############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:systemPipeShiny.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings systemPipeShiny_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/systemPipeShiny.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘systemPipeShiny/DESCRIPTION’ ... OK * this is package ‘systemPipeShiny’ version ‘1.16.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘systemPipeShiny’ 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 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 loading without being on the library search path ... 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 core_topServer : module : : warning in eval(code, env = .GlobalEnv): partial argument match of 'env' to 'envir' .validateGuide: no visible binding for global variable ‘guide_ui’ .validateGuide: no visible binding for global variable ‘guide_content’ .validateGuide : : no visible binding for global variable ‘guide_content’ admin_infoServer : timeDiffString: no visible binding for global variable ‘time_start’ admin_infoServer : getCPU: no visible binding for global variable ‘V2’ appLoadingTime: no visible binding for global variable ‘time_start’ core_topServer : module : : no visible global function definition for ‘dev.off’ core_topServer : module : : no visible binding for '<<-' assignment to ‘.cur_plot’ core_topServer : module : : no visible global function definition for ‘dev.cur’ core_topServer : module : : no visible binding for global variable ‘.cur_plot’ core_topServer : module : : no visible global function definition for ‘recordPlot’ core_topServer : module : : no visible global function definition for ‘png’ core_topServer : module : : no visible binding for global variable ‘.rs_dir’ core_topServer : module : : no visible binding for global variable ‘.plot_num’ core_topServer : module : : no visible global function definition for ‘replayPlot’ core_topServer : module : : no visible binding for '<<-' assignment to ‘.plot_num’ findTabInfo: no visible binding for global variable ‘tab_info’ makeSort: no visible binding for global variable ‘session’ parseGuide: no visible binding for global variable ‘guide_ui’ parseGuide: no visible binding for global variable ‘guide_content’ removeSpsTab: no visible binding for global variable ‘type’ removeSpsTab: no visible binding for global variable ‘tab_file_name’ vs_rnaseq_degServer : module: no visible binding for global variable ‘trans_table’ vs_rnaseq_degServer : module: no visible binding for global variable ‘Sample’ vs_rnaseq_degServer : module: no visible binding for global variable ‘log2FoldChange’ vs_rnaseq_degServer : module: no visible binding for global variable ‘padj’ vs_rnaseq_degServer : module: no visible binding for global variable ‘cmp’ vs_rnaseq_degServer : module: no visible binding for global variable ‘direction’ vs_rnaseq_degServer : module: no visible binding for global variable ‘pass_filter’ vs_rnaseq_degServer : module : : no visible binding for global variable ‘pass_filter’ vs_rnaseq_degServer : module : : no visible binding for global variable ‘cmp’ vs_rnaseq_degServer : module: no visible binding for global variable ‘baseMean’ vs_rnaseq_degServer : module: no visible global function definition for ‘png’ vs_rnaseq_degServer : module: no visible global function definition for ‘dev.off’ vs_rnaseq_dendroServer : module: no visible global function definition for ‘hcl.colors’ vs_rnaseq_dendroServer : module: no visible global function definition for ‘title’ vs_rnaseq_glmServer : module: no visible binding for global variable ‘dim1’ vs_rnaseq_glmServer : module: no visible binding for global variable ‘dim2’ vs_rnaseq_heatmapServer : module: no visible global function definition for ‘png’ vs_rnaseq_heatmapServer : module: no visible global function definition for ‘dev.off’ vs_rnaseq_mdsServer : module: no visible binding for global variable ‘spsRNA_trans’ vs_rnaseq_mdsServer : module: no visible binding for global variable ‘X1’ vs_rnaseq_mdsServer : module: no visible binding for global variable ‘X2’ vs_rnaseq_normalServer : module: no visible binding for '<<-' assignment to ‘spsRNA_trans’ vs_rnaseq_normalServer : module: no visible binding for global variable ‘spsRNA_trans’ vs_rnaseq_normalServer : module: no visible binding for '<<-' assignment to ‘spsDEG’ vs_rnaseq_normalServer : module : : no visible binding for global variable ‘spsRNA_trans’ vs_rnaseq_pcaServer : module: no visible binding for global variable ‘spsRNA_trans’ vs_rnaseq_pcaServer : module: no visible binding for global variable ‘PC1’ vs_rnaseq_pcaServer : module: no visible binding for global variable ‘PC2’ vs_rnaseq_tsneServer : module: no visible binding for global variable ‘dim1’ vs_rnaseq_tsneServer : module: no visible binding for global variable ‘dim2’ wf_runServer : module : : : no visible global function definition for ‘png’ wf_runServer : module : : : no visible binding for global variable ‘.rs_dir’ wf_runServer : module : : : no visible binding for global variable ‘.plot_num’ wf_runServer : module : : : no visible global function definition for ‘dev.cur’ wf_runServer : module : : : no visible global function definition for ‘dev.new’ wf_runServer : module : : : no visible global function definition for ‘dev.control’ wf_runServer : module : : : no visible binding for '<<-' assignment to ‘.plot_num’ wf_runServer : module : : no visible binding for '<<-' assignment to ‘.rs_dir’ wf_runServer : module : : no visible binding for '<<-' assignment to ‘.plot_num’ wf_runServer : module : : no visible binding for '<<-' assignment to ‘.cur_plot’ wf_wfServer : module: no visible binding for global variable ‘input_code’ Undefined global functions or variables: .cur_plot .plot_num .rs_dir PC1 PC2 Sample V2 X1 X2 baseMean cmp dev.control dev.cur dev.new dev.off dim1 dim2 direction guide_content guide_ui hcl.colors input_code log2FoldChange padj pass_filter png recordPlot replayPlot session spsRNA_trans tab_file_name tab_info time_start title trans_table type Consider adding importFrom("grDevices", "dev.control", "dev.cur", "dev.new", "dev.off", "hcl.colors", "png", "recordPlot", "replayPlot") importFrom("graphics", "title") 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/systemPipeShiny.Rcheck/00check.log’ for details.