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CHECK report for openCyto on tokay2

This page was generated on 2019-10-16 12:28:45 -0400 (Wed, 16 Oct 2019).

Package 1143/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
openCyto 1.22.2
Mike Jiang
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/openCyto
Branch: RELEASE_3_9
Last Commit: 230adb5
Last Changed Date: 2019-06-03 16:55:58 -0400 (Mon, 03 Jun 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: openCyto
Version: 1.22.2
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:openCyto.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings openCyto_1.22.2.tar.gz
StartedAt: 2019-10-16 05:44:08 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:51:06 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 418.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: openCyto.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:openCyto.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings openCyto_1.22.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/openCyto.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.22.2'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdiGyK/R.INSTALL22f85bb03fb4/openCyto/man/add_pop.Rd:34: file link 'load_gs' in package 'flowWorkspace' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/openCyto.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'flowWorkspace'
A package should be listed in only one of these fields.
* 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
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'flowViz'
  All declared Imports should be used.
':::' call which should be '::': 'flowWorkspace:::isNegated'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'flowClust:::.ellipsePoints' 'flowStats:::drvkde'
  'flowStats:::warpSetNCDF' 'flowWorkspace:::.cpp_addGate'
  'flowWorkspace:::.getAllDescendants' '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'
.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 'extends'
.gating_gtMethod: no visible global function definition for 'extends'
.gating_refGate : : no visible global function definition
  for 'rectangleGate'
.gating_refGate: no visible global function definition for 'filterList'
.gen_1dgate : : no visible binding for global variable
  'parent'
.gen_1dgate : : no visible binding for global variable
  'gating_method'
.gen_1dgate : : no visible binding for global variable
  'gating_args'
.gen_1dgate : : no visible binding for global variable
  'collapseDataForGating'
.gen_1dgate : : no visible binding for global variable
  'preprocessing_method'
.gen_1dgate : : no visible binding for global variable
  'preprocessing_args'
.gen_dummy_ref_gate: no visible binding for global variable 'parent'
.gen_dummy_ref_gate : : no visible binding for global
  variable 'pop'
.gen_dummy_ref_gate : : no visible binding for global
  variable 'gating_method'
.gen_dummy_ref_gate : : no visible binding for global
  variable 'gating_args'
.gen_dummy_ref_gate : : no visible binding for global
  variable 'collapseDataForGating'
.gen_dummy_ref_gate : : no visible binding for global
  variable 'preprocessing_method'
.gen_dummy_ref_gate : : 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 : : 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 : : no visible global function definition
  for 'sd'
.prior_flowClust1d: no visible binding for global variable 'var'
.prior_flowClust1d : : no visible global function definition
  for 'embed'
.prior_flowClust1d : : no visible binding for global
  variable 'var'
.prior_kmeans : : no visible global function definition for
  'exprs'
.prior_kmeans : : no visible global function definition for
  'kmeans'
.prior_kmeans :  : : no visible global function
  definition for 'cov'
.prior_kmeans : : 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 : : 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.FCS.csv: no visible global function definition for 'parameters<-'
.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'
add_pop: no visible global function definition for 'is'
add_pop_init: no visible global function definition for 'is'
as.data.table.gatingTemplate : : no visible global function
  definition for 'extends'
fcEllipsoidGate: no visible global function definition for 'as'
fcFilterList : : 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'
flowClust.1d: no visible global function definition for 'exprs'
flowClust.1d: no visible global function definition for 'rectangleGate'
flowClust.1d: no visible global function definition for 'abline'
flowClust.1d: no visible global function definition for 'rainbow'
flowClust.1d: no visible global function definition for 'lines'
flowClust.2d: no visible global function definition for 'new'
flowClust.2d: no visible global function definition for 'dist'
flowClust.2d: no visible global function definition for 'qchisq'
flowClust.2d: no visible global function definition for 'exprs'
flowClust.2d: no visible global function definition for 'sd'
flowClust.2d: no visible global function definition for 'polygonGate'
flowClust.2d: no visible global function definition for 'lines'
flowClust.2d: no visible global function definition for 'points'
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 : : 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 : : 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'
mindensity: no visible global function definition for 'exprs'
mindensity: no visible global function definition for 'rectangleGate'
mindensity2: no visible global function definition for 'exprs'
mindensity2: no visible global function definition for 'rectangleGate'
ocRectRefGate: no visible global function definition for 'as'
quadGate.seq : : no visible global function definition for
  'exprs'
quadGate.seq: no visible global function definition for 'filter'
quadGate.seq: no visible global function definition for 'as'
quadGate.seq : : no visible global function definition for
  'rectangleGate'
quadGate.seq: no visible global function definition for 'filters'
quadGate.tmix: no visible global function definition for 'filter'
quadGate.tmix: no visible global function definition for 'as'
quadGate.tmix: no visible global function definition for 'polygonGate'
quadGate.tmix: no visible global function definition for 'filters'
quantileGate: no visible global function definition for 'exprs'
quantileGate: no visible global function definition for 'quantile'
quantileGate: no visible global function definition for 'hist'
quantileGate: no visible global function definition for 'density'
quantileGate: no visible global function definition for 'abline'
quantileGate: no visible global function definition for 'text'
quantileGate: no visible global function definition for 'rectangleGate'
remove_pop: no visible global function definition for 'is'
tailgate: no visible global function definition for 'exprs'
tailgate: no visible global function definition for 'rectangleGate'
tautStringGate: no visible global function definition for 'exprs'
tautStringGate: no visible global function definition for
  'rectangleGate'
add,GatingHierarchy-ocRectRefGate: no visible global function
  definition for 'selectMethod'
coerce,ncdfFlowList-flowFrame: no visible global function definition
  for 'selectMethod'
coerce,ncdfFlowSet-flowFrame: no visible global function definition for
  'fsApply'
coerce,ncdfFlowSet-flowFrame : : no visible global function
  definition for 'exprs'
coerce,ncdfFlowSet-flowFrame: no visible global function definition for
  'new'
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 : : 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
  parameters<- parent points polygonGate pop predict preprocessing_args
  preprocessing_method pt qchisq qf 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 ... WARNING
Codoc mismatches from documentation object 'add_pop_init':
add_pop_init
  Code: function(gs = NULL)
  Docs: function(GatingSet)
  Argument names in code not in docs:
    gs
  Argument names in docs not in code:
    GatingSet
  Mismatches in argument names:
    Position: 1 Code: gs Docs: GatingSet
add_pop_init
  Code: function(gs = NULL)
  Docs: function(GatingSetList)
  Argument names in code not in docs:
    gs
  Argument names in docs not in code:
    GatingSetList
  Mismatches in argument names:
    Position: 1 Code: gs Docs: GatingSetList
add_pop_init
  Code: function(gs = NULL)
  Docs: function()
  Argument names in code not in docs:
    gs

Codoc mismatches from documentation object 'remove_pop':
remove_pop
  Code: function(gs)
  Docs: function(GatingSet)
  Argument names in code not in docs:
    gs
  Argument names in docs not in code:
    GatingSet
  Mismatches in argument names:
    Position: 1 Code: gs Docs: GatingSet
remove_pop
  Code: function(gs)
  Docs: function(GatingSetList)
  Argument names in code not in docs:
    gs
  Argument names in docs not in code:
    GatingSetList
  Mismatches in argument names:
    Position: 1 Code: gs Docs: GatingSetList

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'add_pop_init'
  'GatingSet' 'GatingSetList'

Documented arguments not in \usage in documentation object 'gate_tail':
  'method' 'auto_tol' 'adjust'

Undocumented arguments in documentation object 'remove_pop'
  'GatingSet' 'GatingSetList'
Documented arguments not in \usage in documentation object 'remove_pop':
  'gs'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-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 'C:/Users/biocbuild/bbs-3.9-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 WARNINGs, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-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 https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/openCyto_1.22.2.tar.gz && rm -rf openCyto.buildbin-libdir && mkdir openCyto.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=openCyto.buildbin-libdir openCyto_1.22.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL openCyto_1.22.2.zip && rm openCyto_1.22.2.tar.gz openCyto_1.22.2.zip
###
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install for i386

* installing *source* package 'openCyto' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cpPmden.cpp -o cpPmden.o
cpPmden.cpp: In function 'stringInfo cpPmden(const std::vector&)':
cpPmden.cpp:88:22: warning: comparison between signed and unsigned integer expressions [-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:156:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 0; i < nsamp; i++) {
                        ^
cpPmden.cpp:162:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i=0; i < (nsamp-2); i++) {
                      ^
cpPmden.cpp:186:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 0; i < nsamp; i++) {
                        ^
cpPmden.cpp:212:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (auto i = 0; i < nsamp; i++) {
                          ^
cpPmden.cpp:244:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (auto i = 0; i < nsamp; i++) {
                          ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cppApprox.cpp -o cppApprox.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cppdip.cpp -o cppdip.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dynamic_prog.cpp -o dynamic_prog.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c fill_SMAWK.cpp -o fill_SMAWK.o
fill_SMAWK.cpp: In function 'void reduce_in_place(int, int, int, int, const std::vector&, std::vector&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)':
fill_SMAWK.cpp:80:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(N >= js.size()) {
        ^
fill_SMAWK.cpp:90:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(m > N) { // js_reduced has more than N positions / columns
           ^
fill_SMAWK.cpp:121:25: warning: comparison between signed and unsigned integer expressions [-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&, std::vector >&, std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)':
fill_SMAWK.cpp:164:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(++ r; r < n && js[r]<=jmax; r++) {
                 ^
fill_SMAWK.cpp:164:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(++ r; r < n && js[r]<=jmax; r++) {
                             ^
fill_SMAWK.cpp:168:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(jabs > i) break;
               ^
fill_SMAWK.cpp: In function 'void find_min_from_candidates(int, int, int, int, const std::vector&, std::vector >&, std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)':
fill_SMAWK.cpp:218:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(j_abs > i) break;
                ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getTautStringApprox.cpp -o getTautStringApprox.o
getTautStringApprox.cpp: In function 'Rcpp::List getTautStringApprox(std::vector)':
getTautStringApprox.cpp:32:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 1; i != fullString.size(); ++i) {
                     ^
getTautStringApprox.cpp:56:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i  = 0; i != plotSpecs.size(); ++i) {
                      ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c kMedDP.cpp -o kMedDP.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c kkuiper.cpp -o kkuiper.o
kkuiper.cpp: In function 'void difficultmax(std::vector&, 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&, long int, long int, long int, long int*, long int*, double*)':
kkuiper.cpp:64:15: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *erga=maxi;
               ^
kkuiper.cpp:63:15: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ergb=mini;
               ^
kkuiper.cpp: In function 'void difficultmax(std::vector&, 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 kkuiper(std::vector&, long int, int)':
kkuiper.cpp:64:15: 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:63:15: 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:64:15: 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:63:15: 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&)':
medianAbsoluteDeviation.cpp:28:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i != devs.size(); ++i) 
                      ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c misc.cpp -o misc.o
misc.cpp: In function 'Rcpp::NumericMatrix collapseData(Rcpp::List, Rcpp::StringVector)':
misc.cpp:10:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned i = 0; i < mat_list.size(); i++){
                        ^
misc.cpp:21:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned ind = 0; ind < mat_list.size(); ind++){
                               ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rQuantile.cpp -o rQuantile.o
rQuantile.cpp: In function 'std::vector rQuantile(const std::vector&, std::vector)':
rQuantile.cpp:35:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i != lowInd.size(); ++i) {
                      ^
rQuantile.cpp:41:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i != lowInd.size(); ++i) {
                      ^
rQuantile.cpp:47:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i != offSet.size(); ++i) 
                      ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c singleDip.cpp -o singleDip.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c tautstring.cpp -o tautstring.o
tautstring.cpp: In function 'stringInfo tautString(const std::vector&, const std::vector&, const std::vector&, const std::vector&, double, double, long int, int)':
tautstring.cpp:148:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i < knotst.size(); i++) {
                      ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c tsGates.cpp -o tsGates.o
tsGates.cpp: In function 'std::vector findKmedGates(const std::vector&, const std::vector&, int)':
tsGates.cpp:41:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto j = 0; j != classVector.size(); j++)
                        ^
tsGates.cpp: In function 'std::vector tsGates(const std::vector&, int)':
tsGates.cpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 1; i != (localMins.size()-1); ++i) {
                        ^
tsGates.cpp:86:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 0; i != yvals.size(); ++i) 
                        ^
tsGates.cpp:96:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto j = 0; j != cutValues.size(); ++j) {
                        ^
tsGates.cpp:99:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (auto i = 0; i != ys.size(); ++i) 
                          ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c unlockNamespace.c -o unlockNamespace.o
C:/Rtools/mingw_32/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 -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-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
    add                                     html  
    add_pop                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEdiGyK/R.INSTALL22f85bb03fb4/openCyto/man/add_pop.Rd:34: file link 'load_gs' in package 'flowWorkspace' does not exist and so has been treated as a topic
    add_pop_init                            html  
    finding level-2 HTML links ... done

    as.data.table.gatingTemplate            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  
    flowClust1d                             html  
    flowClust2d                             html  
    gate_mindensity                         html  
    gate_mindensity2                        html  
    gate_quad_sequential                    html  
    gate_quad_tmix                          html  
    gate_quantile                           html  
    gate_tail                               html  
    gating-gtMethod-GatingSet-method        html  
    gating-methods                          html  
    gatingTemplate-class                    html  
    getChildren-gatingTemplate-character-method
                                            html  
    getGate-fcTree-character-method         html  
    getGate-gatingTemplate-character-method
                                            html  
    getNodes-fcTree-method                  html  
    getNodes                                html  
    getParent-gatingTemplate-character-method
                                            html  
    groupBy-gtMethod-method                 html  
    gtMethod-class                          html  
    gtPopulation-class                      html  
    gtSubsets-class                         html  
    isCollapse-gtMethod-method              html  
    listgtMethods                           html  
    names-gtMethod-method                   html  
    names-gtPopulation-method               html  
    ocRectRefGate-class                     html  
    ocRectRefGate                           html  
    ocRectangleGate-class                   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  
    priors-fcFilter-ANY-method              html  
    refGate-class                           html  
    registerPlugins                         html  
    remove_pop                              html  
    show-boolMethod-method                  html  
    show-fcFilter-method                    html  
    show-gatingTemplate-method              html  
    show-gtMethod-method                    html  
    tautString                              html  
    templateGen                             html  
    toggle.helperGates                      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:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cpPmden.cpp -o cpPmden.o
cpPmden.cpp: In function 'stringInfo cpPmden(const std::vector&)':
cpPmden.cpp:88:22: warning: comparison between signed and unsigned integer expressions [-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:156:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 0; i < nsamp; i++) {
                        ^
cpPmden.cpp:162:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i=0; i < (nsamp-2); i++) {
                      ^
cpPmden.cpp:186:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 0; i < nsamp; i++) {
                        ^
cpPmden.cpp:212:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (auto i = 0; i < nsamp; i++) {
                          ^
cpPmden.cpp:244:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (auto i = 0; i < nsamp; i++) {
                          ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cppApprox.cpp -o cppApprox.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cppdip.cpp -o cppdip.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dynamic_prog.cpp -o dynamic_prog.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c fill_SMAWK.cpp -o fill_SMAWK.o
fill_SMAWK.cpp: In function 'void reduce_in_place(int, int, int, int, const std::vector&, std::vector&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)':
fill_SMAWK.cpp:80:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(N >= js.size()) {
        ^
fill_SMAWK.cpp:90:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(m > N) { // js_reduced has more than N positions / columns
           ^
fill_SMAWK.cpp:121:25: warning: comparison between signed and unsigned integer expressions [-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&, std::vector >&, std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)':
fill_SMAWK.cpp:164:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(++ r; r < n && js[r]<=jmax; r++) {
                 ^
fill_SMAWK.cpp:164:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(++ r; r < n && js[r]<=jmax; r++) {
                             ^
fill_SMAWK.cpp:168:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(jabs > i) break;
               ^
fill_SMAWK.cpp: In function 'void find_min_from_candidates(int, int, int, int, const std::vector&, std::vector >&, std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, DISSIMILARITY)':
fill_SMAWK.cpp:218:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(j_abs > i) break;
                ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getTautStringApprox.cpp -o getTautStringApprox.o
getTautStringApprox.cpp: In function 'Rcpp::List getTautStringApprox(std::vector)':
getTautStringApprox.cpp:32:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 1; i != fullString.size(); ++i) {
                     ^
getTautStringApprox.cpp:56:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i  = 0; i != plotSpecs.size(); ++i) {
                      ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c kMedDP.cpp -o kMedDP.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c kkuiper.cpp -o kkuiper.o
kkuiper.cpp: In function 'void difficultmax(std::vector&, 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&, long int, long int, long int, long int*, long int*, double*)':
kkuiper.cpp:64:15: warning: 'maxi' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *erga=maxi;
               ^
kkuiper.cpp:63:15: warning: 'mini' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *ergb=mini;
               ^
kkuiper.cpp: In function 'void difficultmax(std::vector&, 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 kkuiper(std::vector&, long int, int)':
kkuiper.cpp:64:15: 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:63:15: 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:64:15: 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:63:15: 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&)':
medianAbsoluteDeviation.cpp:28:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i != devs.size(); ++i) 
                      ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c misc.cpp -o misc.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rQuantile.cpp -o rQuantile.o
rQuantile.cpp: In function 'std::vector rQuantile(const std::vector&, std::vector)':
rQuantile.cpp:35:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i != lowInd.size(); ++i) {
                      ^
rQuantile.cpp:41:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i != lowInd.size(); ++i) {
                      ^
rQuantile.cpp:47:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i != offSet.size(); ++i) 
                      ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c singleDip.cpp -o singleDip.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c tautstring.cpp -o tautstring.o
tautstring.cpp: In function 'stringInfo tautString(const std::vector&, const std::vector&, const std::vector&, const std::vector&, double, double, long int, int)':
tautstring.cpp:148:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (auto i = 0; i < knotst.size(); i++) {
                      ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c tsGates.cpp -o tsGates.o
tsGates.cpp: In function 'std::vector findKmedGates(const std::vector&, const std::vector&, int)':
tsGates.cpp:41:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto j = 0; j != classVector.size(); j++)
                        ^
tsGates.cpp: In function 'std::vector tsGates(const std::vector&, int)':
tsGates.cpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 1; i != (localMins.size()-1); ++i) {
                        ^
tsGates.cpp:86:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto i = 0; i != yvals.size(); ++i) 
                        ^
tsGates.cpp:96:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (auto j = 0; j != cutValues.size(); ++j) {
                        ^
tsGates.cpp:99:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (auto i = 0; i != ys.size(); ++i) 
                          ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c unlockNamespace.c -o unlockNamespace.o
C:/Rtools/mingw_64/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 -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/openCyto.buildbin-libdir/openCyto/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'openCyto' as openCyto_1.22.2.zip
* DONE (openCyto)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'openCyto' successfully unpacked and MD5 sums checked

Tests output

openCyto.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)
Loading required package: flowWorkspace
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
> 
> test_check("openCyto")
== testthat results  ===========================================================
[ OK: 128 | SKIPPED: 0 | WARNINGS: 9 | FAILED: 0 ]
> 
> #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 
  77.62   17.59   99.32

openCyto.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)
Loading required package: flowWorkspace
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
> 
> test_check("openCyto")
== testthat results  ===========================================================
[ OK: 128 | SKIPPED: 0 | WARNINGS: 9 | FAILED: 0 ]
> 
> #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 
  82.09    8.90  128.29

Example timings

openCyto.Rcheck/examples_i386/openCyto-Ex.timings

nameusersystemelapsed
add_pop000
add_pop_init000
flowClust1d000
flowClust2d000
gate_mindensity000
gate_mindensity2000
gate_quantile000
gate_tail000
gating-methods000
gatingTemplate-class000
getChildren-gatingTemplate-character-method000
getGate-gatingTemplate-character-method000
getNodes000
getParent-gatingTemplate-character-method000
gtMethod-class000
gtPopulation-class000
names-gtMethod-method000
openCyto000
openCyto.options000
plot-fcFilterList-ANY-method000
plot-gatingTemplate-missing-method000
ppMethod-class000
ppMethod-gatingTemplate-character-method000
remove_pop000
toggle.helperGates000

openCyto.Rcheck/examples_x64/openCyto-Ex.timings

nameusersystemelapsed
add_pop000
add_pop_init000
flowClust1d000
flowClust2d000
gate_mindensity000
gate_mindensity2000
gate_quantile000
gate_tail000
gating-methods000
gatingTemplate-class000
getChildren-gatingTemplate-character-method000
getGate-gatingTemplate-character-method000
getNodes000
getParent-gatingTemplate-character-method000
gtMethod-class000
gtPopulation-class000
names-gtMethod-method000
openCyto000
openCyto.options000
plot-fcFilterList-ANY-method000
plot-gatingTemplate-missing-method000
ppMethod-class000
ppMethod-gatingTemplate-character-method000
remove_pop000
toggle.helperGates000