############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ggcyto_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ggcyto.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 ‘ggcyto/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ggcyto’ version ‘1.34.0’ * 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 ... NOTE Found the following non-portable file path: ggcyto/docs/articles/advanced/ggplot.flowSet.overlay_files/accessible-code-block-0.0.1/empty-anchor.js Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for sufficient/correct file permissions ... OK * checking whether package ‘ggcyto’ 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: ‘scales’ All declared Imports should be used. ':::' call which should be '::': ‘flowWorkspace:::gh_pop_is_negated’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘flowWorkspace:::.mergeGates’ ‘flowWorkspace:::compact’ ‘flowWorkspace:::fix_y_axis’ ‘ggplot2:::+.gg’ ‘ggplot2:::add_group’ ‘ggplot2:::as_gg_data_frame’ ‘ggplot2:::check_aesthetics’ ‘ggplot2:::guides_list’ ‘ggplot2:::hex_binwidth’ ‘ggplot2:::is.waive’ ‘ggplot2:::is_calculated_aes’ ‘ggplot2:::make_labels’ ‘ggplot2:::make_scale’ ‘ggplot2:::plot_clone’ ‘ggplot2:::print.ggplot’ ‘ggplot2:::scales_list’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... WARNING grid.draw: function(x, recording) grid.draw.ggcyto_GatingLayout: function(x) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .fr2dt: no visible binding for global variable ‘axis’ .fr2dt: no visible binding for global variable ‘name’ .fs2dt: no visible binding for global variable ‘name’ add_ggcyto: no visible binding for global variable ‘name’ add_ggcyto: no visible global function definition for ‘modifyList’ add_ggcyto: no visible binding for global variable ‘axis’ add_ggcyto: no visible binding for global variable ‘desc’ add_par: no visible global function definition for ‘modifyList’ as.ggplot: no visible binding for global variable ‘axis’ as.ggplot: no visible binding for global variable ‘name’ as.ggplot : : no visible binding for global variable ‘axis’ as.ggplot : : no visible binding for global variable ‘name’ as.ggplot: no visible binding for global variable ‘count’ as.ggplot: no visible global function definition for ‘densCols’ as.ggplot: no visible global function definition for ‘colorRampPalette’ as.ggplot: no visible binding for global variable ‘density’ autoplot.GatingHierarchy : : no visible global function definition for ‘gray’ autoplot.GatingSetList: no visible global function definition for ‘getS3method’ autoplot.cytoframe: no visible global function definition for ‘getS3method’ autoplot.cytoset: no visible global function definition for ‘getS3method’ autoplot.ncdfFlowList: no visible global function definition for ‘getS3method’ density_fr_all : : no visible global function definition for ‘gray’ faust_gating_plot: no visible global function definition for ‘gray’ fortify.GatingSetList: no visible global function definition for ‘getS3method’ fortify.cytoframe: no visible global function definition for ‘getS3method’ fortify.cytoset: no visible global function definition for ‘getS3method’ fortify.ncdfFlowList: no visible global function definition for ‘getS3method’ fortify_fs.GatingSetList: no visible global function definition for ‘getS3method’ getFlowFrame.GatingSetList: no visible global function definition for ‘getS3method’ getFlowFrame.cytoset: no visible global function definition for ‘getS3method’ getFlowFrame.ncdfFlowList: no visible global function definition for ‘getS3method’ ggcyto.GatingSetList: no visible global function definition for ‘getS3method’ ggcyto.cytoset: no visible global function definition for ‘getS3method’ ggcyto.flowSet: no visible binding for global variable ‘axis’ ggcyto.flowSet: no visible binding for global variable ‘name’ ggcyto.ncdfFlowList: no visible global function definition for ‘getS3method’ ggcyto_arrange: no visible binding for global variable ‘name’ stat_position.filter: no visible global function definition for ‘setNames’ Undefined global functions or variables: axis colorRampPalette count densCols density desc getS3method gray modifyList name setNames Consider adding importFrom("grDevices", "colorRampPalette", "densCols", "gray") importFrom("graphics", "axis") importFrom("stats", "density", "setNames") importFrom("utils", "getS3method", "modifyList") 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 ... WARNING Undocumented arguments in Rd file 'faust_gating_plot.Rd' ‘gh’ ‘...’ Documented arguments not in \usage in Rd file 'fortify.multiRangeGate.Rd': ‘nPoints’ Undocumented arguments in Rd file 'geom_multi_range.Rd' ‘stat’ ‘linejoin’ ‘na.rm’ ‘inherit.aes’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed ggcyto_add 10.228 0.112 10.715 autoplot 9.115 0.532 12.365 ggcyto 8.502 0.466 9.427 * 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 WARNINGs, 4 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ggcyto.Rcheck/00check.log’ for details.