############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CytoML.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CytoML_2.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/CytoML.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘CytoML/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CytoML’ version ‘2.18.0’ * 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 ‘CytoML’ can be installed ... WARNING Found the following significant warnings: /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/cytolib/include/cytolib/transformation.hpp:38:27: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] /media/volume/teran2_disk/biocbuild/bbs-3.20-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] ../inst/include/CytoML/wsNode.hpp:27:20: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=] ../inst/include/CytoML/workspace_type.hpp:67:124: warning: ‘boost::filesystem::recursive_directory_iterator::recursive_directory_iterator(const boost::filesystem::path&, boost::filesystem::symlink_option)’ is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations] See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/CytoML.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 55.3Mb sub-directories of 1Mb or more: extdata 4.8Mb libs 49.4Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: AGPL-3.0-only Standardizable: FALSE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘jsonlite’ ‘methods’ A package should be listed in only one of these fields. * 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 'library' or 'require' call to ‘parallel’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespaces in Imports field not imported from: ‘openCyto’ ‘stats’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE addCustomInfo: no visible global function definition for ‘gh_get_transformations’ addGate: no visible binding for global variable ‘id’ addGate: no visible binding for global variable ‘gate_id’ addGate: no visible binding for global variable ‘fcs’ addGate: no visible binding for global variable ‘fcs_file_id’ addGate: no visible binding for global variable ‘gate_def’ addGate: no visible binding for global variable ‘name’ ce_get_panels: no visible binding for global variable ‘panel’ ce_get_panels: no visible binding for global variable ‘n’ constructTree: no visible binding for global variable ‘id’ constructTree: no visible binding for global variable ‘name’ createTransformIdentifier: no visible global function definition for ‘slotNames’ cytobank_to_gatingset.cytobank_experiment: no visible binding for global variable ‘desc’ diva_to_gatingset: no visible binding for global variable ‘specimen’ diva_to_gatingset: no visible binding for global variable ‘sampleSelected’ diva_to_gatingset: no visible global function definition for ‘gh_apply_to_new_fcs’ export_comp_trans: no visible global function definition for ‘gh_get_compensations’ export_comp_trans: no visible global function definition for ‘gh_get_transformations’ export_gates_cytobank: no visible global function definition for ‘gs_get_pop_paths’ export_gates_cytobank: no visible global function definition for ‘gs_pop_get_gate’ extend.polygonGate: no visible binding for global variable ‘..dim’ extend.polygonGate : : no visible binding for global variable ‘y’ extend.polygonGate : : no visible binding for global variable ‘x’ extend.polygonGate: no visible binding for global variable ‘id’ extend.polygonGate: no visible binding for global variable ‘x’ extend.polygonGate: no visible binding for global variable ‘y’ extend.polygonGate: no visible binding for global variable ‘is.smaller’ flinTr: no visible global function definition for ‘lintGml2’ fratioTr: no visible global function definition for ‘ratiotGml2’ generate_trans: no visible global function definition for ‘flowjo_log_trans’ gs_compare_cytobank_counts: no visible binding for global variable ‘population’ gs_compare_cytobank_counts: no visible binding for global variable ‘parent’ gs_compare_cytobank_counts: no visible binding for global variable ‘parent_count’ gs_compare_cytobank_counts: no visible global function definition for ‘.’ gs_compare_cytobank_counts: no visible binding for global variable ‘fcs_filename’ hyperlogTr: no visible global function definition for ‘hyperlogtGml2’ open_cytobank_experiment: no visible global function definition for ‘unzip’ range.GatingHierarchy: no visible global function definition for ‘gh_get_transformations’ read.gatingML.cytobank: no visible binding for global variable ‘id’ read.gatingML.cytobank: no visible binding for global variable ‘comp_ref’ transDg1polynomial: no visible global function definition for ‘dg1polynomial’ transEH: no visible global function definition for ‘EHtrans’ transExponential: no visible global function definition for ‘exponential’ transHyperLog: no visible global function definition for ‘hyperlog’ transHyperbolicSin: no visible global function definition for ‘sinht’ transInvSplitScale: no visible global function definition for ‘invsplitscale’ transInverseHyperbolicSin: no visible global function definition for ‘asinht’ transLogarithm: no visible global function definition for ‘logarithm’ transQuadratic: no visible global function definition for ‘quadratic’ transRatio: no visible global function definition for ‘ratio’ transSplitScale: no visible global function definition for ‘splitscale’ transSquareroot: no visible global function definition for ‘squareroot’ write.gatingML: no visible global function definition for ‘sessionInfo’ xmlVertexNode : : no visible global function definition for ‘format_float’ identifyNode,http...www.isac.net.org.std.Gating.ML.v1.5.gating_DecisionTreeGate: no visible binding for global variable ‘expressionFilter’ identifyNode,http...www.isac.net.org.std.Gating.ML.v1.5.gating_PolytopeGate: no visible global function definition for ‘polytopeGate’ identifyNode,http...www.isac.net.org.std.Gating.ML.v2.0.transformations_spectrumMatrix: no visible global function definition for ‘pseudoinverse’ show,flowjo_workspace: no visible binding for global variable ‘groupName’ show,flowjo_workspace: no visible binding for global variable ‘groupID’ Undefined global functions or variables: . ..dim EHtrans asinht comp_ref desc dg1polynomial exponential expressionFilter fcs fcs_file_id fcs_filename flowjo_log_trans format_float gate_def gate_id gh_apply_to_new_fcs gh_get_compensations gh_get_transformations groupID groupName gs_get_pop_paths gs_pop_get_gate hyperlog hyperlogtGml2 id invsplitscale is.smaller lintGml2 logarithm n name panel parent parent_count polytopeGate population pseudoinverse quadratic ratio ratiotGml2 sampleSelected sessionInfo sinht slotNames specimen splitscale squareroot unzip x y Consider adding importFrom("methods", "slotNames") importFrom("utils", "sessionInfo", "unzip") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) getNodes-graphGML-method.Rd:5: Lost braces; missing escapes or markup? 5 | \title{get nodes from {graphGML} object} | ^ checkRd: (-1) getNodes-graphGML-method.Rd:22: Lost braces; missing escapes or markup? 22 | get nodes from {graphGML} object | ^ * 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 'flowjo_to_gatingset.Rd' ‘backend_dir’ ‘backend’ Documented arguments not in \usage in Rd file 'flowjo_to_gatingset.Rd': ‘h5_dir’ 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 shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... NOTE Package has both ‘src/Makevars.in’ and ‘src/Makevars’. Installation with --no-configure' is unlikely to work. If you intended ‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’ otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a ‘cleanup’ script. * 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’ apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars.in’ * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... WARNING Note: information on .o files is not available File ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/CytoML/libs/CytoML.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 ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 5 WARNINGs, 8 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/CytoML.Rcheck/00check.log’ for details.