############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bgx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bgx_1.72.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/bgx.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bgx/DESCRIPTION’ ... OK * this is package ‘bgx’ version ‘1.72.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘bgx’ can be installed ... WARNING Found the following significant warnings: clang: warning: argument unused during compilation: '-mcpu=pentium2' [-Wunused-command-line-argument] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/bgx.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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 dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rcpp’ All declared Imports should be used. Packages in Depends field not imported from: ‘Biobase’ ‘affy’ 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 bgx: no visible global function definition for ‘geneNames’ bgx: no visible global function definition for ‘sampleNames’ bgx: no visible global function definition for ‘new’ bgx: no visible global function definition for ‘annotation’ bgx: no visible global function definition for ‘description’ bgx: no visible global function definition for ‘assayDataElementReplace’ loessNorm: no visible global function definition for ‘loess’ loessNorm: no visible global function definition for ‘predict’ plotDEDensity: no visible global function definition for ‘density’ plotDEDensity: no visible global function definition for ‘abline’ plotDEHistogram: no visible global function definition for ‘hist’ plotDEHistogram: no visible global function definition for ‘glm’ plotDEHistogram: no visible binding for global variable ‘poisson’ plotDEHistogram: no visible global function definition for ‘lines’ plotDEHistogram: no visible global function definition for ‘points’ plotDiffRank: no visible global function definition for ‘quantile’ plotDiffRank: no visible global function definition for ‘sd’ plotDiffRank: no visible global function definition for ‘segments’ plotDiffRank: no visible global function definition for ‘abline’ plotExpressionDensity: no visible global function definition for ‘density’ plotExpressionDensity: no visible global function definition for ‘lines’ plotExpressionDensity: no visible global function definition for ‘legend’ readSingle.bgx: no visible global function definition for ‘read.delim’ saveAffinityPlot.bgx: no visible global function definition for ‘pdf’ saveAffinityPlot.bgx: no visible global function definition for ‘par’ saveAffinityPlot.bgx: no visible global function definition for ‘dev.off’ setupVars.bgx : calcProbeAffCategories: no visible global function definition for ‘cdfName’ setupVars.bgx : calcProbeAffCategories: no visible global function definition for ‘median’ setupVars.bgx: no visible global function definition for ‘pData’ setupVars.bgx: no visible global function definition for ‘indexProbes’ standalone.bgx: no visible global function definition for ‘write.table’ standalone.bgx: no visible global function definition for ‘geneNames’ standalone.bgx: no visible global function definition for ‘sampleNames’ Undefined global functions or variables: abline annotation assayDataElementReplace cdfName density description dev.off geneNames glm hist indexProbes legend lines loess median new pData par pdf points poisson predict quantile read.delim sampleNames sd segments write.table Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "abline", "hist", "legend", "lines", "par", "points", "segments") importFrom("methods", "new") importFrom("stats", "density", "glm", "loess", "median", "poisson", "predict", "quantile", "sd") importFrom("utils", "read.delim", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE prepare_Rd: analysis.bgx.Rd:48-49: Dropping empty section \examples checkRd: (-1) bgx.Rd:9: Escaped LaTeX specials: \_ \_ checkRd: (-1) bgx.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) bgx.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) bgx.Rd:43: Lost braces in \itemize; meant \describe ? checkRd: (-1) bgx.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) bgx.Rd:45: Lost braces in \itemize; meant \describe ? prepare_Rd: mcmc.bgx.Rd:48-49: Dropping empty section \examples prepare_Rd: readOutput.bgx.Rd:23-24: Dropping empty section \examples prepare_Rd: saveAffinityPlot.bgx.Rd:18-19: Dropping empty section \details prepare_Rd: saveAffinityPlot.bgx.Rd:20-21: Dropping empty section \value prepare_Rd: saveAffinityPlot.bgx.Rd:26-27: Dropping empty section \examples prepare_Rd: setupVars.bgx.Rd:21-22: Dropping empty section \details prepare_Rd: setupVars.bgx.Rd:43-44: Dropping empty section \examples * 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 line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... NOTE Package has both ‘src/Makevars.in’ and ‘src/Makevars’. Installation with --no-configure' is unlikely to work. If you intended ‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’ otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a ‘cleanup’ script. * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed bgx 16.115 0.285 16.537 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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, 7 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/bgx.Rcheck/00check.log’ for details.