############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:openCyto.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings openCyto_2.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/openCyto.Rcheck’ * using R Under development (unstable) (2024-11-14 r87333) * 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 ‘openCyto/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘openCyto’ version ‘2.19.0’ * 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 ‘openCyto’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * checking C++ specification ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: AGPL-3.0-only Standardizable: FALSE * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... NOTE Namespace in Imports field not imported from: ‘flowViz’ All declared Imports should be used. Missing objects imported by ':::' calls: ‘ncdfFlow:::toBitVec’ ‘ncdfFlow:::toLogical’ Unexported objects imported by ':::' calls: ‘flowClust:::.ellipsePoints’ ‘flowWorkspace:::.addGate’ ‘flowWorkspace:::.getAllDescendants’ ‘flowWorkspace:::cpp_addGate’ ‘flowWorkspace:::cpp_boolGating’ ‘flowWorkspace:::cpp_setIndices’ ‘flowWorkspace:::filter_to_list.booleanFilter’ ‘flowWorkspace:::filter_to_list.rectangleGate’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘groupBy’ ‘isCollapse’ ‘ppMethod’ ‘unlockNamespace’ * checking S3 generic/method consistency ... WARNING as.data.table: function(x, keep.rownames, ...) as.data.table.gatingTemplate: function(x, keep.rownames) 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 Found the following possibly unsafe calls: File ‘openCyto/R/pluginFramework.R’: unlockBinding(methodName, ENV) unlockBinding(methodName, ENV) .boundary: no visible global function definition for ‘rectangleGate’ .center_mode: no visible global function definition for ‘density’ .find_peaks: no visible global function definition for ‘density’ .find_peaks: no visible global function definition for ‘points’ .find_valleys: no visible global function definition for ‘density’ .gateToFilterResult: no visible global function definition for ‘exprs’ .gateToFilterResult: no visible global function definition for ‘as’ .gatingTemplate: no visible global function definition for ‘as’ .gatingTemplate: no visible global function definition for ‘new’ .gatingTemplate: no visible binding for global variable ‘pop’ .gatingTemplate: no visible binding for global variable ‘gating_method’ .gatingTemplate: no visible binding for global variable ‘gating_args’ .gatingTemplate: no visible binding for global variable ‘collapseDataForGating’ .gatingTemplate: no visible binding for global variable ‘preprocessing_method’ .gatingTemplate: no visible binding for global variable ‘preprocessing_args’ .gatingTemplate: no visible global function definition for ‘extends’ .gating_adaptor: no visible global function definition for ‘as’ .gating_adaptor: no visible global function definition for ‘na.omit’ .gating_adaptor: no visible global function definition for ‘rectangleGate’ .gating_adaptor: no visible global function definition for ‘filters’ .gating_adaptor: no visible global function definition for ‘extends’ .gating_gtMethod: no visible global function definition for ‘na.omit’ .gating_gtMethod : : no visible global function definition for ‘extends’ .gating_gtMethod: no visible global function definition for ‘extends’ .gating_gtMethod: no visible global function definition for ‘is’ .gating_gtMethod : : no visible global function definition for ‘filters’ .gating_polyFunctions: no visible global function definition for ‘permutations’ .gating_refGate : : no visible global function definition for ‘rectangleGate’ .gating_refGate: no visible global function definition for ‘filterList’ .gating_refGate: no visible global function definition for ‘is’ .gen_1dgate : : no visible binding for global variable ‘parent’ .gen_1dgate : : no visible binding for global variable ‘gating_method’ .gen_1dgate : : no visible binding for global variable ‘gating_args’ .gen_1dgate : : no visible binding for global variable ‘collapseDataForGating’ .gen_1dgate : : no visible binding for global variable ‘preprocessing_method’ .gen_1dgate : : no visible binding for global variable ‘preprocessing_args’ .gen_dummy_ref_gate: no visible binding for global variable ‘parent’ .gen_dummy_ref_gate : : no visible binding for global variable ‘pop’ .gen_dummy_ref_gate : : no visible binding for global variable ‘gating_method’ .gen_dummy_ref_gate : : no visible binding for global variable ‘gating_args’ .gen_dummy_ref_gate : : no visible binding for global variable ‘collapseDataForGating’ .gen_dummy_ref_gate : : no visible binding for global variable ‘preprocessing_method’ .gen_dummy_ref_gate : : no visible binding for global variable ‘preprocessing_args’ .gen_refGate: no visible binding for global variable ‘parent’ .gen_refGate: no visible binding for global variable ‘gating_args’ .getEllipse: no visible global function definition for ‘qf’ .getEllipse: no visible global function definition for ‘qchisq’ .getEllipseGate: no visible global function definition for ‘qf’ .getEllipseGate: no visible global function definition for ‘qchisq’ .getEllipseGate: no visible global function definition for ‘polygonGate’ .getEllipseGate: no visible global function definition for ‘ellipsoidGate’ .getFullPath: no visible binding for global variable ‘parent’ .improvedMindensity: no visible global function definition for ‘density’ .improvedMindensity: no visible global function definition for ‘smooth.spline’ .improvedMindensity: no visible global function definition for ‘predict’ .improvedMindensity: no visible global function definition for ‘median’ .improvedMindensity : .plots: no visible global function definition for ‘abline’ .improvedMindensity: no visible global function definition for ‘par’ .improvedMindensity: no visible global function definition for ‘abline’ .plotTree: no visible global function definition for ‘as’ .plotTree: no visible global function definition for ‘par’ .plotTree: no visible global function definition for ‘legend’ .polyfunction_nodes: no visible global function definition for ‘permutations’ .preprocess_csv: no visible binding for global variable ‘pop’ .preprocess_csv: no visible binding for global variable ‘parent’ .preprocess_csv: no visible binding for global variable ‘gating_method’ .preprocess_csv: no visible binding for global variable ‘gating_args’ .preprocess_csv: no visible binding for global variable ‘collapseDataForGating’ .preprocess_csv: no visible binding for global variable ‘preprocessing_method’ .preprocess_csv: no visible binding for global variable ‘preprocessing_args’ .preprocess_row: no visible binding for global variable ‘pop’ .preprocess_row: no visible binding for global variable ‘gating_method’ .preprocess_row: no visible binding for global variable ‘parent’ .preprocess_row: no visible binding for global variable ‘gating_args’ .preprocess_row: no visible binding for global variable ‘preprocessing_method’ .preprocess_row: no visible binding for global variable ‘preprocessing_args’ .prior_flowClust1d: no visible global function definition for ‘fsApply’ .prior_flowClust1d : : no visible global function definition for ‘exprs’ .prior_flowClust1d: no visible global function definition for ‘hclust’ .prior_flowClust1d: no visible global function definition for ‘dist’ .prior_flowClust1d: no visible global function definition for ‘median’ .prior_flowClust1d: no visible global function definition for ‘cutree’ .prior_flowClust1d: no visible global function definition for ‘kmeans’ .prior_flowClust1d : : no visible global function definition for ‘sd’ .prior_flowClust1d: no visible binding for global variable ‘var’ .prior_flowClust1d : : no visible global function definition for ‘embed’ .prior_flowClust1d : : no visible binding for global variable ‘var’ .prior_kmeans : : no visible global function definition for ‘exprs’ .prior_kmeans : : no visible global function definition for ‘kmeans’ .prior_kmeans : : : no visible global function definition for ‘cov’ .prior_kmeans : : no visible global function definition for ‘dist’ .prior_kmeans: no visible binding for global variable ‘cov.wt’ .quadGate2rectangleGates: no visible global function definition for ‘rectangleGate’ .quadGate2rectangleGates: no visible global function definition for ‘filters’ .quantile_flowClust : cdf_target : : no visible global function definition for ‘pt’ .quantile_flowClust : cdf_target: no visible global function definition for ‘weighted.mean’ .quantile_flowClust: no visible global function definition for ‘uniroot’ .read.FCS.csv: no visible global function definition for ‘new’ .read.flowSet.csv: no visible global function definition for ‘flowSet’ .scale_huber: no visible global function definition for ‘mad’ .standardize_flowFrame: no visible global function definition for ‘exprs’ .standardize_flowFrame: no visible global function definition for ‘exprs<-’ .standardize_flowset: no visible global function definition for ‘fsApply’ .standardize_flowset: no visible global function definition for ‘flowSet’ .standardize_flowset: no visible global function definition for ‘as’ .truncate_flowframe: no visible global function definition for ‘rectangleGate’ .truncate_flowframe: no visible global function definition for ‘Subset’ .truncate_flowset: no visible global function definition for ‘rectangleGate’ .truncate_flowset: no visible global function definition for ‘Subset’ .unique_check_alias: no visible binding for global variable ‘parent’ as.data.table.gatingTemplate : : no visible global function definition for ‘extends’ fast_coerce: no visible global function definition for ‘fsApply’ fast_coerce : : no visible global function definition for ‘exprs’ fast_coerce: no visible global function definition for ‘new’ fcEllipsoidGate: no visible global function definition for ‘as’ fcFilterList : : no visible global function definition for ‘extends’ fcFilterList: no visible global function definition for ‘filterList’ fcFilterList: no visible global function definition for ‘as’ fcPolygonGate: no visible global function definition for ‘as’ fcRectangleGate: no visible global function definition for ‘as’ fcTree: no visible global function definition for ‘as’ fcTree: no visible global function definition for ‘new’ gate_flowclust_1d: no visible global function definition for ‘exprs’ gate_flowclust_1d: no visible global function definition for ‘rectangleGate’ gate_flowclust_1d: no visible global function definition for ‘abline’ gate_flowclust_1d: no visible global function definition for ‘rainbow’ gate_flowclust_1d: no visible global function definition for ‘lines’ gate_flowclust_2d: no visible global function definition for ‘new’ gate_flowclust_2d: no visible global function definition for ‘dist’ gate_flowclust_2d: no visible global function definition for ‘qchisq’ gate_flowclust_2d: no visible global function definition for ‘exprs’ gate_flowclust_2d: no visible global function definition for ‘sd’ gate_flowclust_2d: no visible global function definition for ‘polygonGate’ gate_flowclust_2d: no visible global function definition for ‘lines’ gate_flowclust_2d: no visible global function definition for ‘points’ gate_mindensity: no visible global function definition for ‘exprs’ gate_mindensity: no visible global function definition for ‘rectangleGate’ gate_mindensity2: no visible global function definition for ‘exprs’ gate_mindensity2: no visible global function definition for ‘rectangleGate’ gate_quad_sequential : : no visible global function definition for ‘exprs’ gate_quad_sequential: no visible global function definition for ‘filter’ gate_quad_sequential: no visible global function definition for ‘as’ gate_quad_sequential : : no visible global function definition for ‘rectangleGate’ gate_quad_sequential: no visible global function definition for ‘filters’ gate_quad_tmix: no visible global function definition for ‘filter’ gate_quad_tmix: no visible global function definition for ‘as’ gate_quad_tmix: no visible global function definition for ‘polygonGate’ gate_quad_tmix: no visible global function definition for ‘filters’ gate_quantile: no visible global function definition for ‘exprs’ gate_quantile: no visible global function definition for ‘quantile’ gate_quantile: no visible global function definition for ‘hist’ gate_quantile: no visible global function definition for ‘density’ gate_quantile: no visible global function definition for ‘abline’ gate_quantile: no visible global function definition for ‘text’ gate_quantile: no visible global function definition for ‘rectangleGate’ gate_singlet: no visible global function definition for ‘exprs’ gate_singlet: no visible global function definition for ‘as.formula’ gate_singlet: no visible global function definition for ‘predict’ gate_singlet: no visible global function definition for ‘polygonGate’ gs_add_gating_method: no visible global function definition for ‘is’ gs_add_gating_method_init: no visible global function definition for ‘is’ gs_remove_gating_method: no visible global function definition for ‘is’ mindensity: no visible global function definition for ‘exprs’ mindensity: no visible global function definition for ‘rectangleGate’ ocRectRefGate: no visible global function definition for ‘as’ prior_flowclust : : no visible global function definition for ‘is’ quadGate.tmix: no visible global function definition for ‘quad_gate_tmix’ robust_m_estimator: no visible global function definition for ‘median’ singletGate: no visible global function definition for ‘exprs’ singletGate: no visible global function definition for ‘as.formula’ singletGate: no visible global function definition for ‘predict’ singletGate: no visible global function definition for ‘polygonGate’ coerce,ncdfFlowList-flowFrame: no visible global function definition for ‘selectMethod’ gatingTemplate,character: no visible binding for global variable ‘isMultiPops’ gatingTemplate,character: no visible binding for global variable ‘pop’ gatingTemplate,character: no visible binding for global variable ‘gating_args’ gatingTemplate,data.table: no visible binding for global variable ‘isMultiPops’ gatingTemplate,data.table: no visible binding for global variable ‘pop’ gatingTemplate,data.table: no visible binding for global variable ‘gating_args’ plot,fcFilterList-ANY : : no visible global function definition for ‘dnorm’ plot,fcFilterList-ANY: no visible global function definition for ‘hist’ plot,fcFilterList-ANY: no visible global function definition for ‘exprs’ plot,fcFilterList-ANY: no visible global function definition for ‘lines’ plot,fcFilterList-ANY: no visible global function definition for ‘rainbow’ plot,fcFilterList-ANY: no visible global function definition for ‘abline’ show,fcFilter: no visible global function definition for ‘callNextMethod’ Undefined global functions or variables: Subset abline as as.formula callNextMethod collapseDataForGating cov cov.wt cutree density dist dnorm ellipsoidGate embed exprs exprs<- extends filter filterList filters flowSet fsApply gating_args gating_method hclust hist is isMultiPops kmeans legend lines mad median na.omit new par parent permutations points polygonGate pop predict preprocessing_args preprocessing_method pt qchisq qf quad_gate_tmix quantile rainbow rectangleGate sd selectMethod smooth.spline text uniroot var weighted.mean Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "abline", "hist", "legend", "lines", "par", "points", "text") importFrom("methods", "as", "callNextMethod", "extends", "is", "new", "selectMethod") importFrom("stats", "as.formula", "cov", "cov.wt", "cutree", "density", "dist", "dnorm", "embed", "filter", "hclust", "kmeans", "mad", "median", "na.omit", "predict", "pt", "qchisq", "qf", "quantile", "sd", "smooth.spline", "uniroot", "var", "weighted.mean") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) gs_add_gating_method.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) gs_add_gating_method.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) gs_add_gating_method.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) gt_gating.Rd:19: Lost braces in \itemize; meant \describe ? checkRd: (-1) gt_gating.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) gt_gating.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) gt_gating.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) gt_gating.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) gt_gating.Rd:24: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link(s) in Rd file 'gate_quad_sequential.Rd': ‘tailgate’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: gate_flowclust_1d.Rd: flowClust gate_flowclust_2d.Rd: flowClust gate_quad_sequential.Rd: tailgate gate_quad_tmix.Rd: flowClust gs_add_gating_method_init.Rd: load_gs Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'robust_m_estimator.Rd' ‘x’ ‘sd’ 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/openCyto/libs/openCyto.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) File ‘openCyto/libs/openCyto.so’: Found non-API calls to R: ‘ENVFLAGS’, ‘SET_ENVFLAGS’ Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points. * 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 ... NOTE Package vignette with \VignetteEngine{} not specifying an engine package: ‘openCytoVignette.Rmd’ Engines should be specified as \VignetteEngine{PKG::ENG}. * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 WARNINGs, 6 NOTEs See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/openCyto.Rcheck/00check.log’ for details.