############################################################################## ############################################################################## ### ### 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_1.21.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DeMixT.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DeMixT/DESCRIPTION’ ... OK * this is package ‘DeMixT’ version ‘1.21.1’ * 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' 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-3.20-bioc/meat/DeMixT.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * 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 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 whether 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’ 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 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 ... WARNING Codoc mismatches from Rd file 'DeMixT_preprocessing.Rd': DeMixT_preprocessing Code: function(count.matrix, normal.id, tumor.id, selected.genes = 9000, cutoff_normal_range = c(0.1, 1), cutoff_tumor_range = c(0, 2.5), cutoff_step = 0.2) Docs: function(count.matrix, normal.id, tumor.id, cutoff_normal_range = c(0.1, 1), cutoff_tumor_range = c(0, 2.5), cutoff_step = 0.2) Argument names in code not in docs: selected.genes Mismatches in argument names: Position: 4 Code: selected.genes Docs: cutoff_normal_range Position: 5 Code: cutoff_normal_range Docs: cutoff_tumor_range Position: 6 Code: cutoff_tumor_range Docs: cutoff_step * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'detect_suspicious_sample_by_hierarchical_clustering_2comp.Rd' ‘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 19.577 0.012 19.591 * checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: ‘calibrate’ * 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: 3 WARNINGs, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/DeMixT.Rcheck/00check.log’ for details.