Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:10 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the marray package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/marray.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1033/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
marray 1.70.0 (landing page) Yee Hwa (Jean) Yang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: marray |
Version: 1.70.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:marray.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings marray_1.70.0.tar.gz |
StartedAt: 2021-10-15 01:21:12 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 01:22:58 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 106.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: marray.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:marray.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings marray_1.70.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/marray.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'marray/DESCRIPTION' ... OK * this is package 'marray' version '1.70.0' * 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 'marray' can be installed ... OK * checking installed package size ... NOTE installed size is 7.5Mb sub-directories of 1Mb or more: swirldata 5.5Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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' call to 'tkWidgets' in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: 'limma' 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 ... NOTE Found the following apparent S3 methods exported but not registered: length.na log.na mean.na prod.na quantile.na scale.na sum.na 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 widget.marrayInfo : inputInfo: warning in assign(newname, newInfo, env = .GlobalEnv): partial argument match of 'env' to 'envir' widget.marrayLayout : inputLayout: warning in assign(newname, newLayout, env = .GlobalEnv): partial argument match of 'env' to 'envir' widget.marrayRaw : inputRaw: warning in assign(newname, newRaw, env = .GlobalEnv): partial argument match of 'env' to 'envir' maA,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument match of 'nr' to 'nrow' maA,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument match of 'nc' to 'ncol' maM,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument match of 'nr' to 'nrow' maM,marrayRaw: warning in matrix(nr = 0, nc = 0): partial argument match of 'nc' to 'ncol' addLines: no visible global function definition for 'loess.control' cor.na: no visible global function definition for 'cor' findID: no visible binding for global variable 'gnames' findID: no visible global function definition for 'phenoData' htmlPage: no visible binding for global variable 'Gnames' ma2D: no visible global function definition for 'loess.control' ma2D: no visible binding for global variable 'na.omit' ma2D: no visible global function definition for 'loess' ma2D: no visible global function definition for 'predict' maColorBar: no visible global function definition for 'heat.colors' maColorBar: no visible global function definition for 'axis' maColorBar: no visible global function definition for 'par' maColorBar: no visible global function definition for 'box' maCompNormA : <anonymous>: no visible global function definition for 'ecdf' maImage: no visible global function definition for 'rainbow' maImage: no visible global function definition for 'layout' maImage: no visible global function definition for 'par' maImage.func: no visible global function definition for 'heat.colors' maImage.func: no visible global function definition for 'axis' maImage.func: no visible global function definition for 'contour' maImage.func: no visible global function definition for 'box' maImage.func: no visible global function definition for 'abline' maLoess: no visible global function definition for 'loess.control' maLoess: no visible binding for global variable 'na.omit' maLoess: no visible global function definition for 'loess' maLoess: no visible global function definition for 'predict' maLoessLines: no visible global function definition for 'loess.control' maLoessLines : <anonymous>: no visible binding for global variable 'loess' maLoessLines : <anonymous>: no visible global function definition for 'quantile' maLoessLines : <anonymous>: no visible global function definition for 'predict' maLowessLines : <anonymous>: no visible global function definition for 'lowess' maMAD: no visible global function definition for 'mad' maMed: no visible global function definition for 'median' maPalette: no visible global function definition for 'col2rgb' maPalette: no visible global function definition for 'rgb' maPlot: no visible global function definition for 'loess.control' maPlot: no visible global function definition for 'abline' maTop: no visible global function definition for 'quantile' maTwoSamples: no visible global function definition for 'gpTools' quantile.na: no visible global function definition for 'quantile' read.Agilent: no visible binding for global variable 'read.table' read.Galfile: no visible binding for global variable 'read.table' read.marrayInfo: no visible global function definition for 'read.table' read.marrayRaw: no visible global function definition for 'read.table' scale.na: no visible global function definition for 'applyy' table2html: no visible global function definition for 'browseURL' var.na: no visible global function definition for 'var' widget.TwoSamples: no visible binding for global variable 'fileBrowser' widget.TwoSamples: no visible global function definition for 'widgetRender' widget.TwoSamples: no visible global function definition for 'values.Widget' widget.mapGeneInfo: no visible global function definition for 'widgetRender' widget.mapGeneInfo: no visible global function definition for 'values.Widget' widget.marrayInfo : inputInfo: no visible global function definition for 'tclvalue' widget.marrayInfo : fileBrow: no visible global function definition for 'tkdelete' widget.marrayInfo : fileBrow: no visible global function definition for 'fileBrowser' widget.marrayInfo : fileBrow: no visible global function definition for 'tkinsert' widget.marrayInfo: no visible global function definition for 'tktoplevel' widget.marrayInfo: no visible global function definition for 'tkwm.title' widget.marrayInfo: no visible global function definition for 'tkframe' widget.marrayInfo: no visible global function definition for 'tkpack' widget.marrayInfo: no visible global function definition for 'tklabel' widget.marrayInfo: no visible global function definition for 'tkentry' widget.marrayInfo: no visible global function definition for 'tkbutton' widget.marrayInfo: no visible global function definition for 'tkgrid' widget.marrayInfo: no visible global function definition for 'tkgrid.configure' widget.marrayInfo : <anonymous>: no visible global function definition for 'tkdestroy' widget.marrayLayout : inputLayout: no visible global function definition for 'tclvalue' widget.marrayLayout : listColnames: no visible global function definition for 'tktoplevel' widget.marrayLayout : listColnames: no visible global function definition for 'tkwm.title' widget.marrayLayout : listColnames: no visible global function definition for 'tkframe' widget.marrayLayout : listColnames: no visible global function definition for 'tkpack' widget.marrayLayout : listColnames: no visible global function definition for 'tklabel' widget.marrayLayout : listColnames: no visible global function definition for 'tkcheckbutton' widget.marrayLayout : listColnames : getResults: no visible global function definition for 'tclvalue' widget.marrayLayout : listColnames : getResults: no visible global function definition for 'tkdestroy' widget.marrayLayout : listColnames: no visible global function definition for 'tkbutton' widget.marrayLayout : fileBrow: no visible global function definition for 'tkdelete' widget.marrayLayout : fileBrow: no visible global function definition for 'fileBrowser' widget.marrayLayout : fileBrow: no visible global function definition for 'tkinsert' widget.marrayLayout: no visible global function definition for 'tktoplevel' widget.marrayLayout: no visible global function definition for 'tkwm.title' widget.marrayLayout: no visible global function definition for 'tkframe' widget.marrayLayout: no visible global function definition for 'tkpack' widget.marrayLayout: no visible global function definition for 'tklabel' widget.marrayLayout: no visible global function definition for 'tkentry' widget.marrayLayout: no visible global function definition for 'tkgrid' widget.marrayLayout: no visible global function definition for 'tkgrid.configure' widget.marrayLayout: no visible global function definition for 'tkconfigure' widget.marrayLayout: no visible global function definition for 'tkbutton' widget.marrayLayout : <anonymous>: no visible global function definition for 'tclvalue' widget.marrayLayout : <anonymous>: no visible global function definition for 'tkdestroy' widget.marrayRaw : inputRaw: no visible global function definition for 'tclvalue' widget.marrayRaw : filesClick: no visible global function definition for 'fileBrowser' widget.marrayRaw : browserToEntry: no visible global function definition for 'objectBrowser' widget.marrayRaw : browserToEntry: no visible global function definition for 'tkdelete' widget.marrayRaw : browserToEntry: no visible global function definition for 'tkinsert' widget.marrayRaw: no visible global function definition for 'tktoplevel' widget.marrayRaw: no visible global function definition for 'tkwm.title' widget.marrayRaw: no visible global function definition for 'tkframe' widget.marrayRaw: no visible global function definition for 'tkpack' widget.marrayRaw: no visible global function definition for 'tkbutton' widget.marrayRaw: no visible global function definition for 'tklabel' widget.marrayRaw: no visible global function definition for 'tkentry' widget.marrayRaw: no visible global function definition for 'tkgrid' widget.marrayRaw: no visible global function definition for 'tkgrid.configure' widget.marrayRaw : <anonymous>: no visible global function definition for 'tkdestroy' write.list: no visible global function definition for 'write.table' write.marray: no visible global function definition for 'write.table' write.xls: no visible binding for global variable 'write.table' show,ShowLargeObject: no visible global function definition for 'printHead' Undefined global functions or variables: Gnames abline applyy axis box browseURL col2rgb contour cor ecdf fileBrowser gnames gpTools heat.colors layout loess loess.control lowess mad median na.omit objectBrowser par phenoData predict printHead quantile rainbow read.table rgb tclvalue tkbutton tkcheckbutton tkconfigure tkdelete tkdestroy tkentry tkframe tkgrid tkgrid.configure tkinsert tklabel tkpack tktoplevel tkwm.title values.Widget var widgetRender write.table Consider adding importFrom("grDevices", "col2rgb", "heat.colors", "rainbow", "rgb") importFrom("graphics", "abline", "axis", "box", "contour", "layout", "par") importFrom("stats", "cor", "ecdf", "loess", "loess.control", "lowess", "mad", "median", "na.omit", "predict", "quantile", "var") importFrom("utils", "browseURL", "read.table", "write.table") to your NAMESPACE file. * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed maNormMain 7.36 0.02 7.37 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed maNormMain 6.7 0 6.7 * 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: 5 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/marray.Rcheck/00check.log' for details.
marray.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/marray_1.70.0.tar.gz && rm -rf marray.buildbin-libdir && mkdir marray.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=marray.buildbin-libdir marray_1.70.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL marray_1.70.0.zip && rm marray_1.70.0.tar.gz marray_1.70.0.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 2825k 100 2825k 0 0 4809k 0 --:--:-- --:--:-- --:--:-- 4820k install for i386 * installing *source* package 'marray' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'marray' finding HTML links ... done boxplot html bracketMethods html cbind html checkTargetInfo html coerce-methods html dim html findID html htmlPage html image html ma2D html maBoxplot html maColorBar html maCompCoord html maCompInd html maCompLayout html maCompNormA html maCompPlate html maCoord2Ind html maDefaultPar html maDotsDefaults html maDotsMatch html maGenControls html maGeneTable html maImage html maImage.func html maInd2Coord html maLegendLines html maLoess html maLoessLines html maMAD html maMed html maNA html maNorm html maNorm2D html maNormLoess html maNormMAD html maNormMain html maNormMed html maNormScale html maNum2Logic html maPalette html maPlot html maPlot.func html maSelectGnames html maText html maTop html maTwoSamples html mapGeneInfo html marray-internal html marrayInfo-class html marrayLayout-class html marrayNorm-class html marrayRaw-class html opVersionID html plotMA html print-methods html read.Galfile html read.marrayInfo html read.marrayLayout html read.marrayRaw html rm.na html showLargeObject html stat.confband.text html stat.gnames html swirl html write.list html write.marray html write.xls 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 'marray' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'marray' as marray_1.70.0.zip * DONE (marray) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'marray' successfully unpacked and MD5 sums checked
marray.Rcheck/examples_i386/marray-Ex.timings
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marray.Rcheck/examples_x64/marray-Ex.timings
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