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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:openCyto.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings openCyto_2.12.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/openCyto.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'openCyto/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'openCyto' version '2.12.0'
* 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 whether package 'openCyto' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking C++ specification ... OK
  Not all R platforms support C++17
* 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 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 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 : <anonymous>: 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 : <anonymous>: no visible global function definition
  for 'filters'
.gating_polyFunctions: no visible global function definition for
  'permutations'
.gating_refGate : <anonymous>: 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 : <anonymous>: no visible binding for global variable
  'parent'
.gen_1dgate : <anonymous>: no visible binding for global variable
  'gating_method'
.gen_1dgate : <anonymous>: no visible binding for global variable
  'gating_args'
.gen_1dgate : <anonymous>: no visible binding for global variable
  'collapseDataForGating'
.gen_1dgate : <anonymous>: no visible binding for global variable
  'preprocessing_method'
.gen_1dgate : <anonymous>: no visible binding for global variable
  'preprocessing_args'
.gen_dummy_ref_gate: no visible binding for global variable 'parent'
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
  variable 'pop'
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
  variable 'gating_method'
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
  variable 'gating_args'
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
  variable 'collapseDataForGating'
.gen_dummy_ref_gate : <anonymous>: no visible binding for global
  variable 'preprocessing_method'
.gen_dummy_ref_gate : <anonymous>: 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 : <anonymous>: 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 : <anonymous>: no visible global function definition
  for 'sd'
.prior_flowClust1d: no visible binding for global variable 'var'
.prior_flowClust1d : <anonymous>: no visible global function definition
  for 'embed'
.prior_flowClust1d : <anonymous>: no visible binding for global
  variable 'var'
.prior_kmeans : <anonymous>: no visible global function definition for
  'exprs'
.prior_kmeans : <anonymous>: no visible global function definition for
  'kmeans'
.prior_kmeans : <anonymous> : <anonymous>: no visible global function
  definition for 'cov'
.prior_kmeans : <anonymous>: 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 : <anonymous>: 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 : <anonymous>: no visible global function
  definition for 'extends'
fast_coerce: no visible global function definition for 'fsApply'
fast_coerce : <anonymous>: 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 : <anonymous>: 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 : <anonymous>: 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 : <anonymous>: 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'
id: no visible global function definition for '%||%'
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 : <anonymous>: 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 : <anonymous>: 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'gate_quad_sequential.Rd':
  'tailgate'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'robust_m_estimator'
  '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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/openCyto/libs/x64/openCyto.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 4 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/openCyto.Rcheck/00check.log'
for details.