############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellscape.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellscape_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/cellscape.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-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 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cellscape/DESCRIPTION’ ... OK * this is package ‘cellscape’ version ‘1.24.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘cellscape’ 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 * 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: ‘plyr’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE cellscape: no visible global function definition for ‘setNames’ cellscape: no visible global function definition for ‘melt’ cellscape: no visible global function definition for ‘na.omit’ cellscape: no visible global function definition for ‘combn’ cellscape: no visible binding for global variable ‘site’ cellscape: no visible binding for global variable ‘genotype’ cellscape: no visible binding for global variable ‘VAF’ cellscape: no visible global function definition for ‘n’ cellscape: no visible binding for global variable ‘n_gt’ cellscape: no visible binding for global variable ‘n’ cellscape: no visible binding for global variable ‘timepoint’ cellscape: no visible binding for global variable ‘single_cell_id’ getCNVHeatmapForEachSC: no visible binding for global variable ‘single_cell_id’ getCNVHeatmapForEachSC: no visible binding for global variable ‘px’ getCNVHeatmapForEachSC: no visible binding for global variable ‘px_width’ getCNVHeatmapForEachSC: no visible binding for global variable ‘chr’ getCNVHeatmapForEachSC: no visible binding for global variable ‘chrom_index’ getCNVHeatmapForEachSC: no visible binding for global variable ‘copy_number’ getCNVHeatmapForEachSC: no visible binding for global variable ‘sc_id’ getCNVHeatmapForEachSC: no visible binding for global variable ‘mode_cnv’ getCNVHeatmapForEachSC: no visible binding for global variable ‘cumsum_values’ getMutOrder: no visible global function definition for ‘dist’ getMutOrder: no visible global function definition for ‘hclust’ getMutOrder: no visible binding for global variable ‘site’ getMutOrder: no visible binding for global variable ‘VAF’ getMutOrder: no visible global function definition for ‘lm’ getMutOrder: no visible binding for global variable ‘na.omit’ getMutOrder: no visible global function definition for ‘coef’ getMutationsData: no visible binding for global variable ‘show_warnings’ getTargetedHeatmapForEachSC: no visible binding for global variable ‘single_cell_id’ getTargetedHeatmapForEachSC: no visible binding for global variable ‘chr’ getTargetedHeatmapForEachSC: no visible binding for global variable ‘coord’ Undefined global functions or variables: VAF chr chrom_index coef combn coord copy_number cumsum_values dist genotype hclust lm melt mode_cnv n n_gt na.omit px px_width sc_id setNames show_warnings single_cell_id site timepoint Consider adding importFrom("stats", "coef", "dist", "hclust", "lm", "na.omit", "setNames") importFrom("utils", "combn") 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 Duplicated \argument entries in documentation object 'dfs_tree': ‘chrom_bounds’ ‘ncols’ ‘chrom_bounds’ ‘cnv_data’ ‘chrom_bounds’ ‘n_bp_per_pixel’ ‘mut_data’ ‘width’ ‘height’ ‘mutations’ ‘height’ ‘width’ ‘clonal_prev’ ‘tree_edges’ ‘alpha’ ‘clonal_prev’ ‘tree_edges’ ‘genotype_position’ ‘clone_colours’ ‘perturbations’ ‘mutations’ ‘tree_edges’ ‘clonal_prev’ ‘clonal_prev’ ‘tree_edges’ ‘clone_colours’ ‘mutations’ 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 files in ‘vignettes’ ... OK * checking examples ... 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 ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/cellscape.Rcheck/00check.log’ for details.