Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:28 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 machv2


To the developers/maintainers of the openCyto package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1338/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
openCyto 2.6.0  (landing page)
Mike Jiang ,Jake Wagner
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/openCyto
git_branch: RELEASE_3_14
git_last_commit: f3e02cd
git_last_commit_date: 2021-10-26 12:10:31 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: openCyto
Version: 2.6.0
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_2.6.0.tar.gz
StartedAt: 2022-04-12 16:21:02 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 16:26:06 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 304.7 seconds
RetCode: 0
Status:   OK  
CheckDir: openCyto.Rcheck
Warnings: 0

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_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/openCyto.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘openCyto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘openCyto’ version ‘2.6.0’
* 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 ‘openCyto’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Namespace in Imports field not imported from: ‘flowViz’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘flowClust:::.ellipsePoints’ ‘flowStats:::drvkde’
  ‘flowWorkspace:::.addGate’ ‘flowWorkspace:::.cpp_addGate’
  ‘flowWorkspace:::.cpp_boolGating’ ‘flowWorkspace:::.cpp_setIndices’
  ‘flowWorkspace:::.getAllDescendants’
  ‘flowWorkspace:::filter_to_list.booleanFilter’
  ‘flowWorkspace:::filter_to_list.rectangleGate’ ‘lattice:::updateList’
  ‘ncdfFlow:::toBitVec’ ‘ncdfFlow:::toLogical’
  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 ... OK
* 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’
.gate_tail: no visible global function definition for ‘exprs’
.gate_tail: no visible global function definition for ‘exprs<-’
.gate_tail: no visible global function definition for ‘rectangleGate’
.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_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’
.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’
.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’
.tailgate: no visible global function definition for ‘exprs’
.tailgate: no visible global function definition for ‘exprs<-’
.tailgate: no visible global function definition for ‘rectangleGate’
.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_tail: no visible global function definition for ‘exprs’
gate_tail: no visible global function definition for ‘rectangleGate’
gate_tautstring: no visible global function definition for ‘exprs’
gate_tautstring: no visible global function definition for
  ‘rectangleGate’
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’
tailgate: no visible global function definition for ‘exprs’
tailgate: no visible global function definition for ‘rectangleGate’
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’
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 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 median na.omit new par
  parent 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", "cov", "cov.wt", "cutree", "density", "dist",
             "dnorm", "embed", "filter", "hclust", "kmeans", "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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* 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
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/openCyto.Rcheck/00check.log’
for details.



Installation output

openCyto.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘openCyto’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cpPmden.cpp -o cpPmden.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cppApprox.cpp -o cppApprox.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cppdip.cpp -o cppdip.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c dynamic_prog.cpp -o dynamic_prog.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c fill_SMAWK.cpp -o fill_SMAWK.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c getTautStringApprox.cpp -o getTautStringApprox.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c kMedDP.cpp -o kMedDP.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c kkuiper.cpp -o kkuiper.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c local_density.cpp -o local_density.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c medianAbsoluteDeviation.cpp -o medianAbsoluteDeviation.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c misc.cpp -o misc.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c rQuantile.cpp -o rQuantile.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c singleDip.cpp -o singleDip.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c tautstring.cpp -o tautstring.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c tsGates.cpp -o tsGates.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c unlockNamespace.c -o unlockNamespace.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o openCyto.so RcppExports.o cpPmden.o cppApprox.o cppdip.o dynamic_prog.o fill_SMAWK.o getTautStringApprox.o kMedDP.o kkuiper.o local_density.o medianAbsoluteDeviation.o misc.o rQuantile.o singleDip.o tautstring.o tsGates.o unlockNamespace.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/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


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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> library(testthat)
> library(openCyto)
> 
> test_check("openCyto")
Loading required package: RcppArmadillo
Loading required package: BH
[ FAIL 0 | WARN 4 | SKIP 1 | PASS 148 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• dir.exists(file.path(localPath, "misc")) is not TRUE (1)

[ FAIL 0 | WARN 4 | SKIP 1 | PASS 148 ]
> 
> #devtools::test()
> 
> #taking quite some time , thus only for internal testing
> #test_file("~/rglab/workspace/openCyto/tests/testthat/gating-testSuite.R")
> 
> proc.time()
   user  system elapsed 
 90.617   2.403  93.144 

Example timings

openCyto.Rcheck/openCyto-Ex.timings

nameusersystemelapsed
gate_flowclust_1d0.0010.0000.001
gate_flowclust_2d0.0010.0000.001
gate_mindensity0.0000.0010.001
gate_mindensity20.0000.0000.001
gate_quantile0.0000.0000.001
gate_tail0.0000.0010.001
gatingTemplate-class0.0000.0010.000
gh_generate_template0.1600.0190.180
gs_add_gating_method0.0000.0010.000
gs_add_gating_method_init0.0000.0010.000
gs_remove_gating_method0.0000.0010.000
gtMethod-class000
gtPopulation-class0.0000.0000.001
gt_gating0.0000.0000.001
gt_get_children000
gt_get_gate000
gt_get_nodes0.0000.0010.001
gt_get_parent000
gt_toggle_helpergates0.0000.0000.001
names-gtMethod-method0.0000.0000.001
openCyto0.0000.0000.001
openCyto.options0.0000.0000.001
plot-fcFilterList-ANY-method0.0000.0000.001
plot-gatingTemplate-missing-method0.0000.0010.000
ppMethod-class0.0000.0000.001
ppMethod-gatingTemplate-character-method0.0000.0000.001