############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:marray.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings marray_1.85.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/marray.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘marray/DESCRIPTION’ ... OK * this is package ‘marray’ version ‘1.85.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 for sufficient/correct file permissions ... OK * checking whether package ‘marray’ can be installed ... OK * checking installed package size ... INFO installed size is 5.1Mb sub-directories of 1Mb or more: swirldata 4.1Mb * 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 code 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 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 loading without being on the library search path ... 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 ... OK * 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 : : 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 : : no visible binding for global variable ‘loess’ maLoessLines : : no visible global function definition for ‘quantile’ maLoessLines : : no visible global function definition for ‘predict’ maLowessLines : : 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 : : 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 : : no visible global function definition for ‘tclvalue’ widget.marrayLayout : : 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 : : 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed maNormMain 6.24 0.008 6.25 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/marray.Rcheck/00check.log’ for details.