############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:treekoR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings treekoR_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/treekoR.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘treekoR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘treekoR’ version ‘1.15.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘treekoR’ 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 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 addFreqBars: no visible binding for global variable ‘freq’ addFreqBars: no visible binding for global variable ‘xmax’ addFreqBars: no visible binding for global variable ‘y’ addFreqBars: no visible binding for global variable ‘xmin’ addFreqBars: no visible binding for global variable ‘ymin’ addFreqBars: no visible binding for global variable ‘ymax’ addFreqBars: no visible binding for global variable ‘x_label’ addFreqBars: no visible binding for global variable ‘freq_label’ addHeatMap: no visible binding for global variable ‘variable’ addHeatMap: no visible binding for global variable ‘value’ addHeatMap: no visible binding for global variable ‘y’ addHeatMap: no visible binding for global variable ‘label’ addHeatMap: no visible binding for global variable ‘.’ addHeatMap: no visible binding for global variable ‘x’ colourTree: no visible binding for global variable ‘stat_parent’ colourTree: no visible binding for global variable ‘x’ colourTree: no visible binding for global variable ‘y’ colourTree: no visible binding for global variable ‘stat_total’ colourTree: no visible binding for global variable ‘label’ getCellGMeans: no visible binding for global variable ‘cluster_id’ getCellGMeans: no visible binding for global variable ‘sample_id’ getCellProp: no visible binding for global variable ‘cluster_id’ getCellProp: no visible binding for global variable ‘sample_id’ getCellProp: no visible binding for global variable ‘.’ getClusterTree: no visible binding for global variable ‘cluster_id’ plotInteractiveHeatmap: no visible binding for global variable ‘label’ plotInteractiveHeatmap: no visible binding for global variable ‘node’ plotSigScatter: no visible binding for global variable ‘stat_total’ plotSigScatter: no visible binding for global variable ‘stat_parent’ plotSigScatter: no visible binding for global variable ‘isTip’ plotSigScatter: no visible binding for global variable ‘label’ runEdgeRTests: no visible binding for global variable ‘PValue’ runEdgeRTests: no visible binding for global variable ‘logFC’ runEdgeRTests: no visible binding for global variable ‘node’ runEdgeRTests: no visible binding for global variable ‘stat_parent’ runEdgeRTests: no visible binding for global variable ‘pval_parent’ runEdgeRTests: no visible binding for global variable ‘FDR_parent’ runEdgeRTests: no visible binding for global variable ‘PValue_total’ runEdgeRTests: no visible binding for global variable ‘logFC_total’ runEdgeRTests: no visible binding for global variable ‘stat_total’ runEdgeRTests: no visible binding for global variable ‘pval_total’ runEdgeRTests: no visible binding for global variable ‘FDR_total’ runGLMMTests: no visible binding for global variable ‘isTip’ runGLMMTests: no visible binding for global variable ‘node’ Undefined global functions or variables: . FDR_parent FDR_total PValue PValue_total cluster_id freq freq_label isTip label logFC logFC_total node pval_parent pval_total sample_id stat_parent stat_total value variable x x_label xmax xmin y ymax ymin * 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 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/treekoR.Rcheck/00check.log’ for details.