############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings flowWorkspace_4.12.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/flowWorkspace.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘flowWorkspace/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘flowWorkspace’ version ‘4.12.2’ * 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 ... WARNING Found the following significant warnings: /home/biocbuild/bbs-3.17-bioc/R/site-library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable ‘range’ creates a copy from type ‘const pb::Range’ [-Wrange-loop-construct] See ‘/home/biocbuild/bbs-3.17-bioc/meat/flowWorkspace.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 35.4Mb sub-directories of 1Mb or more: libs 34.3Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. 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 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 loading without being on the library search path ... OK * checking startup messages can be suppressed ... 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 ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE generate_gatingset_example_archive: warning in list.files(dataDir, pattern = "gs_manual", full = TRUE): partial argument match of 'full' to 'full.names' .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’ convert_backend: no visible global function definition for ‘cf_write_tile’ 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_plot_pop_count_cv: no visible global function definition for ‘barchart’ gh_plot_pop_count_cv: no visible binding for global variable ‘ggplot2like’ 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 barchart callNextMethod cf_write_tile count desc extends ggplot2like 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 'convert' ‘backend’ Undocumented arguments in documentation object 'cs_get_uri' ‘x’ 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. * 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 ... WARNING Non-portable flags in variable 'PKG_CPPFLAGS': -Wno-pedantic * 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 ... WARNING Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/flowWorkspace/libs/flowWorkspace.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) Found ‘__sprintf_chk’, possibly from ‘sprintf’ (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) Found ‘stderr’, possibly from ‘stderr’ (C) Found ‘stdout’, possibly from ‘stdout’ (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 nor [v]sprintf. 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 ... ‘HowToMergeGatingSet.Rmd’ using ‘UTF-8’... OK ‘flowWorkspace-Introduction.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 6 WARNINGs, 7 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/flowWorkspace.Rcheck/00check.log’ for details.