Package: flowWorkspace

Version: 3.34.1

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowWorkspace.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings flowWorkspace_3.34.1.tar.gz

StartedAt: 2020-04-15 03:15:52 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:19:23 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 210.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowWorkspace.Rcheck

Warnings: 4

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowWorkspace.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings flowWorkspace_3.34.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowWorkspace/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowWorkspace' version '3.34.1'
* 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 'flowWorkspace' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCqwvNP/R.INSTALL1d3c4fffcdf/flowWorkspace/man/flowjo_biexp_trans.Rd:13: file link 'flowJoTrans' in package 'flowWorkspace' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 13.2Mb
  sub-directories of 1Mb or more:
    lib    7.3Mb
    libs   4.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Versioned 'LinkingTo' values for
  'BH' 'RProtoBufLib' 'cytolib'
are only usable in R >= 3.0.2
* 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
Namespaces in Imports field not imported from:
  'RBGL' 'grDevices' 'graphics' 'utils'
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  'flowCore:::.estimateLogicle' 'flowCore:::checkClass'
  'flowCore:::copyFlowSet' 'flowCore:::guid'
  'flowCore:::logicle_transform' 'flowCore:::updateTransformKeywords'
  'graph:::.makeEdgeKeys' 'lattice:::updateList'
  'ncdfFlow:::.isValidSamples' 'stats:::.splinefun'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.addGatingHierarchies: no visible global function definition for 'is'
.addGatingHierarchies : <anonymous>: no visible global function
  definition for 'fj_ws_get_keywords'
.computeCV : <anonymous>: no visible binding for global variable
  'xml.count'
.computeCV : <anonymous>: no visible binding for global variable
  'openCyto.count'
.computeCV : <anonymous> : <anonymous>: no visible global function
  definition for 'IQR'
.computeCV : <anonymous> : <anonymous>: no visible global function
  definition for 'median'
.computeCV_gh : <anonymous>: no visible global function definition for
  'IQR'
.computeCV_gh : <anonymous>: no visible global function definition for
  'median'
.graph_handler : asGraphNEL: no visible global function definition for
  'new'
.graph_handler : asGraphNEL: no visible global function definition for
  'validObject'
.load_gs: no visible global function definition for 'new'
.load_gs: no visible global function definition for '.hasSlot'
.load_gs: no visible global function definition for 'slot'
.load_gs: no visible global function definition for 'is'
.mergeGates : <anonymous>: no visible global function definition for
  'extends'
.plotGate: no visible global function definition for 'new'
.plotGate: no visible global function definition for 'as.formula'
.preplot: no visible global function definition for 'as'
.preprocessMap: no visible binding for global variable 'old'
.preprocessMap: no visible binding for global variable '.'
GatingSetList: no visible global function definition for 'as'
GatingSetList: no visible global function definition for 'validObject'
booleanFilter: no visible global function definition for 'new'
booleanFilter: no visible global function definition for 'is'
char2booleanFilter: no visible global function definition for 'new'
flowWorkspace.par.init: no visible global function definition for
  'gray'
gh_apply_to_new_fcs: no visible global function definition for 'new'
gh_pop_compare_stats: no visible binding for global variable 'node'
gh_pop_get_count: no visible binding for global variable 'count'
gh_pop_get_proportion: no visible binding for global variable 'percent'
gh_pop_get_stats_tfilter: no visible global function definition for
  'is'
gs_get_singlecell_expression: no visible global function definition for
  'is'
gs_get_singlecell_expression: no visible binding for global variable
  'parallel'
gs_pop_add: no visible global function definition for 'is'
gs_pop_get_count_fast: no visible global function definition for 'is'
gs_pop_get_count_with_meta: no visible binding for global variable
  'sampleName'
gs_pop_set_gate: no visible global function definition for 'is'
gs_remove_redundant_nodes : <anonymous>: no visible global function
  definition for 'is'
gslist_to_gs: no visible global function definition for 'new'
gslist_to_gs: no visible binding for global variable 'slot'
mkformula: no visible global function definition for 'as.formula'
parse_transformer: no visible global function definition for 'is'
pop.MFI: no visible binding for global variable 'desc'
save_gslist: no visible binding for global variable 'slot'
transformerList: no visible global function definition for 'is'
transformerList: no visible binding for global variable 'is'
GatingSet,flowSet-ANY: no visible global function definition for 'new'
[,GatingSet-ANY: no visible global function definition for 'new'
[,GatingSet-ANY: no visible global function definition for 'extends'
[,GatingSetList-ANY: no visible global function definition for
  'callNextMethod'
[,GatingSetList-ANY: no visible global function definition for 'as'
[[,GatingSet-character: no visible global function definition for 'as'
flowData,GatingSet: no visible binding for global variable 'obj'
gs_cyto_data,GatingSet: no visible global function definition for 'is'
keyword,GatingSetList-character: no visible global function definition
  for 'selectMethod'
keyword,GatingSetList-missing: no visible global function definition
  for 'selectMethod'
pData<-,GatingSetList-data.frame: no visible global function definition
  for 'callNextMethod'
pData<-,GatingSetList-data.frame: no visible global function definition
  for 'as'
plotGate,GatingSetList-character: no visible global function definition
  for 'selectMethod'
recompute,GatingSetList: no visible global function definition for
  'selectMethod'
setNode,GatingSet-character-ANY: no visible global function definition
  for 'is'
transform,GatingSet: no visible global function definition for 'is'
transform,GatingSet : <anonymous>: no visible global function
  definition for 'is'
Undefined global functions or variables:
  . .hasSlot IQR as as.formula callNextMethod count desc extends
  fj_ws_get_keywords gray is median new node obj old openCyto.count
  parallel percent sampleName selectMethod slot validObject xml.count
Consider adding
  importFrom("grDevices", "gray")
  importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
             "is", "new", "selectMethod", "slot", "validObject")
  importFrom("stats", "IQR", "as.formula", "median")
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 ... WARNING
Undocumented code objects:
  'getChildren' 'getData' 'getGate' 'getNodes' 'getParent'
  'getPopStats' 'gh_pop_get_stats_tfilter' 'gs_cyto_data<-'
  'gs_pop_get_stats_tfilter'
Undocumented S4 methods:
  generic 'flowData<-' and siglist 'GatingSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'GatingSet-class':
Slots for class 'GatingSet'
  Code: FCSPath axis compensation data flag guid name pointer
        transformation
  Docs: FCSPath axis compensation data flag guid pointer transformation

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'GatingSet-class'
  'value'

Undocumented arguments in documentation object 'GatingSet,flowSet,ANY-method'
  'x'

Undocumented arguments in documentation object 'flowjo_log_trans'
  'n' 'equal.space' 'max_val' 'min_val'

Documented arguments not in \usage in documentation object 'GatingSet,GatingHierarchy,character-method':
  'swap_cols'

Undocumented arguments in documentation object 'flowData'
  '...'

Duplicated \argument entries in documentation object 'getPopStats,GatingSet-method':
  'x' '...'

Documented arguments not in \usage in documentation object 'isGated':
  '...'

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 ... NOTE
GNU make is a SystemRequirements.
* 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-3.10-bioc/R/library/flowWorkspace/libs/i386/flowWorkspace.dll':
  Found '_exit', possibly from '_exit' (C)
  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-3.10-bioc/R/library/flowWorkspace/libs/x64/flowWorkspace.dll':
  Found '_exit', possibly from '_exit' (C)
  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: 4 WARNINGs, 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/flowWorkspace_3.34.1.tar.gz && rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowWorkspace.buildbin-libdir flowWorkspace_3.34.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL flowWorkspace_3.34.1.zip && rm flowWorkspace_3.34.1.tar.gz flowWorkspace_3.34.1.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 2642k  100 2642k    0     0  28.0M      0 --:--:-- --:--:-- --:--:-- 29.3M

install for i386

* installing *source* package 'flowWorkspace' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c R_API.cpp -o R_API.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c R_GatingSet.cpp -o R_GatingSet.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c getDescendants.cpp -o getDescendants.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c getPopStats.cpp -o getPopStats.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
getSingleCellExpression.cpp: In function 'Rcpp::NumericMatrix getSingleCellExpressionByGate(Rcpp::XPtr<GatingSet>, std::string, Rcpp::List, Rcpp::NumericMatrix, Rcpp::CharacterVector, bool)':
getSingleCellExpression.cpp:73:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned j = 0; j < pops.size(); ++j){
                           ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c setCounts.cpp -o setCounts.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
mkdir -p "C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o
C:\Rtools\mingw_32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386/libflowWorkspace.a
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/lib/i386/GatingSet.pb.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/lib/i386/libprotobuf.a -LC:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowWorkspace'
    finding HTML links ... done
    GatingHierarchy-class                   html  
    GatingSet-class                         html  
    GatingSet-methods                       html  
    GatingSetList-class                     html  
    asinh_Gml2                              html  
    asinhtGml2_trans                        html  
    booleanFilter-class                     html  
    finding level-2 HTML links ... done

    compensate                              html  
    compute_timestep                        html  
    estimateLogicle.GatingHierarchy         html  
    extract_cluster_pop_name_from_node      html  
    filterObject                            html  
    fix_channel_slash                       html  
    flowJo_flog                             html  
    flowWorkspace-deprecated                html  
    flowWorkspace-package                   html  
    flowWorkspace.par.get                   html  
    flowWorkspace.par.init                  html  
    flow_breaks                             html  
    flow_trans                              html  
    flowjo_biexp                            html  
    flowjo_biexp_trans                      html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCqwvNP/R.INSTALL1d3c4fffcdf/flowWorkspace/man/flowjo_biexp_trans.Rd:13: file link 'flowJoTrans' in package 'flowWorkspace' does not exist and so has been treated as a topic
    flowjo_fasinh                           html  
    flowjo_fasinh_trans                     html  
    gh_apply_to_new_fcs                     html  
    gh_copy_gate                            html  
    gh_get_cluster_labels                   html  
    gh_get_compensations                    html  
    gh_get_transformations                  html  
    gh_pop_compare_stats                    html  
    gh_pop_get_cluster_name                 html  
    gh_pop_get_descendants                  html  
    gh_pop_get_full_path                    html  
    gh_pop_get_gate                         html  
    gh_pop_get_indices                      html  
    gh_pop_get_indices_mat                  html  
    gh_pop_get_proportion                   html  
    gh_pop_move                             html  
    gh_pop_set_indices                      html  
    gh_pop_set_xml_count                    html  
    gs_check_redundant_nodes                html  
    gs_clone                                html  
    gs_cyto_data                            html  
    gs_get_compensation_internal            html  
    gs_get_leaf_nodes                       html  
    gs_get_pop_paths                        html  
    gs_get_singlecell_expression            html  
    gs_is_h5                                html  
    gs_plot_diff_tree                       html  
    gs_plot_pop_count_cv                    html  
    gs_pop_add                              html  
    gs_pop_get_children                     html  
    gs_pop_get_count_fast                   html  
    gs_pop_get_data                         html  
    gs_pop_get_stats                        html  
    gs_pop_set_gate                         html  
    gs_pop_set_name                         html  
    gs_pop_set_visibility                   html  
    gs_remove_redundant_channels            html  
    gs_remove_redundant_nodes               html  
    gs_split_by_channels                    html  
    gs_split_by_tree                        html  
    gs_update_channels                      html  
    gslist_to_gs                            html  
    keyword                                 html  
    lapply-methods                          html  
    length                                  html  
    logicleGml2_trans                       html  
    logicle_trans                           html  
    loglevel                                html  
    logtGml2_trans                          html  
    markernames                             html  
    mkformula                               html  
    ncFlowSet-methods                       html  
    nodeflags                               html  
    openWorkspace                           html  
    pData-methods                           html  
    plot-methods                            html  
    plotGate-methods                        html  
    pop_add                                 html  
    prettyAxis                              html  
    recompute                               html  
    rotate_gate                             html  
    sampleNames                             html  
    save_gs                                 html  
    scale_gate                              html  
    shift_gate                              html  
    standardize-GatingSet                   html  
    stats.fun                               html  
    subset                                  html  
    swap_data_cols                          html  
    transform                               html  
    transform_gate                          html  
    transformerList                         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 'flowWorkspace' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c R_API.cpp -o R_API.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c R_GatingSet.cpp -o R_GatingSet.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c getDescendants.cpp -o getDescendants.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c getPopStats.cpp -o getPopStats.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c setCounts.cpp -o setCounts.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function 'virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
mkdir -p "C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o
C:\Rtools\mingw_64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/lib/x64/libprotobuf.a -LC:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowWorkspace' as flowWorkspace_3.34.1.zip
* DONE (flowWorkspace)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'flowWorkspace' successfully unpacked and MD5 sums checked

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(flowWorkspace)
> library(flowCore)
> library(ncdfFlow)
Loading required package: RcppArmadillo
Loading required package: BH
> 
> test_check("flowWorkspace")

Attaching package: 'dplyr'

The following objects are masked from 'package:data.table':

    between, first, last

The following object is masked from 'package:ncdfFlow':

    filter

The following object is masked from 'package:flowCore':

    filter

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:dplyr':

    combine, intersect, setdiff, union

The following object is masked from 'package:flowCore':

    normalize

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

== testthat results  ===========================================================
[ OK: 903 | SKIPPED: 3 | WARNINGS: 40 | FAILED: 0 ]
> 
> #devtools::test("~/rglab/workspace/flowWorkspace")
> #devtools::check_man()
> #test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-archive.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-parseWorkspace.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/GatingHierarchy-testSuite.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/GatingSet-testSuite.R")
> 
> proc.time()
   user  system elapsed 
  29.73    3.95   34.70 

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(flowWorkspace)
> library(flowCore)
> library(ncdfFlow)
Loading required package: RcppArmadillo
Loading required package: BH
> 
> test_check("flowWorkspace")

Attaching package: 'dplyr'

The following objects are masked from 'package:data.table':

    between, first, last

The following object is masked from 'package:ncdfFlow':

    filter

The following object is masked from 'package:flowCore':

    filter

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:dplyr':

    combine, intersect, setdiff, union

The following object is masked from 'package:flowCore':

    normalize

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

== testthat results  ===========================================================
[ OK: 903 | SKIPPED: 3 | WARNINGS: 40 | FAILED: 0 ]
> 
> #devtools::test("~/rglab/workspace/flowWorkspace")
> #devtools::check_man()
> #test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-archive.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-parseWorkspace.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/GatingHierarchy-testSuite.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/GatingSet-testSuite.R")
> 
> proc.time()
   user  system elapsed 
  31.93    3.73   35.71