Multiple platform build/check report for BioC 3.21 - CHECK results for openCyto on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4748
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4459
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4396
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4110
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for openCyto on kjohnson3

To the developers/maintainers of the openCyto package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/openCyto.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: openCyto

Version: 2.19.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:openCyto.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings openCyto_2.19.0.tar.gz

StartedAt: 2024-11-27 02:19:06 -0500 (Wed, 27 Nov 2024)

EndedAt: 2024-11-27 02:23:37 -0500 (Wed, 27 Nov 2024)

EllapsedTime: 270.6 seconds

RetCode: 0

Status: WARNINGS

CheckDir: openCyto.Rcheck

Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:openCyto.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings openCyto_2.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/openCyto.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘openCyto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘openCyto’ version ‘2.19.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 : <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’
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 ... 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 ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/openCyto/libs/openCyto.so’:
  Found ‘__ZNSt3__14cerrE’, 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/openCyto.Rcheck/00check.log’
for details.

Installation output

openCyto.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL openCyto
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘openCyto’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c Hungarian.cpp -o Hungarian.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c cpp11.cpp -o cpp11.o
In file included from cpp11.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include/cpp11/declarations.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include/cpp11.hpp:3:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
        ^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
        ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c misc.cpp -o misc.o
In file included from misc.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include/cpp11.hpp:3:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
        ^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
        ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c rlm.cpp -o rlm.o
In file included from rlm.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include/cpp11.hpp:3:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
        ^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
        ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c solve_LSAP.cpp -o solve_LSAP.o
In file included from solve_LSAP.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include/cpp11.hpp:3:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
        ^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
        ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c unlockNamespace.cpp -o unlockNamespace.o
In file included from unlockNamespace.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include/cpp11.hpp:3:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
        ^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
        ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o openCyto.so Hungarian.o cpp11.o misc.o rlm.o solve_LSAP.o unlockNamespace.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-openCyto/00new/openCyto/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (openCyto)

Tests output

openCyto.Rcheck/tests/testthat.Rout


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Platform: aarch64-apple-darwin20

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> library(testthat)
> library(openCyto)
> 
> test_check("openCyto")
Loading required package: BH
[ FAIL 0 | WARN 5 | SKIP 2 | PASS 145 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• dir.exists(file.path(localPath, "misc")) is not TRUE (1):
  'test-gating-suite.R:8:1'
• no longer supported (1): 'test-polyfunction.R:4:3'

[ FAIL 0 | WARN 5 | SKIP 2 | PASS 145 ]
> 
> 
> #taking quite some time , thus only for internal testing
> #test_file("~/rglab/workspace/openCyto/tests/testthat/gating-testSuite.R")
> 
> proc.time()
   user  system elapsed 
 13.982   0.512  14.501

Example timings

openCyto.Rcheck/openCyto-Ex.timings

name	user	system	elapsed
gate_flowclust_1d	0.000	0.000	0.001
gate_flowclust_2d	0	0	0
gate_mindensity	0	0	0
gate_mindensity2	0	0	0
gate_quantile	0	0	0
gatingTemplate-class	0	0	0
gh_generate_template	0.033	0.004	0.038
gs_add_gating_method	0	0	0
gs_add_gating_method_init	0.000	0.000	0.001
gs_remove_gating_method	0	0	0
gtMethod-class	0	0	0
gtPopulation-class	0.000	0.001	0.000
gt_gating	0	0	0
gt_get_children	0	0	0
gt_get_gate	0	0	0
gt_get_nodes	0	0	0
gt_get_parent	0	0	0
gt_toggle_helpergates	0	0	0
names-gtMethod-method	0	0	0
openCyto	0	0	0
openCyto.options	0	0	0
plot-fcFilterList-ANY-method	0	0	0
plot-gatingTemplate-missing-method	0.001	0.000	0.000
ppMethod-class	0	0	0
ppMethod-gatingTemplate-character-method	0	0	0
prior_flowclust	0	0	0