Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-08-02 12:04:53 -0400 (Mon, 02 Aug 2021).

CHECK results for openCyto on riesling1

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? here 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 1297/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
openCyto 2.5.4  (landing page)
Mike Jiang ,Jake Wagner
Snapshot Date: 2021-08-01 14:50:04 -0400 (Sun, 01 Aug 2021)
URL: https://git.bioconductor.org/packages/openCyto
Branch: master
Last Commit: 22c609b
Last Changed Date: 2021-07-30 13:41:51 -0400 (Fri, 30 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  NO, package depends on 'flowWorkspace' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: openCyto
Version: 2.5.4
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:openCyto.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings openCyto_2.5.4.tar.gz
StartedAt: 2021-08-02 01:29:04 -0400 (Mon, 02 Aug 2021)
EndedAt: 2021-08-02 01:33:05 -0400 (Mon, 02 Aug 2021)
EllapsedTime: 240.8 seconds
RetCode: 0
Status:   OK  
CheckDir: openCyto.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:openCyto.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings openCyto_2.5.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/openCyto.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'openCyto/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'openCyto' version '2.5.4'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.14-bioc/R/library/openCyto/libs/i386/openCyto.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'D:/biocbuild/bbs-3.14-bioc/R/library/openCyto/libs/x64/openCyto.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'D:/biocbuild/bbs-3.14-bioc/meat/openCyto.Rcheck/00check.log'
for details.



Installation output

openCyto.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/openCyto_2.5.4.tar.gz && rm -rf openCyto.buildbin-libdir && mkdir openCyto.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=openCyto.buildbin-libdir openCyto_2.5.4.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL openCyto_2.5.4.zip && rm openCyto_2.5.4.tar.gz openCyto_2.5.4.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1101k  100 1101k    0     0  4985k      0 --:--:-- --:--:-- --:--:-- 5008k

install for i386

* installing *source* package 'openCyto' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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]
   for (auto i = 0; i < (nsamp-1); i++) {
                    ~~^~~~~~~~~~~
cpPmden.cpp:100:17: warning: variable 'newaccx' set but not used [-Wunused-but-set-variable]
     double rhs, newaccx;
                 ^~~~~~~
cpPmden.cpp:157:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
     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]
     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]
     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]
       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]
       for (auto i = 0; i < nsamp; i++) {
                        ~~^~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cppApprox.cpp -o cppApprox.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cppdip.cpp -o cppdip.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dynamic_prog.cpp -o dynamic_prog.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fill_SMAWK.cpp -o fill_SMAWK.o
fill_SMAWK.cpp: In function 'void reduce_in_place(int, int, int, int, const std::vector<unsigned int>&, std::vector<unsigned int>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<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<unsigned int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   if(N >= js.size()) {
      ~~^~~~~~~~~~~~
fill_SMAWK.cpp:90:11: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   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 'unsigned int'} [-Wsign-compare]
   for(int r=(left+1); r < m; ++r) {
                       ~~^~~
fill_SMAWK.cpp: In function 'void fill_even_positions(int, int, int, int, const std::vector<unsigned int>&, std::vector<std::vector<double> >&, std::vector<std::vector<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 'unsigned int'} [-Wsign-compare]
     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 unsigned int'} and 'int' [-Wsign-compare]
     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 unsigned int'} and 'int' [-Wsign-compare]
       if(jabs > i) break;
          ~~~~~^~~
fill_SMAWK.cpp: In function 'void find_min_from_candidates(int, int, int, int, const std::vector<unsigned int>&, std::vector<std::vector<double> >&, std::vector<std::vector<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 unsigned int'} and 'int' [-Wsign-compare]
       if(j_abs > i) break;
          ~~~~~~^~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 'unsigned int'} [-Wsign-compare]
   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 'unsigned int'} [-Wsign-compare]
   for (int i  = 0; i != plotSpecs.size(); ++i) {
                    ~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kMedDP.cpp -o kMedDP.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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]
   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]
     *erga=maxi;
     ~~~~~^~~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *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]
       *erga=minis[maxi];
                       ^
kkuiper.cpp: In function 'std::vector<double> kkuiper(std::vector<double>&, long int, int)':
kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *erga=maxi;
     ~~~~~^~~~~
kkuiper.cpp:44:15: note: 'maxi' was declared here
   long i,mini,maxi;
               ^~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ergb=mini;
     ~~~~~^~~~~
kkuiper.cpp:44:10: note: 'mini' was declared here
   long i,mini,maxi;
          ^~~~
kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *erga=maxi;
     ~~~~~^~~~~
kkuiper.cpp:44:15: note: 'maxi' was declared here
   long i,mini,maxi;
               ^~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ergb=mini;
     ~~~~~^~~~~
kkuiper.cpp:44:10: note: 'mini' was declared here
   long i,mini,maxi;
          ^~~~
kkuiper.cpp:58:3: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(mini<maxi) {
   ^~
kkuiper.cpp:44:15: note: 'maxi' was declared here
   long i,mini,maxi;
               ^~~~
kkuiper.cpp:58:3: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(mini<maxi) {
   ^~
kkuiper.cpp:44:10: note: 'mini' was declared here
   long i,mini,maxi;
          ^~~~
kkuiper.cpp:197:9: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
     a[0]=maxi;
kkuiper.cpp:196:9: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     b[0]=mini;
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c local_density.cpp -o local_density.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 'unsigned int'} [-Wsign-compare]
   for (auto i = 0; i != devs.size(); ++i)
                    ~~^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c misc.cpp -o misc.o
misc.cpp: In function 'Rcpp::NumericMatrix collapseData(Rcpp::List, Rcpp::StringVector)':
misc.cpp:10:24: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
  for(unsigned i = 0; i < mat_list.size(); i++){
                      ~~^~~~~~~~~~~~~~~~~
misc.cpp:21:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for(unsigned ind = 0; ind < mat_list.size(); ind++){
                           ~~~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 'unsigned int'} [-Wsign-compare]
   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 'unsigned int'} [-Wsign-compare]
   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 'unsigned int'} [-Wsign-compare]
   for (auto i = 0; i != offSet.size(); ++i)
                    ~~^~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c singleDip.cpp -o singleDip.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 'unsigned int'} [-Wsign-compare]
   for (auto i = 0; i < knotst.size(); i++) {
                    ~~^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 'unsigned int'} [-Wsign-compare]
     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 'unsigned int'} [-Wsign-compare]
     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 'unsigned int'} [-Wsign-compare]
     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 'unsigned int'} [-Wsign-compare]
     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 'unsigned int'} [-Wsign-compare]
       for (auto i = 0; i != ys.size(); ++i)
                        ~~^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c unlockNamespace.c -o unlockNamespace.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o openCyto.dll tmp.def 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 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/openCyto.buildbin-libdir/00LOCK-openCyto/00new/openCyto/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'openCyto'
    finding HTML links ... done
    CytoExploreR_exports                    html  
    add                                     html  
    as.data.table                           html  
    boolMethod-class                        html  
    dims-gtMethod-method                    html  
    dummyMethod-class                       html  
    fcEllipsoidGate-class                   html  
    fcEllipsoidGate                         html  
    fcFilter-class                          html  
    fcFilterList-class                      html  
    fcFilterList                            html  
    fcPolygonGate-class                     html  
    fcPolygonGate                           html  
    fcRectangleGate-class                   html  
    fcRectangleGate                         html  
    fcTree-class                            html  
    fcTree                                  html  
    gate_flowclust_1d                       html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.14-bioc/meat/openCyto.buildbin-libdir/00LOCK-openCyto/00new/openCyto/help/gate_flowClust_1d.html
    finding level-2 HTML links ... done

    gate_flowclust_2d                       html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.14-bioc/meat/openCyto.buildbin-libdir/00LOCK-openCyto/00new/openCyto/help/gate_flowClust_2d.html
    gate_mindensity                         html  
    gate_mindensity2                        html  
    gate_quad_sequential                    html  
    gate_quad_tmix                          html  
    gate_quantile                           html  
    gate_tail                               html  
    gate_tautstring                         html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.14-bioc/meat/openCyto.buildbin-libdir/00LOCK-openCyto/00new/openCyto/help/tautString.html
    gatingTemplate-class                    html  
    getGate-fcTree-character-method         html  
    getNodes-fcTree-method                  html  
    gh_generate_template                    html  
    groupBy-gtMethod-method                 html  
    gs_add_gating_method                    html  
    gs_add_gating_method_init               html  
    gs_remove_gating_method                 html  
    gtMethod-class                          html  
    gtPopulation-class                      html  
    gtSubsets-class                         html  
    gt_gating                               html  
    gt_get_children                         html  
    gt_get_gate                             html  
    gt_get_nodes                            html  
    gt_get_parent                           html  
    gt_list_methods                         html  
    gt_toggle_helpergates                   html  
    isCollapse-gtMethod-method              html  
    names-gtMethod-method                   html  
    names-gtPopulation-method               html  
    ocRectRefGate-class                     html  
    ocRectRefGate                           html  
    ocRectangleGate-class                   html  
    openCyto-deprecated                     html  
    openCyto                                html  
    openCyto.options                        html  
    parameters-gtMethod-method              html  
    plot-fcFilterList-ANY-method            html  
    plot-fcTree-character-method            html  
    plot-gatingTemplate-missing-method      html  
    polyFunctions-class                     html  
    posteriors-fcFilter-ANY-method          html  
    ppMethod-class                          html  
    ppMethod-gatingTemplate-character-method
                                            html  
    preprocessing-ppMethod-GatingSet-method
                                            html  
    prior_flowclust                         html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.14-bioc/meat/openCyto.buildbin-libdir/00LOCK-openCyto/00new/openCyto/help/prior_flowClust.html
    priors-fcFilter-ANY-method              html  
    refGate-class                           html  
    register_plugins                        html  
    show-boolMethod-method                  html  
    show-fcFilter-method                    html  
    show-gatingTemplate-method              html  
    show-gtMethod-method                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'openCyto' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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]
   for (auto i = 0; i < (nsamp-1); i++) {
                    ~~^~~~~~~~~~~
cpPmden.cpp:100:17: warning: variable 'newaccx' set but not used [-Wunused-but-set-variable]
     double rhs, newaccx;
                 ^~~~~~~
cpPmden.cpp:157:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
     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]
     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]
     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]
       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]
       for (auto i = 0; i < nsamp; i++) {
                        ~~^~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cppApprox.cpp -o cppApprox.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cppdip.cpp -o cppdip.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dynamic_prog.cpp -o dynamic_prog.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 long unsigned int>&, std::vector<long long unsigned int>&, const std::vector<std::vector<double> >&, const std::vector<std::vector<long 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 long unsigned int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   if(N >= js.size()) {
      ~~^~~~~~~~~~~~
fill_SMAWK.cpp:90:11: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   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 long unsigned int'} [-Wsign-compare]
   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 long unsigned int>&, std::vector<std::vector<double> >&, std::vector<std::vector<long 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 long unsigned int'} [-Wsign-compare]
     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 long unsigned int'} and 'int' [-Wsign-compare]
     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 long unsigned int'} and 'int' [-Wsign-compare]
       if(jabs > i) break;
          ~~~~~^~~
fill_SMAWK.cpp: In function 'void find_min_from_candidates(int, int, int, int, const std::vector<long long unsigned int>&, std::vector<std::vector<double> >&, std::vector<std::vector<long 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 long unsigned int'} and 'int' [-Wsign-compare]
       if(j_abs > i) break;
          ~~~~~~^~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 long unsigned int'} [-Wsign-compare]
   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 long unsigned int'} [-Wsign-compare]
   for (int i  = 0; i != plotSpecs.size(); ++i) {
                    ~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kMedDP.cpp -o kMedDP.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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]
   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]
     *erga=maxi;
     ~~~~~^~~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *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]
       *erga=minis[maxi];
                       ^
kkuiper.cpp: In function 'std::vector<double> kkuiper(std::vector<double>&, long int, int)':
kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *erga=maxi;
     ~~~~~^~~~~
kkuiper.cpp:44:15: note: 'maxi' was declared here
   long i,mini,maxi;
               ^~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ergb=mini;
     ~~~~~^~~~~
kkuiper.cpp:44:10: note: 'mini' was declared here
   long i,mini,maxi;
          ^~~~
kkuiper.cpp:64:10: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *erga=maxi;
     ~~~~~^~~~~
kkuiper.cpp:44:15: note: 'maxi' was declared here
   long i,mini,maxi;
               ^~~~
kkuiper.cpp:63:10: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ergb=mini;
     ~~~~~^~~~~
kkuiper.cpp:44:10: note: 'mini' was declared here
   long i,mini,maxi;
          ^~~~
kkuiper.cpp:58:3: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(mini<maxi) {
   ^~
kkuiper.cpp:44:15: note: 'maxi' was declared here
   long i,mini,maxi;
               ^~~~
kkuiper.cpp:58:3: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(mini<maxi) {
   ^~
kkuiper.cpp:44:10: note: 'mini' was declared here
   long i,mini,maxi;
          ^~~~
kkuiper.cpp:197:9: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
     a[0]=maxi;
kkuiper.cpp:196:9: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     b[0]=mini;
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c local_density.cpp -o local_density.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 long unsigned int'} [-Wsign-compare]
   for (auto i = 0; i != devs.size(); ++i)
                    ~~^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c misc.cpp -o misc.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 long unsigned int'} [-Wsign-compare]
   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 long unsigned int'} [-Wsign-compare]
   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 long unsigned int'} [-Wsign-compare]
   for (auto i = 0; i != offSet.size(); ++i)
                    ~~^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c singleDip.cpp -o singleDip.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 long unsigned int'} [-Wsign-compare]
   for (auto i = 0; i < knotst.size(); i++) {
                    ~~^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 long unsigned int'} [-Wsign-compare]
     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 long unsigned int'} [-Wsign-compare]
     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 long unsigned int'} [-Wsign-compare]
     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 long unsigned int'} [-Wsign-compare]
     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 long unsigned int'} [-Wsign-compare]
       for (auto i = 0; i != ys.size(); ++i)
                        ~~^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c unlockNamespace.c -o unlockNamespace.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o openCyto.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/openCyto.buildbin-libdir/openCyto/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'openCyto' as openCyto_2.5.4.zip
* DONE (openCyto)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'openCyto' successfully unpacked and MD5 sums checked

Tests output

openCyto.Rcheck/tests_i386/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(openCyto)
> 
> test_check("openCyto")
Loading required package: RcppArmadillo
Loading required package: BH
== Skipped tests ===============================================================
* dir.exists(file.path(localPath, "misc")) is not TRUE (1)

[ FAIL 0 | WARN 79 | SKIP 1 | PASS 148 ]
There were 36 warnings (use warnings() to see them)
> 
> #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 
  36.18    2.65   39.25 

openCyto.Rcheck/tests_x64/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(openCyto)
> 
> test_check("openCyto")
Loading required package: RcppArmadillo
Loading required package: BH
== Skipped tests ===============================================================
* dir.exists(file.path(localPath, "misc")) is not TRUE (1)

[ FAIL 0 | WARN 79 | SKIP 1 | PASS 148 ]
There were 36 warnings (use warnings() to see them)
> 
> #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 
  39.68    2.62   42.67 

Example timings

openCyto.Rcheck/examples_i386/openCyto-Ex.timings

nameusersystemelapsed
gate_flowclust_1d000
gate_flowclust_2d000
gate_mindensity000
gate_mindensity2000
gate_quantile000
gate_tail000
gatingTemplate-class000
gh_generate_template0.150.020.17
gs_add_gating_method000
gs_add_gating_method_init000
gs_remove_gating_method000
gtMethod-class000
gtPopulation-class000
gt_gating000
gt_get_children000
gt_get_gate000
gt_get_nodes000
gt_get_parent000
gt_toggle_helpergates000
names-gtMethod-method000
openCyto000
openCyto.options000
plot-fcFilterList-ANY-method000
plot-gatingTemplate-missing-method000
ppMethod-class000
ppMethod-gatingTemplate-character-method000

openCyto.Rcheck/examples_x64/openCyto-Ex.timings

nameusersystemelapsed
gate_flowclust_1d000
gate_flowclust_2d000
gate_mindensity000
gate_mindensity2000
gate_quantile000
gate_tail000
gatingTemplate-class000
gh_generate_template0.060.020.08
gs_add_gating_method000
gs_add_gating_method_init000
gs_remove_gating_method000
gtMethod-class000
gtPopulation-class000
gt_gating000
gt_get_children000
gt_get_gate000
gt_get_nodes000
gt_get_parent000
gt_toggle_helpergates000
names-gtMethod-method000
openCyto000
openCyto.options000
plot-fcFilterList-ANY-method000
plot-gatingTemplate-missing-method000
ppMethod-class000
ppMethod-gatingTemplate-character-method000