############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DeMixT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DeMixT_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/DeMixT.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DeMixT/DESCRIPTION’ ... OK * this is package ‘DeMixT’ version ‘1.18.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'parallel', 'Rcpp', 'SummarizedExperiment', 'knitr', 'KernSmooth', 'matrixcalc', 'rmarkdown', 'DSS', 'dendextend', 'psych', 'sva' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘DeMixT’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’ Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’ Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’ See ‘/Users/biocbuild/bbs-3.18-bioc/meat/DeMixT.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 ... 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 * 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 startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE DeMixT_GS: no visible global function definition for ‘qchisq’ DeMixT_preprocessing: no visible global function definition for ‘quantile_normalization’ detect_suspicious_sample_by_hierarchical_clustering_2comp : : no visible global function definition for ‘wilcox.test’ detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for ‘prcomp’ detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for ‘dist’ detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for ‘hclust’ detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for ‘par’ detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for ‘as.dendrogram’ detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible global function definition for ‘legend’ plot_dim: no visible global function definition for ‘prcomp’ plot_dim: no visible global function definition for ‘rainbow’ plot_dim: no visible global function definition for ‘abline’ plot_dim: no visible global function definition for ‘segments’ plot_dim: no visible global function definition for ‘points’ plot_dim: no visible global function definition for ‘legend’ plot_sd: no visible global function definition for ‘par’ scale_normalization_75th_percentile: no visible global function definition for ‘median’ simulate_2comp: no visible global function definition for ‘SimpleList’ simulate_2comp: no visible global function definition for ‘DataFrame’ simulate_3comp: no visible global function definition for ‘SimpleList’ simulate_3comp: no visible global function definition for ‘DataFrame’ Undefined global functions or variables: DataFrame SimpleList abline as.dendrogram dist hclust legend median par points prcomp qchisq quantile_normalization rainbow segments wilcox.test Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "abline", "legend", "par", "points", "segments") importFrom("stats", "as.dendrogram", "dist", "hclust", "median", "prcomp", "qchisq", "wilcox.test") 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 ... WARNING Undocumented arguments in documentation object 'detect_suspicious_sample_by_hierarchical_clustering_2comp' ‘labels’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed DeMixT_S2 118.804 0.535 127.336 * checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: ‘calibrate’ * 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: 2 WARNINGs, 4 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc/meat/DeMixT.Rcheck/00check.log’ for details.