############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowWorkspace_4.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/flowWorkspace.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flowWorkspace/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘flowWorkspace’ version ‘4.8.0’ * 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 ‘flowWorkspace’ can be installed ... OK * checking installed package size ... NOTE installed size is 7.9Mb sub-directories of 1Mb or more: libs 6.5Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R 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 ... NOTE Namespaces in Imports field not imported from: ‘RBGL’ ‘RProtoBufLib’ ‘ggplot2’ ‘grDevices’ ‘graphics’ ‘utils’ All declared Imports should be used. Unexported objects imported by ':::' calls: ‘DelayedArray:::simplify_NULL_dimnames’ ‘flowCore:::.estimateLogicle’ ‘flowCore:::.spillover_pattern’ ‘flowCore:::checkClass’ ‘flowCore:::guid’ ‘flowCore:::logicle_transform’ ‘flowCore:::parse_pd_for_read_fs’ ‘flowCore:::txt2spillmatrix’ ‘flowCore:::updateTransformKeywords’ ‘flowCore:::validFilterResultList’ ‘graph:::.makeEdgeKeys’ ‘ncdfFlow:::.isValidSamples’ ‘stats:::.splinefun’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: print.cytoctx See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .computeCV : : no visible binding for global variable ‘xml.count’ .computeCV : : no visible binding for global variable ‘openCyto.count’ .computeCV : : : no visible global function definition for ‘IQR’ .computeCV : : : no visible global function definition for ‘median’ .computeCV_gh : : no visible global function definition for ‘IQR’ .computeCV_gh : : no visible global function definition for ‘median’ .graph_handler : asGraphNEL: no visible global function definition for ‘new’ .graph_handler : asGraphNEL: no visible global function definition for ‘validObject’ .load_legacy: no visible global function definition for ‘is’ .load_legacy: no visible global function definition for ‘new’ .load_legacy: no visible global function definition for ‘.hasSlot’ .load_legacy : : no visible global function definition for ‘is’ .mergeGates : : no visible global function definition for ‘extends’ .preprocessMap: no visible binding for global variable ‘old’ .preprocessMap: no visible binding for global variable ‘.’ GatingSetList: no visible global function definition for ‘as’ GatingSetList: no visible global function definition for ‘validObject’ booleanFilter: no visible global function definition for ‘new’ booleanFilter: no visible global function definition for ‘is’ cf_append_cols: no visible global function definition for ‘new’ cf_flush_meta: no visible global function definition for ‘is’ cf_get_uri: no visible global function definition for ‘is’ cf_keyword_delete: no visible global function definition for ‘is’ cf_keyword_insert: no visible global function definition for ‘is’ cf_keyword_rename: no visible global function definition for ‘is’ cf_keyword_rename: no visible binding for global variable ‘na_idx’ cf_keyword_set: no visible global function definition for ‘is’ cf_load_meta: no visible global function definition for ‘is’ cf_lock: no visible global function definition for ‘is’ cf_rename_channel: no visible global function definition for ‘is’ cf_rename_marker: no visible global function definition for ‘is’ cf_rename_marker: no visible binding for global variable ‘desc’ cf_scale_time_channel: no visible global function definition for ‘is’ cf_unlock: no visible global function definition for ‘is’ cf_write_disk: no visible global function definition for ‘is’ char2booleanFilter: no visible global function definition for ‘new’ check_comp: no visible global function definition for ‘is’ convert_backend: no visible binding for global variable ‘output’ copy_view.cytoframe: no visible global function definition for ‘new’ copy_view.cytoset: no visible global function definition for ‘new’ cs_add_cytoframe: no visible global function definition for ‘is’ cs_get_cytoframe: no visible global function definition for ‘is’ cs_get_cytoframe: no visible global function definition for ‘new’ cs_get_uri: no visible global function definition for ‘is’ cs_keyword_delete: no visible global function definition for ‘is’ cs_keyword_insert: no visible global function definition for ‘is’ cs_keyword_rename: no visible global function definition for ‘is’ cs_keyword_rename : : no visible binding for global variable ‘keys’ cs_keyword_set: no visible global function definition for ‘is’ cs_set_cytoframe: no visible global function definition for ‘is’ cytoframe_to_flowFrame: no visible global function definition for ‘as’ cytoset: no visible global function definition for ‘new’ cytoset_to_flowSet: no visible global function definition for ‘as’ get_cytoframe_from_cs: no visible global function definition for ‘is’ get_cytoframe_from_cs: no visible global function definition for ‘new’ gh_apply_to_cs: no visible global function definition for ‘new’ gh_pop_compare_stats: no visible binding for global variable ‘node’ gh_pop_get_count: no visible binding for global variable ‘count’ gh_pop_get_proportion: no visible binding for global variable ‘percent’ gh_pop_get_stats_tfilter: no visible global function definition for ‘is’ gh_pop_get_stats_tfilter : : no visible binding for global variable ‘Population’ gh_pop_set_gate: no visible global function definition for ‘is’ gs_clone: no visible global function definition for ‘new’ gs_copy_tree_only: no visible global function definition for ‘new’ gs_get_singlecell_expression: no visible global function definition for ‘is’ gs_get_singlecell_expression: no visible binding for global variable ‘parallel’ gs_pop_add: no visible global function definition for ‘is’ gs_pop_get_count_fast: no visible global function definition for ‘is’ gs_pop_get_count_with_meta: no visible binding for global variable ‘sampleName’ gs_pop_get_data: no visible global function definition for ‘new’ gs_pop_set_gate: no visible global function definition for ‘is’ gs_remove_redundant_nodes : : no visible global function definition for ‘is’ gslist_to_gs: no visible global function definition for ‘new’ load_cytoframe: no visible global function definition for ‘new’ load_cytoframe_from_fcs: no visible global function definition for ‘new’ load_cytoset_from_fcs: no visible global function definition for ‘new’ load_gs: no visible global function definition for ‘new’ load_gslist : : no visible global function definition for ‘is’ merge_list_to_gs: no visible global function definition for ‘is’ merge_list_to_gs: no visible global function definition for ‘new’ parse_transformer: no visible global function definition for ‘is’ pop.MFI: no visible binding for global variable ‘desc’ realize_view.cytoframe: no visible global function definition for ‘new’ realize_view.cytoset: no visible global function definition for ‘new’ transformerList: no visible global function definition for ‘is’ transformerList: no visible binding for global variable ‘is’ validitycheck: no visible global function definition for ‘is’ GatingSet,cytoset-ANY: no visible global function definition for ‘new’ Subset,cytoset-filterResultList : : no visible global function definition for ‘as’ Subset,cytoset-list: no visible global function definition for ‘is’ [,GatingSet-ANY: no visible global function definition for ‘extends’ [,GatingSet-ANY: no visible global function definition for ‘new’ [,GatingSetList-ANY: no visible global function definition for ‘callNextMethod’ [,GatingSetList-ANY: no visible global function definition for ‘as’ [[,GatingSet-character: no visible global function definition for ‘as’ compensate,GatingSet-ANY: no visible global function definition for ‘selectMethod’ compensate,cytoset-ANY: no visible global function definition for ‘selectMethod’ flowData,GatingSet: no visible binding for global variable ‘obj’ fsApply,cytoset: no visible global function definition for ‘callNextMethod’ gs_cyto_data,GatingSet: no visible global function definition for ‘new’ keyword,GatingSetList-character: no visible global function definition for ‘selectMethod’ keyword,GatingSetList-missing: no visible global function definition for ‘selectMethod’ keyword<-,cytoframe-list: no visible binding for global variable ‘kwdError’ pData<-,GatingSetList-data.frame: no visible global function definition for ‘callNextMethod’ pData<-,GatingSetList-data.frame: no visible global function definition for ‘as’ parameters,cytoframe: no visible global function definition for ‘new’ phenoData,cytoset: no visible global function definition for ‘new’ sampleNames<-,cytoset-ANY: no visible global function definition for ‘selectMethod’ setNode,GatingSet-character-ANY: no visible global function definition for ‘is’ show,cytoframe: no visible global function definition for ‘selectMethod’ transform,GatingSet: no visible global function definition for ‘is’ transform,GatingSet : : no visible global function definition for ‘is’ transform,cytoframe: no visible global function definition for ‘is’ transform,cytoset: no visible global function definition for ‘is’ transform,cytoset : : no visible global function definition for ‘is’ Undefined global functions or variables: . .hasSlot IQR Population as callNextMethod count desc extends is keys kwdError median na_idx new node obj old openCyto.count output parallel percent sampleName selectMethod validObject xml.count Consider adding importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends", "is", "new", "selectMethod", "validObject") importFrom("stats", "IQR", "median") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘gs_clone’ ‘gs_copy_tree_only’ Undocumented S4 methods: generic 'dimnames' and siglist 'cytoframe' generic 'rownames' and siglist 'cytoframe' generic 'rownames<-' and siglist 'cytoframe' generic 'show' and siglist 'cytoframe' generic 'transform' and siglist 'cytoframe' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Documented arguments not in \usage in documentation object 'GatingSet-methods': ‘...’ Undocumented arguments in documentation object 'cf_append_cols' ‘ctx’ Undocumented arguments in documentation object 'convert' ‘backend’ Undocumented arguments in documentation object 'cs_get_uri' ‘x’ Undocumented arguments in documentation object 'cytoctx' ‘...’ Undocumented arguments in documentation object 'delete_gs' ‘ctx’ Undocumented arguments in documentation object 'gh_apply_to_new_fcs' ‘files’ Undocumented arguments in documentation object 'keyword-mutators' ‘cs’ Undocumented arguments in documentation object 'load_cytoframe_from_fcs' ‘backend’ ‘uri’ Undocumented arguments in documentation object 'load_cytoset_from_fcs' ‘backend’ ‘backend_dir’ Undocumented arguments in documentation object 'save_gs' ‘cdf’ ‘backend_readonly’ 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. S3 methods shown with full name in documentation object 'cytoctx': ‘print.cytoctx’ The \usage entries for S3 methods should use the \method markup and not their full name. 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 ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... WARNING apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’ * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/flowWorkspace/libs/flowWorkspace.so’: Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++) Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++) Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_exit’, possibly from ‘exit’ (C) Found ‘_rand’, possibly from ‘rand’ (C) Found ‘_rand_r’, possibly from ‘rand_r’ (C) Found ‘_srand’, possibly from ‘srand’ (C) 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. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 7 NOTEs See ‘/Users/biocbuild/bbs-3.15-bioc/meat/flowWorkspace.Rcheck/00check.log’ for details.