############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CAFE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CAFE_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CAFE.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 'CAFE/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CAFE' 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 'CAFE' 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. * 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 ... WARNING '::' or ':::' import not declared from: 'BiocManager' 'loadNamespace' or 'requireNamespace' call not declared from: 'BiocManager' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Armchisqr: no visible global function definition for 'chisq.test' ArmfisherExact: no visible global function definition for 'fisher.test' ProcessCels: no visible global function definition for 'install.packages' ProcessCels: no visible global function definition for 'download.file' ProcessCels: no visible global function definition for 'read.table' ProcessCels: no visible global function definition for 'txtProgressBar' ProcessCels: no visible global function definition for 'setTxtProgressBar' ProcessCels: no visible global function definition for 'na.omit' allBandsOnChrom: no visible global function definition for 'fisher.test' allBandsOnChromChi: no visible global function definition for 'chisq.test' armStats: no visible global function definition for 'p.adjust' bandStats: no visible global function definition for 'p.adjust' chisqr: no visible global function definition for 'chisq.test' chromosomeStats: no visible global function definition for 'p.adjust' discontPlot: no visible global function definition for 'png' discontPlot: no visible global function definition for 'dev.off' discontPlot: no visible global function definition for 'data' facetPlot: no visible global function definition for 'png' facetPlot: no visible global function definition for 'dev.off' facetPlot: no visible global function definition for 'na.omit' fisher.method: no visible global function definition for 'pchisq' fisherExact: no visible global function definition for 'fisher.test' makelevels: no visible global function definition for 'na.omit' rawPlot: no visible global function definition for 'png' rawPlot: no visible global function definition for 'dev.off' rawPlot: no visible global function definition for 'data' slidPlot: no visible global function definition for 'png' slidPlot: no visible global function definition for 'dev.off' slidPlot: no visible global function definition for 'data' Undefined global functions or variables: chisq.test data dev.off download.file fisher.test install.packages na.omit p.adjust pchisq png read.table setTxtProgressBar txtProgressBar Consider adding importFrom("grDevices", "dev.off", "png") importFrom("stats", "chisq.test", "fisher.test", "na.omit", "p.adjust", "pchisq") importFrom("utils", "data", "download.file", "install.packages", "read.table", "setTxtProgressBar", "txtProgressBar") 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 ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... Running 'runTests.R' 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: 1 WARNING, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CAFE.Rcheck/00check.log' for details.