############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DEGreport_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/DEGreport.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DEGreport/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DEGreport’ version ‘1.40.0’ * package encoding: UTF-8 * 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: .travis.yml 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 ‘DEGreport’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .benckmark_cutoff: no visible binding for global variable ‘cutoff’ .benckmark_cutoff: no visible binding for global variable ‘cluster’ .convertIDs: no visible global function definition for ‘keys’ .correct_fdr: no visible global function definition for ‘fdrtool’ .generate_scatter_plot: no visible binding for global variable ‘compare’ .generate_scatter_plot: no visible binding for global variable ‘covar’ .get_counts: no visible global function definition for ‘counts’ .model: no visible global function definition for ‘lm’ .plot_raw: no visible binding for global variable ‘.x’ .plot_shrunken: no visible binding for global variable ‘.x’ .process: no visible binding for global variable ‘genes’ .process: no visible binding for global variable ‘cluster’ .reduce : : : no visible global function definition for ‘boxplot’ .reduce_covariates : : no visible binding for global variable ‘fdr’ .reduce_covariates : : no visible binding for global variable ‘compare’ .reduce_covariates : : no visible binding for global variable ‘r’ .reduce_covariates : : no visible binding for global variable ‘p.value’ .run_cluster_profiler: no visible global function definition for ‘enrichGO’ .run_cluster_profiler: no visible global function definition for ‘simplify’ .select_concensus_genes: no visible global function definition for ‘desc’ .select_concensus_genes: no visible binding for global variable ‘score’ .select_concensus_genes: no visible binding for global variable ‘k’ .select_concensus_genes: no visible binding for global variable ‘itemConsensus’ .summarise_res: no visible global function definition for ‘matches’ .summarise_res: no visible binding for global variable ‘comparison’ .summarise_res: no visible binding for global variable ‘gene’ .summarise_res: no visible binding for global variable ‘value_fdr’ .summarise_res: no visible binding for global variable ‘value_fc’ .table_w_fc: no visible binding for global variable ‘comp’ .table_w_fc: no visible binding for global variable ‘log2FoldChange’ degCheckFactors: no visible binding for global variable ‘ratios’ degCorCov: no visible binding for global variable ‘compare’ degCovariates: no visible binding for global variable ‘x’ degCovariates: no visible binding for global variable ‘y’ degCovariates: no visible binding for global variable ‘xend’ degCovariates: no visible binding for global variable ‘yend’ degCovariates: no visible binding for global variable ‘pvalue’ degMA: no visible binding for global variable ‘base_mean’ degMA: no visible binding for global variable ‘log2fc’ degMV: no visible binding for global variable ‘min_median’ degMV: no visible binding for global variable ‘max_sd’ degPatterns: no visible global function definition for ‘rowMedians’ degPatterns: no visible binding for global variable ‘genes’ degPatterns: no visible global function definition for ‘color_branches’ degPatterns: no visible global function definition for ‘set’ degPlotCluster: no visible binding for global variable ‘genes’ degPlotCluster: no visible binding for global variable ‘cluster’ degPlotWide : : no visible binding for global variable ‘count’ significants,TopTags: no visible binding for global variable ‘FDR’ significants,TopTags: no visible binding for global variable ‘logFC’ significants,list : : no visible global function definition for ‘matches’ Undefined global functions or variables: .x FDR base_mean boxplot cluster color_branches comp compare comparison count counts covar cutoff desc enrichGO fdr fdrtool gene genes itemConsensus k keys lm log2FoldChange log2fc logFC matches max_sd min_median p.value pvalue r ratios rowMedians score set simplify value_fc value_fdr x xend y yend Consider adding importFrom("graphics", "boxplot") importFrom("stats", "lm") 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 ... OK * 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed degResults 8.949 0.126 13.508 degColors 8.520 0.137 12.159 degPlot 8.132 0.115 12.680 degQC 6.631 0.096 10.227 degComps 6.538 0.090 9.406 significants 6.223 0.083 8.957 degSummary 6.042 0.097 9.228 DEGSet 5.891 0.192 8.541 degVar 5.907 0.088 9.135 degVB 5.887 0.089 9.013 degMB 5.640 0.093 8.051 degPlotWide 5.492 0.079 8.325 degMV 4.771 0.078 7.011 degMean 4.539 0.052 6.536 degMA 3.590 0.058 5.098 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/DEGreport.Rcheck/00check.log’ for details.