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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:openCyto.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings openCyto_2.8.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/openCyto.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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 ‘2.8.4’
* 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’
  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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/openCyto.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL openCyto
###
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘openCyto’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cpPmden.cpp -o cpPmden.o
cpPmden.cpp: In function ‘stringInfo cpPmden(const std::vector<double>&)’:
cpPmden.cpp:88:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
   88 |   for (auto i = 0; i < (nsamp-1); i++) {
      |                    ~~^~~~~~~~~~~
cpPmden.cpp:100:17: warning: variable ‘newaccx’ set but not used [-Wunused-but-set-variable]
  100 |     double rhs, newaccx;
      |                 ^~~~~~~
cpPmden.cpp:157:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  157 |     for (auto i = 0; i < nsamp; i++) {
      |                      ~~^~~~~~~
cpPmden.cpp:164:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  164 |     for (auto i=0; i < (nsamp-2); i++) {
      |                    ~~^~~~~~~~~~~
cpPmden.cpp:193:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  193 |     for (auto i = 0; i < nsamp; i++) {
      |                      ~~^~~~~~~
cpPmden.cpp:219:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  219 |       for (auto i = 0; i < nsamp; i++) {
      |                        ~~^~~~~~~
cpPmden.cpp:251:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
  251 |       for (auto i = 0; i < nsamp; i++) {
      |                        ~~^~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cppApprox.cpp -o cppApprox.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cppdip.cpp -o cppdip.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c dynamic_prog.cpp -o dynamic_prog.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fill_SMAWK.cpp -o fill_SMAWK.o
fill_SMAWK.cpp: In function ‘void reduce_in_place(int, int, int, int, const std::vector<long unsigned int>&, std::vector<long unsigned int>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<long unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)’:
fill_SMAWK.cpp:80:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   80 |   if(N >= js.size()) {
      |      ~~^~~~~~~~~~~~
fill_SMAWK.cpp:90:11: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   90 |   while(m > N) { // js_reduced has more than N positions / columns
      |         ~~^~~
fill_SMAWK.cpp:121:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  121 |   for(int r=(left+1); r < m; ++r) {
      |                       ~~^~~
fill_SMAWK.cpp: In function ‘void fill_even_positions(int, int, int, int, const std::vector<long unsigned int>&, std::vector<std::vector<double> >&, std::vector<std::vector<long unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)’:
fill_SMAWK.cpp:164:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  164 |     for(++ r; r < n && js[r]<=jmax; r++) {
      |               ~~^~~
fill_SMAWK.cpp:164:29: warning: comparison of integer expressions of different signedness: ‘const value_type’ {aka ‘const long unsigned int’} and ‘int’ [-Wsign-compare]
  164 |     for(++ r; r < n && js[r]<=jmax; r++) {
fill_SMAWK.cpp:168:15: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘int’ [-Wsign-compare]
  168 |       if(jabs > i) break;
      |          ~~~~~^~~
fill_SMAWK.cpp: In function ‘void find_min_from_candidates(int, int, int, int, const std::vector<long unsigned int>&, std::vector<std::vector<double> >&, std::vector<std::vector<long unsigned int> >&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, DISSIMILARITY)’:
fill_SMAWK.cpp:218:16: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘int’ [-Wsign-compare]
  218 |       if(j_abs > i) break;
      |          ~~~~~~^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getTautStringApprox.cpp -o getTautStringApprox.o
getTautStringApprox.cpp: In function ‘Rcpp::List getTautStringApprox(std::vector<double>)’:
getTautStringApprox.cpp:32:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   32 |   for (int i = 1; i != fullString.size(); ++i) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~
getTautStringApprox.cpp:56:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<stringPairs>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   56 |   for (int i  = 0; i != plotSpecs.size(); ++i) {
      |                    ~~^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c kMedDP.cpp -o kMedDP.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c kkuiper.cpp -o kkuiper.o
kkuiper.cpp: In function ‘void difficultmax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)’:
kkuiper.cpp:77:10: warning: variable ‘min’ set but not used [-Wunused-but-set-variable]
   77 |   double min, max;
      |          ^~~
kkuiper.cpp: In function ‘void easymax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)’:
kkuiper.cpp:64:10: warning: ‘maxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   64 |     *erga=maxi;
      |     ~~~~~^~~~~
kkuiper.cpp:63:10: warning: ‘mini’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   63 |     *ergb=mini;
      |     ~~~~~^~~~~
kkuiper.cpp: In function ‘void difficultmax(std::vector<double>&, long int, long int, long int, long int*, long int*, double*)’:
kkuiper.cpp:161:23: warning: ‘maxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  161 |       *erga=minis[maxi];
      |                       ^
kkuiper.cpp: In function ‘std::vector<double> kkuiper(std::vector<double>&, long int, int)’:
kkuiper.cpp:176:15: warning: ‘maxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  176 |   long i,mini,maxi,maxa,maxb,newa,newb,einordnen ;
      |               ^~~~
kkuiper.cpp:176:10: warning: ‘mini’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  176 |   long i,mini,maxi,maxa,maxb,newa,newb,einordnen ;
      |          ^~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c local_density.cpp -o local_density.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c medianAbsoluteDeviation.cpp -o medianAbsoluteDeviation.o
medianAbsoluteDeviation.cpp: In function ‘double medianAbsoluteDeviation(const std::vector<double>&)’:
medianAbsoluteDeviation.cpp:28:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   28 |   for (auto i = 0; i != devs.size(); ++i)
      |                    ~~^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c misc.cpp -o misc.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rQuantile.cpp -o rQuantile.o
rQuantile.cpp: In function ‘std::vector<double> rQuantile(const std::vector<double>&, std::vector<double>)’:
rQuantile.cpp:35:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   35 |   for (auto i = 0; i != lowInd.size(); ++i) {
      |                    ~~^~~~~~~~~~~~~~~~
rQuantile.cpp:41:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   41 |   for (auto i = 0; i != lowInd.size(); ++i) {
      |                    ~~^~~~~~~~~~~~~~~~
rQuantile.cpp:47:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   47 |   for (auto i = 0; i != offSet.size(); ++i)
      |                    ~~^~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c singleDip.cpp -o singleDip.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c tautstring.cpp -o tautstring.o
tautstring.cpp: In function ‘stringInfo tautString(const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&, double, double, long int, int)’:
tautstring.cpp:148:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  148 |   for (auto i = 0; i < knotst.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c tsGates.cpp -o tsGates.o
tsGates.cpp: In function ‘std::vector<double> findKmedGates(const std::vector<double>&, const std::vector<int>&, int)’:
tsGates.cpp:41:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   41 |     for (auto j = 0; j != classVector.size(); j++)
      |                      ~~^~~~~~~~~~~~~~~~~~~~~
tsGates.cpp: In function ‘std::vector<double> tsGates(const std::vector<double>&, int)’:
tsGates.cpp:81:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   81 |     for (auto i = 1; i != (localMins.size()-1); ++i) {
      |                      ~~^~~~~~~~~~~~~~~~~~~~~~~
tsGates.cpp:86:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   86 |     for (auto i = 0; i != yvals.size(); ++i)
      |                      ~~^~~~~~~~~~~~~~~
tsGates.cpp:96:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   96 |     for (auto j = 0; j != cutValues.size(); ++j) {
      |                      ~~^~~~~~~~~~~~~~~~~~~
tsGates.cpp:99:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   99 |       for (auto i = 0; i != ys.size(); ++i)
      |                        ~~^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c unlockNamespace.c -o unlockNamespace.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.15-bioc/R/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 -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-openCyto/00new/openCyto/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘flowViz::contour’ by ‘graphics::contour’ when loading ‘flowStats’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘flowViz::contour’ by ‘graphics::contour’ when loading ‘flowStats’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘flowViz::contour’ by ‘graphics::contour’ when loading ‘flowStats’
** testing if installed package keeps a record of temporary installation path
* DONE (openCyto)

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(testthat)
> library(openCyto)
Warning message:
replacing previous import 'flowViz::contour' by 'graphics::contour' when loading 'flowStats' 
> 
> test_check("openCyto")
Loading required package: RcppArmadillo
Loading required package: BH
[ FAIL 0 | WARN 8 | SKIP 1 | PASS 154 ]

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

[ FAIL 0 | WARN 8 | SKIP 1 | PASS 154 ]
> 
> #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 
 58.055   1.991  60.038