############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings DEGreport_1.38.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DEGreport.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘DEGreport/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DEGreport’ version ‘1.38.5’ * 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 ... 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 loading without being on the library search path ... 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 6.199 0.060 6.259 degPlot 5.608 0.036 5.645 degColors 5.151 0.191 5.343 degComps 5.199 0.031 5.231 degMB 4.950 0.080 5.031 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘DEGreport.Rmd’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/DEGreport.Rcheck/00check.log’ for details.