points' MA.plot.miRNA: no visible global function definition for 'fitted' MA.plot.miRNA: no visible global function definition for 'loess' MA.plot.miRNA: no visible global function definition for 'legend' MA.plot.miRNA: no visible global function definition for 'title' PCAplotMicroRna: no visible global function definition for 'is' PCAplotMicroRna: no visible global function definition for 'exprs' PCAplotMicroRna: no visible global function definition for 'na.omit' PCAplotMicroRna: no visible global function definition for 'exprs<-' PCAplotMicroRna: no visible global function definition for 'plotPCA' PCAplotMicroRna: no visible global function definition for 'dev.new' RleMicroRna: no visible binding for global variable 'median' RleMicroRna: no visible global function definition for 'par' RleMicroRna: no visible global function definition for 'plot' RleMicroRna: no visible global function definition for 'boxplot' RleMicroRna: no visible global function definition for 'points' RleMicroRna: no visible global function definition for 'lines' RleMicroRna: no visible global function definition for 'title' RleMicroRna: no visible global function definition for 'abline' basicLimma: no visible global function definition for 'is' basicLimma: no visible global function definition for 'exprs' basicLimma: no visible global function definition for 'lmFit' basicLimma: no visible global function definition for 'contrasts.fit' basicLimma: no visible global function definition for 'eBayes' boxplotMicroRna: no visible global function definition for 'par' boxplotMicroRna: no visible global function definition for 'plot' boxplotMicroRna: no visible global function definition for 'boxplot' boxplotMicroRna: no visible global function definition for 'points' boxplotMicroRna: no visible global function definition for 'lines' boxplotMicroRna: no visible global function definition for 'title' cv.array: no visible binding for global variable 'median' cvArray: no visible global function definition for 'is' esetMicroRna: no visible global function definition for 'is' esetMicroRna: no visible global function definition for 'new' esetMicroRna: no visible global function definition for 'dev.new' esetMicroRna: no visible global function definition for 'exprs' filter.IsGeneDetected: no visible global function definition for 'is' filter.control.miRNA: no visible global function definition for 'is' filter.wellaboveNEG.miRNA: no visible global function definition for 'is' filter.wellaboveNEG.miRNA: no visible binding for global variable 'sd' filterMicroRna: no visible global function definition for 'is' filterMicroRna: no visible global function definition for 'dev.new' getDecideTests: no visible global function definition for 'is' getDecideTests: no visible global function definition for 'decideTests' hierclusMicroRna: no visible binding for global variable 'var' hierclusMicroRna: no visible global function definition for 'dist' hierclusMicroRna: no visible global function definition for 'as.dist' hierclusMicroRna: no visible global function definition for 'cor' hierclusMicroRna: no visible global function definition for 'hclust' hierclusMicroRna: no visible global function definition for 'plot' hierclusMicroRna: no visible global function definition for 'title' mvaBASIC: no visible binding for global variable 'median' mvaBASIC: no visible global function definition for 'plot' mvaBASIC: no visible global function definition for 'title' mvaBASIC: no visible global function definition for 'abline' mvaMicroRna: no visible binding for global variable 'median' mvaMicroRna: no visible global function definition for 'plot' mvaMicroRna: no visible global function definition for 'points' mvaMicroRna: no visible global function definition for 'fitted' mvaMicroRna: no visible global function definition for 'loess' mvaMicroRna: no visible global function definition for 'title' mvaMicroRna: no visible global function definition for 'abline' mvaMicroRna: no visible global function definition for 'legend' plotDensityMicroRna: no visible global function definition for 'rainbow' plotDensityMicroRna: no visible global function definition for 'density' plotDensityMicroRna: no visible global function definition for 'plot' plotDensityMicroRna: no visible global function definition for 'lines' plotDensityMicroRna: no visible global function definition for 'title' plotDensityMicroRna: no visible global function definition for 'legend' pvalHistogram: no visible global function definition for 'p.adjust' pvalHistogram: no visible global function definition for 'hist' pvalHistogram: no visible global function definition for 'dev.new' qcPlots: no visible global function definition for 'is' qcPlots: no visible global function definition for 'dev.new' read.agiMicroRna: no visible global function definition for 'read.columns' read.agiMicroRna: no visible global function definition for 'new' readMicroRnaAFE: no visible global function definition for 'is' readTargets: no visible global function definition for 'read.table' rmaMicroRna: no visible global function definition for 'is' rmaMicroRna: no visible global function definition for 'rma.background.correct' rmaMicroRna: no visible global function definition for 'normalizeBetweenArrays' rmaMicroRna: no visible binding for global variable 'median' significantMicroRna: no visible global function definition for 'is' significantMicroRna: no visible global function definition for 'exprs' significantMicroRna: no visible global function definition for 'p.adjust' tgsMicroRna: no visible global function definition for 'is' tgsMicroRna: no visible global function definition for 'dev.new' tgsNormalization: no visible global function definition for 'is' tgsNormalization: no visible global function definition for 'dev.new' tgsNormalization: no visible global function definition for 'normalizeBetweenArrays' write.LIST.miRNA: no visible global function definition for 'is' write.LIST.miRNA: no visible global function definition for 'write.table' write.control.out.miRNA: no visible global function definition for 'is' write.control.out.miRNA: no visible global function definition for 'write.table' write.filt.out.miRNA: no visible global function definition for 'is' write.filt.out.miRNA: no visible global function definition for 'write.table' writeEset: no visible global function definition for 'is' writeEset: no visible global function definition for 'exprs' writeEset: no visible global function definition for 'featureNames' writeEset: no visible global function definition for 'write.table' show,uRNAList: no visible global function definition for 'slotNames' show,uRNAList: no visible global function definition for 'slot' Undefined global functions or variables: abline as.dist boxplot contrasts.fit cor decideTests density dev.new dist eBayes exprs exprs<- featureNames fitted hclust heatmap.2 hist is legend lines lmFit loess maPalette median na.omit new normalizeBetweenArrays p.adjust par plot plotPCA points rainbow read.columns read.table rma.background.correct sd slot slotNames title var write.table Consider adding importFrom("grDevices", "dev.new", "rainbow") importFrom("graphics", "abline", "boxplot", "hist", "legend", "lines", "par", "plot", "points", "title") importFrom("methods", "is", "new", "slot", "slotNames") importFrom("stats", "as.dist", "cor", "density", "dist", "fitted", "hclust", "loess", "median", "na.omit", "p.adjust", "sd", "var") importFrom("utils", "read.table", "write.table") 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed mvaMicroRna 14.75 0.26 15.02 rmaMicroRna 6.38 0.07 6.46 HeatMapMicroRna 1.20 0.03 8.14 significantMicroRna 0.79 0.07 6.04 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed mvaMicroRna 11.75 0.05 11.81 rmaMicroRna 5.97 0.03 6.00 * 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: 6 NOTEs See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/AgiMicroRna.Rcheck/00check.log' for details.
AgiMicroRna.Rcheck/00install.out
install for i386 * installing *source* package 'AgiMicroRna' ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'AgiMicroRna' finding HTML links ... done HeatMapMicroRna html PCAplotMicroRna html RleMicroRna html basicLimma html boxplotMicroRna html cvArray html dd.micro html ddPROC html dim.uRNAList html dimnames.uRNAList html esetMicroRna html filterMicroRna html getDecideTests html hierclusMicroRna html mvaBASIC html mvaMicroRna html plotDensityMicroRna html pvalHistogram html qcPlots html readMicroRnaAFE html readTargets html rmaMicroRna html significantMicroRna html summary.uRNAList html targets.micro html tgsMicroRna html tgsNormalization html uRNAList html writeEset html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'AgiMicroRna' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'AgiMicroRna' as AgiMicroRna_2.28.0.zip * DONE (AgiMicroRna) In R CMD INSTALL In R CMD INSTALL
AgiMicroRna.Rcheck/examples_i386/AgiMicroRna-Ex.timings
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AgiMicroRna.Rcheck/examples_x64/AgiMicroRna-Ex.timings
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