############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scMAGeCK.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scMAGeCK_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/scMAGeCK.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scMAGeCK/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scMAGeCK’ version ‘1.4.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt 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 ‘scMAGeCK’ 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. License components which are templates and need '+ file LICENSE': BSD_2_clause * 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 'library' or 'require' call to ‘utils’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE get_rank_tables: no visible global function definition for ‘getoriginalgseascore’ get_sc_signature: no visible binding for global variable ‘gs_c2_exps’ plot_gi_genes: no visible global function definition for ‘ggplot’ plot_gi_genes: no visible global function definition for ‘aes’ plot_gi_genes: no visible binding for global variable ‘Type’ plot_gi_genes: no visible binding for global variable ‘Expression’ plot_gi_genes: no visible global function definition for ‘geom_violin’ plot_gi_genes: no visible global function definition for ‘geom_point’ plot_gi_genes: no visible global function definition for ‘position_jitter’ plot_gi_genes: no visible global function definition for ‘ggtitle’ plot_gi_genes: no visible global function definition for ‘scale_y_log10’ plot_single_genes: no visible binding for global variable ‘targetobj’ plot_single_genes: no visible global function definition for ‘ggplot’ plot_single_genes: no visible global function definition for ‘aes’ plot_single_genes: no visible binding for global variable ‘Type’ plot_single_genes: no visible binding for global variable ‘Expression’ plot_single_genes: no visible global function definition for ‘geom_violin’ plot_single_genes: no visible global function definition for ‘geom_point’ plot_single_genes: no visible global function definition for ‘position_jitter’ plot_single_genes: no visible global function definition for ‘ggtitle’ plot_single_genes: no visible global function definition for ‘scale_y_log10’ Undefined global functions or variables: Expression Type aes geom_point geom_violin getoriginalgseascore ggplot ggtitle gs_c2_exps position_jitter scale_y_log10 targetobj * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed scMAGeCK-package 30.156 1.242 32.019 scMAGeCK_LR 27.416 0.934 28.366 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/scMAGeCK.Rcheck/00check.log’ for details.