Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ggcyto_1.38.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ggcyto.Rcheck’* using R version 4.5.2 (2025-10-31)* using platform: x86_64-pc-linux-gnu* R was compiled by    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0* running under: Ubuntu 24.04.3 LTS* using session charset: UTF-8* checking for file ‘ggcyto/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘ggcyto’ version ‘1.38.0’* 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 ... NOTEFound the following hidden files and directories:  .travis.ymlThese were most likely included in error. See section ‘Packagestructure’ in the ‘Writing R Extensions’ manual.* checking for portable file names ... NOTEFound the following non-portable file path:  ggcyto/docs/articles/advanced/ggplot.flowSet.overlay_files/accessible-code-block-0.0.1/empty-anchor.jsTarballs are only required to store paths of up to 100 bytes and cannotstore those of more than 256 bytes, with restrictions including to 100bytes 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 ... NOTENamespace 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.Missing object imported by a ':::' call: ‘ggplot2:::+.gg’Unexported objects imported by ':::' calls:  ‘flowWorkspace:::.mergeGates’ ‘flowWorkspace:::compact’  ‘flowWorkspace:::fix_y_axis’ ‘ggplot2:::add_group’  ‘ggplot2:::as_gg_data_frame’ ‘ggplot2:::check_aesthetics’  ‘ggplot2:::guides_list’ ‘ggplot2:::hex_binwidth’  ‘ggplot2:::is_calculated_aes’ ‘ggplot2:::make_labels’  ‘ggplot2:::make_scale’ ‘ggplot2:::plot_clone’ ‘ggplot2:::scales_list’  See the note in ?`:::` about the use of this operator.* checking S3 generic/method consistency ... WARNINGgrid.draw:  function(x, recording)grid.draw.ggcyto_GatingLayout:  function(x)See section ‘Generic functions and methods’ in the ‘Writing RExtensions’ 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 : <anonymous>: no visible binding for global variable ‘axis’as.ggplot : <anonymous>: 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 : <anonymous>: 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 : <anonymous>: 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 setNamesConsider adding  importFrom("grDevices", "colorRampPalette", "densCols", "gray")  importFrom("graphics", "axis")  importFrom("stats", "density", "setNames")  importFrom("utils", "getS3method", "modifyList")to your NAMESPACE file.* checking Rd files ... NOTEcheckRd: (-1) geom_hvline.Rd:44: Non-ASCII contents without declared encoding:  ‘•’checkRd: (-1) geom_hvline.Rd:44: Non-ASCII contents without declared encoding:  ‘→’checkRd: (-1) geom_hvline.Rd:44: Non-ASCII contents without declared encoding:  ‘→ via’checkRd: (-1) geom_hvline.Rd:44: Non-ASCII contents without declared encoding:  ‘→ inferred’checkRd: (-1) geom_multi_range.Rd:48: Non-ASCII contents without declared encoding:  ‘•’checkRd: (-1) geom_multi_range.Rd:48: Non-ASCII contents without declared encoding:  ‘→’checkRd: (-1) geom_multi_range.Rd:48: Non-ASCII contents without declared encoding:  ‘→ via’checkRd: (-1) geom_multi_range.Rd:48: Non-ASCII contents without declared encoding:  ‘→ inferred’* checking Rd metadata ... OK* checking Rd cross-references ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors:  autoplot.Rd: gs_get_pop_paths  geom_hvline.Rd: geom_hline, geom_vline, aes, aes_string, layer  geom_multi_range.Rd: geom_rect, aes, aes_string, layerPlease provide package anchors for all Rd \link{} targets not in thepackage itself and the base packages.* checking for missing documentation entries ... OK* checking for code/documentation mismatches ... OK* checking Rd \usage sections ... WARNINGUndocumented 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 \aliasentries, and all their arguments documented.The \usage entries must correspond to syntactically valid R code.See chapter ‘Writing R documentation files’ in the ‘Writing RExtensions’ manual.* checking Rd contents ... OK* checking for unstated dependencies in examples ... OK* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s               user system elapsedautoplot     13.041  0.270  13.024ggcyto       10.151  0.302  10.318ggcyto_add    9.869  0.096   9.865getFlowFrame  5.158  0.082   5.242* 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* DONEStatus: 2 WARNINGs, 6 NOTEsSee  ‘/home/biocbuild/bbs-3.22-bioc/meat/ggcyto.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ggcyto###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘ggcyto’ ...** this is package ‘ggcyto’ version ‘1.38.0’** using staged installation** R** inst** byte-compile and prepare package for lazy loading** help*** installing help indices*** copying figures** building package indices** installing vignettes** testing if installed package can be loaded from temporary location** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (ggcyto)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: x86_64-pc-linux-gnuR is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain conditions.Type 'license()' or 'licence()' for distribution details.R is a collaborative project with many contributors.Type 'contributors()' for more information and'citation()' on how to cite R or R packages in publications.Type 'demo()' for some demos, 'help()' for on-line help, or'help.start()' for an HTML browser interface to help.Type 'q()' to quit R.> library(testthat)> library(ggcyto)Loading required package: ggplot2Loading required package: flowCoreLoading required package: ncdfFlowLoading required package: BHLoading required package: flowWorkspaceAs part of improvements to flowWorkspace, some behavior ofGatingSet objects has changed. For details, please read the sectiontitled "The cytoframe and cytoset classes" in the package vignette:  vignette("flowWorkspace-Introduction", "flowWorkspace")> library(vdiffr)> > test_check("ggcyto")`stat_bin()` using `bins = 30`. Pick better value `binwidth`.`stat_bin()` using `bins = 30`. Pick better value `binwidth`.Scale for fill is already present.Adding another scale for fill, which will replace the existing scale.[ FAIL 0 | WARN 1 | SKIP 8 | PASS 7 ]══ Skipped tests (8) ═══════════════════════════════════════════════════════════• On CRAN (8): 'test-autoplot.R:8:1', 'test-autoplot.R:13:1',  'test-autoplot.R:20:1', 'test-ggcyto-fs.R:10:1', 'test-ggcyto-gs.R:25:1',  'test-ggcyto-gs.R:79:1', 'test-ggcyto-gs.R:95:1', 'test-multiRangeGate.R:7:1'[ FAIL 0 | WARN 1 | SKIP 8 | PASS 7 ]> > proc.time()   user  system elapsed  48.711   1.249  49.421