##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowWorkspace.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings flowWorkspace_4.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '4.4.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'flowWorkspace' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 24.0Mb
  sub-directories of 1Mb or more:
    lib    5.5Mb
    libs  15.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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' 'RProtoBufLib' 'ggplot2' 'grDevices' 'graphics' 'utils'
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  'DelayedArray:::simplify_NULL_dimnames' 'flowCore:::.estimateLogicle'
  'flowCore:::.spillover_pattern' 'flowCore:::checkClass'
  'flowCore:::guid' 'flowCore:::logicle_transform'
  'flowCore:::parse_pd_for_read_fs' 'flowCore:::txt2spillmatrix'
  'flowCore:::updateTransformKeywords'
  'flowCore:::validFilterResultList' 'graph:::.makeEdgeKeys'
  'ncdfFlow:::.isValidSamples' 'stats:::.splinefun'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  print.cytoctx
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.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_legacy: no visible global function definition for 'is'
.load_legacy: no visible global function definition for 'new'
.load_legacy: no visible global function definition for '.hasSlot'
.load_legacy : <anonymous>: no visible global function definition for
  'is'
.mergeGates : <anonymous>: no visible global function definition for
  'extends'
.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'
cf_append_cols: no visible global function definition for 'new'
cf_flush_meta: no visible global function definition for 'is'
cf_get_uri: no visible global function definition for 'is'
cf_keyword_delete: no visible global function definition for 'is'
cf_keyword_insert: no visible global function definition for 'is'
cf_keyword_rename: no visible global function definition for 'is'
cf_keyword_rename: no visible binding for global variable 'na_idx'
cf_keyword_set: no visible global function definition for 'is'
cf_load_meta: no visible global function definition for 'is'
cf_lock: no visible global function definition for 'is'
cf_rename_channel: no visible global function definition for 'is'
cf_rename_marker: no visible global function definition for 'is'
cf_rename_marker: no visible binding for global variable 'desc'
cf_scale_time_channel: no visible global function definition for 'is'
cf_unlock: no visible global function definition for 'is'
cf_write_disk: no visible global function definition for 'is'
char2booleanFilter: no visible global function definition for 'new'
check_comp: no visible global function definition for 'is'
convert_backend: no visible binding for global variable 'output'
copy_view.cytoframe: no visible global function definition for 'new'
copy_view.cytoset: no visible global function definition for 'new'
cs_add_cytoframe: no visible global function definition for 'is'
cs_get_cytoframe: no visible global function definition for 'is'
cs_get_cytoframe: no visible global function definition for 'new'
cs_get_uri: no visible global function definition for 'is'
cs_keyword_delete: no visible global function definition for 'is'
cs_keyword_insert: no visible global function definition for 'is'
cs_keyword_rename: no visible global function definition for 'is'
cs_keyword_rename : <anonymous>: no visible binding for global variable
  'keys'
cs_keyword_set: no visible global function definition for 'is'
cs_set_cytoframe: no visible global function definition for 'is'
cytoframe_to_flowFrame: no visible global function definition for 'as'
cytoset: no visible global function definition for 'new'
cytoset_to_flowSet: no visible global function definition for 'as'
get_cytoframe_from_cs: no visible global function definition for 'is'
get_cytoframe_from_cs: no visible global function definition for 'new'
gh_apply_to_cs: 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'
gh_pop_get_stats_tfilter : <anonymous>: no visible binding for global
  variable 'Population'
gh_pop_set_gate: no visible global function definition for 'is'
gs_clone: no visible global function definition for 'new'
gs_copy_tree_only: no visible global function definition for 'new'
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_get_data: no visible global function definition for 'new'
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'
load_cytoframe: no visible global function definition for 'new'
load_cytoframe_from_fcs: no visible global function definition for
  'new'
load_cytoset_from_fcs: no visible global function definition for 'new'
load_gs: no visible global function definition for 'new'
load_gslist : <anonymous>: no visible global function definition for
  'is'
merge_list_to_gs: no visible global function definition for 'is'
merge_list_to_gs: no visible global function definition for 'new'
parse_transformer: no visible global function definition for 'is'
pop.MFI: no visible binding for global variable 'desc'
realize_view.cytoframe: no visible global function definition for 'new'
realize_view.cytoset: no visible global function definition for 'new'
transformerList: no visible global function definition for 'is'
transformerList: no visible binding for global variable 'is'
validitycheck: no visible global function definition for 'is'
GatingSet,cytoset-ANY: no visible global function definition for 'new'
Subset,cytoset-filterResultList : <anonymous>: no visible global
  function definition for 'as'
Subset,cytoset-list: no visible global function definition for 'is'
[,GatingSet-ANY: no visible global function definition for 'extends'
[,GatingSet-ANY: no visible global function definition for 'new'
[,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'
compensate,GatingSet-ANY: no visible global function definition for
  'selectMethod'
compensate,cytoset-ANY: no visible global function definition for
  'selectMethod'
flowData,GatingSet: no visible binding for global variable 'obj'
fsApply,cytoset: no visible global function definition for
  'callNextMethod'
gs_cyto_data,GatingSet: no visible global function definition for 'new'
keyword,GatingSetList-character: no visible global function definition
  for 'selectMethod'
keyword,GatingSetList-missing: no visible global function definition
  for 'selectMethod'
keyword<-,cytoframe-list: no visible binding for global variable
  'kwdError'
pData<-,GatingSetList-data.frame: no visible global function definition
  for 'callNextMethod'
pData<-,GatingSetList-data.frame: no visible global function definition
  for 'as'
parameters,cytoframe: no visible global function definition for 'new'
phenoData,cytoset: no visible global function definition for 'new'
sampleNames<-,cytoset-ANY: no visible global function definition for
  'selectMethod'
setNode,GatingSet-character-ANY: no visible global function definition
  for 'is'
show,cytoframe: no visible global function definition for
  'selectMethod'
transform,GatingSet: no visible global function definition for 'is'
transform,GatingSet : <anonymous>: no visible global function
  definition for 'is'
transform,cytoframe: no visible global function definition for 'is'
transform,cytoset: no visible global function definition for 'is'
transform,cytoset : <anonymous>: no visible global function definition
  for 'is'
Undefined global functions or variables:
  . .hasSlot IQR Population as callNextMethod count desc extends is
  keys kwdError median na_idx new node obj old openCyto.count output
  parallel percent sampleName selectMethod validObject xml.count
Consider adding
  importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
             "is", "new", "selectMethod", "validObject")
  importFrom("stats", "IQR", "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:
  'gs_clone' 'gs_copy_tree_only'
Undocumented S4 methods:
  generic 'dimnames' and siglist 'cytoframe'
  generic 'rownames' and siglist 'cytoframe'
  generic 'rownames<-' and siglist 'cytoframe'
  generic 'show' and siglist 'cytoframe'
  generic 'transform' and siglist 'cytoframe'
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 ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'GatingSet-methods':
  '...'

Undocumented arguments in documentation object 'cf_append_cols'
  'ctx'

Undocumented arguments in documentation object 'convert'
  'backend'

Undocumented arguments in documentation object 'cs_get_uri'
  'x'

Undocumented arguments in documentation object 'cytoctx'
  '...'

Undocumented arguments in documentation object 'delete_gs'
  'ctx'

Undocumented arguments in documentation object 'gh_apply_to_new_fcs'
  'files'

Undocumented arguments in documentation object 'keyword-mutators'
  'cs'

Undocumented arguments in documentation object 'load_cytoframe_from_fcs'
  'backend' 'uri'

Undocumented arguments in documentation object 'load_cytoset_from_fcs'
  'backend' 'backend_dir'

Undocumented arguments in documentation object 'save_gs'
  'cdf' 'backend_readonly'

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.
S3 methods shown with full name in documentation object 'cytoctx':
  'print.cytoctx'

The \usage entries for S3 methods should use the \method markup and not
their full name.
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) ... WARNING
  apparently using $(BLAS_LIBS) without following $(FLIBS) in 'src/Makevars'
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/libs/i386/flowWorkspace.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowWorkspace/libs/x64/flowWorkspace.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (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, 7 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/flowWorkspace_4.4.0.tar.gz && rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowWorkspace.buildbin-libdir flowWorkspace_4.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL flowWorkspace_4.4.0.zip && rm flowWorkspace_4.4.0.tar.gz flowWorkspace_4.4.0.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
 11 4651k   11  537k    0     0  1188k      0  0:00:03 --:--:--  0:00:03 1190k
 72 4651k   72 3351k    0     0  2255k      0  0:00:02  0:00:01  0:00:01 2255k
100 4651k  100 4651k    0     0  2501k      0  0:00:01  0:00:01 --:--:-- 2500k

install for i386

* installing *source* package 'flowWorkspace' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_API.cpp -o R_API.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_GatingSet.cpp -o R_GatingSet.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:46,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
                 from ../inst/include/flowWorkspace.h:6,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]':
RcppExports.cpp:629:43:   required from here
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type 'cytolib::CytoFrameView' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete obj;
     ^~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cytoctxAPI.cpp -o cytoctxAPI.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from cytoctxAPI.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from cytoctxAPI.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from cytoctxAPI.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cytoframeAPI.cpp -o cytoframeAPI.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
                 from cytoframeAPI.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
                 from cytoframeAPI.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from cytoframeAPI.cpp:3:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:46,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
                 from cytoframeAPI.cpp:3:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]':
cytoframeAPI.cpp:9:43:   required from here
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type 'cytolib::CytoFrameView' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete obj;
     ^~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cytosetAPI.cpp -o cytosetAPI.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
                 from cytosetAPI.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
                 from cytosetAPI.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from cytosetAPI.cpp:2:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
cytosetAPI.cpp: In function 'Rcpp::XPtr<cytolib::CytoFrameView> get_cytoframe(Rcpp::XPtr<cytolib::GatingSet>, Rcpp::RObject, Rcpp::RObject)':
cytosetAPI.cpp:206:29: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
       for(unsigned i = 0; i < j_val.size(); i++){
                           ~~^~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:46,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
                 from cytosetAPI.cpp:2:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]':
cytosetAPI.cpp:38:81:   required from here
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type 'cytolib::CytoFrameView' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete obj;
     ^~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getDescendants.cpp -o getDescendants.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getDescendants.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getDescendants.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getDescendants.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getPopStats.cpp -o getPopStats.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getPopStats.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getPopStats.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getPopStats.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getSingleCellExpression.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getSingleCellExpression.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getSingleCellExpression.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
getSingleCellExpression.cpp: In function 'Rcpp::NumericMatrix getSingleCellExpressionByGate(Rcpp::XPtr<cytolib::GatingSet>, std::__cxx11::string, Rcpp::List, Rcpp::NumericMatrix, Rcpp::CharacterVector, bool)':
getSingleCellExpression.cpp:74:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'R_xlen_t' {aka 'int'} [-Wsign-compare]
     for(unsigned j = 0; j < pops.size(); ++j){
                         ~~^~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c h5_error_r_handler.cpp -o h5_error_r_handler.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from h5_error_r_handler.cpp:8:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from h5_error_r_handler.cpp:8:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from h5_error_r_handler.cpp:8:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c setCounts.cpp -o setCounts.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from setCounts.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from setCounts.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from setCounts.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
mkdir -p "C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386"
"C:/rtools40/mingw32/bin/"ar rs "C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoctxAPI.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o
C:\rtools40\mingw32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386/libflowWorkspace.a
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoctxAPI.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/lib/i386/libcytolib.a C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/i386/GatingSet.pb.o -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/i386 -lprotobuf -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -lws2_32 -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-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

    brackets                                html  
    cf_append_cols                          html  
    cf_backend_type                         html  
    cf_get_uri                              html  
    cf_write_disk                           html  
    cf_write_h5                             html  
    cf_write_tile                           html  
    cleanup                                 html  
    cleanup_temp                            html  
    compensate                              html  
    convert                                 html  
    convert_backend                         html  
    convert_legacy                          html  
    cs_add_cytoframe                        html  
    cs_get_uri                              html  
    cs_set_cytoframe                        html  
    cytoctx                                 html  
    cytoframe-labels                        html  
    cytoframe                               html  
    cytoset                                 html  
    default_backend                         html  
    delete_gs                               html  
    estimateLogicle                         html  
    extract_cluster_pop_name_from_node      html  
    filter_to_list                          html  
    flowWorkspace-deprecated                html  
    flowWorkspace-package                   html  
    flow_breaks                             html  
    flow_trans                              html  
    flowjo_biexp                            html  
    flowjo_biexp_trans                      html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/help/flowJo_biexp_trans.html
    flowjo_fasinh                           html  
    flowjo_fasinh_trans                     html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/help/flowJo_fasinh_trans.html
    flowjo_log_trans                        html  
    gh_apply_to_cs                          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_data                         html  
    gh_pop_get_descendants                  html  
    gh_pop_get_full_path                    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_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_persistent                        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_gate                         html  
    gs_pop_get_gs                           html  
    gs_pop_get_stats                        html  
    gs_pop_get_stats_tfilter                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  
    identifier-methods                      html  
    is_subsetted                            html  
    is_tiledb_support                       html  
    keyword-mutators                        html  
    keyword                                 html  
    lapply-methods                          html  
    length                                  html  
    load_cytoframe                          html  
    load_cytoframe_from_fcs                 html  
    load_cytoset_from_fcs                   html  
    load_meta                               html  
    lock                                    html  
    logicleGml2_trans                       html  
    logicle_trans                           html  
    loglevel                                html  
    logtGml2_trans                          html  
    markernames                             html  
    merge_list_to_gs                        html  
    ncFlowSet-methods                       html  
    nodeflags                               html  
    openWorkspace                           html  
    pData-methods                           html  
    plot-methods                            html  
    plotGate-methods-defunct                html  
    pop_add                                 html  
    prettyAxis                              html  
    recompute                               html  
    rotate_gate                             html  
    sampleNames                             html  
    save_cytoset                            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:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_API.cpp -o R_API.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_GatingSet.cpp -o R_GatingSet.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:46,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
                 from ../inst/include/flowWorkspace.h:6,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]':
RcppExports.cpp:629:43:   required from here
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type 'cytolib::CytoFrameView' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete obj;
     ^~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cytoctxAPI.cpp -o cytoctxAPI.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from cytoctxAPI.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from cytoctxAPI.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from cytoctxAPI.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cytoframeAPI.cpp -o cytoframeAPI.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
                 from cytoframeAPI.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
                 from cytoframeAPI.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from cytoframeAPI.cpp:3:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:46,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
                 from cytoframeAPI.cpp:3:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]':
cytoframeAPI.cpp:9:43:   required from here
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type 'cytolib::CytoFrameView' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete obj;
     ^~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cytosetAPI.cpp -o cytosetAPI.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
                 from cytosetAPI.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
                 from cytosetAPI.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from cytosetAPI.cpp:2:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp.h:46,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:32,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
                 from cytosetAPI.cpp:2:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of 'void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]':
cytosetAPI.cpp:38:81:   required from here
C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type 'cytolib::CytoFrameView' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete obj;
     ^~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getDescendants.cpp -o getDescendants.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getDescendants.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getDescendants.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getDescendants.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getPopStats.cpp -o getPopStats.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getPopStats.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getPopStats.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getPopStats.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getSingleCellExpression.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getSingleCellExpression.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getSingleCellExpression.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c h5_error_r_handler.cpp -o h5_error_r_handler.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from h5_error_r_handler.cpp:8:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from h5_error_r_handler.cpp:8:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from h5_error_r_handler.cpp:8:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DRCPP_PARALLEL_USE_TBB=1 -fpermissive  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c setCounts.cpp -o setCounts.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from setCounts.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from setCounts.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from setCounts.cpp:1:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
mkdir -p "C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64"
"C:/rtools40/mingw64/bin/"ar rs "C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoctxAPI.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o
C:\rtools40\mingw64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoctxAPI.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/lib/x64/libcytolib.a C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/x64 -lprotobuf -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowWorkspace' as flowWorkspace_4.4.0.zip
* DONE (flowWorkspace)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'flowWorkspace' successfully unpacked and MD5 sums checked