############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tkWidgets.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings tkWidgets_1.72.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/tkWidgets.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'tkWidgets/DESCRIPTION' ... OK * this is package 'tkWidgets' version '1.72.0' * 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 'tkWidgets' 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 to packages already attached by Depends: 'DynDoc' 'methods' 'tools' 'widgetTools' Please remove these calls from your code. 'library' or 'require' call to 'Biobase' in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: 'DynDoc' 'methods' 'tools' 'widgetTools' 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: print.Widget print.pWidget 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 File 'tkWidgets/R/zzz.R': .onLoad calls: require("methods", quietly = TRUE) require("widgetTools", quietly = TRUE) require("DynDoc", quietly = TRUE) require(Biobase) Package startup functions should not change the search path. See section 'Good practice' in '?.onAttach'. .getPackNames: warning in .packages(all = TRUE): partial argument match of 'all' to 'all.available' .popPackList: warning in .packages(all = TRUE): partial argument match of 'all' to 'all.available' assignArgs: warning in assign("argsList", value, env = env): partial argument match of 'env' to 'envir' assignLineData: warning in assign("lineData", lineData, env = env): partial argument match of 'env' to 'envir' eExplorer : export: warning in assign(i, temp[[i]], env = .GlobalEnv): partial argument match of 'env' to 'envir' fileWizard : view: warning in read.table(file = args$file, head = args$header, sep = args$sep, as.is = TRUE): partial argument match of 'head' to 'header' fileWizard : finish: warning in read.table(file = args$file, head = args$header, sep = args$sep, as.is = TRUE): partial argument match of 'head' to 'header' finish: warning in assign(dataName, dataFile, env = .GlobalEnv): partial argument match of 'env' to 'envir' getRowNames: warning in read.table(file.name, sep = sep, nrow = 3, header = header, skip = skip): partial argument match of 'nrow' to 'nrows' objNameToList: warning in get(objNames[i], env = env): partial argument match of 'env' to 'envir' objectBrowser : viewEnv: warning in ls(env = env, all = TRUE): partial argument match of 'env' to 'envir' objectBrowser : viewEnv: warning in ls(env = env, all = TRUE): partial argument match of 'all' to 'all.names' objectBrowser : doEnv: warning in ls(env = get(item)): partial argument match of 'env' to 'envir' objectBrowser : up: warning in ls(env = get(selectedObj)): partial argument match of 'env' to 'envir' viewVignette : export: warning in assign(i, temp[[i]], env = .GlobalEnv): partial argument match of 'env' to 'envir' fileWizard : brows: no visible global function definition for 'tkcmd' objNameToList: no visible global function definition for 'package.contents' vExplorer : write2VigList: no visible global function definition for 'pkgVignettes' Undefined global functions or variables: package.contents pkgVignettes tkcmd * 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 ** running examples for arch 'x64' ... OK * 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-3.14-bioc/meat/tkWidgets.Rcheck/00check.log' for details.