############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scBubbletree.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scBubbletree_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/scBubbletree.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 ‘scBubbletree/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scBubbletree’ version ‘1.8.0’ * 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 ‘scBubbletree’ 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 dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘base’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE compare_bubbletrees: no visible binding for global variable ‘isTip’ compare_bubbletrees: no visible binding for global variable ‘Cells’ compare_bubbletrees: no visible binding for global variable ‘lab_short’ compare_bubbletrees: no visible binding for global variable ‘label’ compare_bubbletrees: no visible binding for global variable ‘JD’ compare_bubbletrees: no visible binding for global variable ‘intersection’ get_dendrogram: no visible binding for global variable ‘isTip’ get_dendrogram: no visible binding for global variable ‘Cells’ get_dendrogram: no visible binding for global variable ‘label’ get_dendrogram: no visible binding for global variable ‘lab_short’ get_dendrogram: no visible binding for global variable ‘lab_long’ get_num_cell_tiles: no visible binding for global variable ‘cluster’ ggplot_cat_tiles: no visible binding for global variable ‘feature’ ggplot_cat_tiles: no visible binding for global variable ‘cluster’ ggplot_cat_tiles: no visible binding for global variable ‘percent’ ggplot_num_cell_tiles: no visible binding for global variable ‘cluster’ ggplot_num_cell_tiles: no visible binding for global variable ‘f’ ggplot_num_tiles: no visible binding for global variable ‘feature’ ggplot_num_tiles: no visible binding for global variable ‘cluster’ ggplot_num_tiles: no visible binding for global variable ‘value’ ggplot_num_violins: no visible binding for global variable ‘cluster’ ggplot_num_violins: no visible binding for global variable ‘value’ Undefined global functions or variables: Cells JD cluster f feature intersection isTip lab_long lab_short label percent value * 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 get_bubbletree_comparison 16.246 0.105 19.265 get_r 11.350 0.005 12.130 get_num_cell_tiles 11.181 0.009 12.043 get_num_tiles 10.753 0.017 12.497 get_bubbletree_kmeans 10.620 0.011 11.899 get_bubbletree_graph 9.047 0.020 9.639 get_num_violins 8.700 0.017 10.339 get_cat_tiles 8.090 0.011 12.326 get_gini_k 7.718 0.001 9.171 get_bubbletree_dummy 5.348 0.008 6.145 * 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: 2 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/scBubbletree.Rcheck/00check.log’ for details.