Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-07-31 12:06:01 -0400 (Sat, 31 Jul 2021).

CHECK results for CytoML on riesling1

To the developers/maintainers of the CytoML package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CytoML.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 427/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoML 2.5.3  (landing page)
Mike Jiang
Snapshot Date: 2021-07-30 14:50:06 -0400 (Fri, 30 Jul 2021)
URL: https://git.bioconductor.org/packages/CytoML
Branch: master
Last Commit: a1c6ddb
Last Changed Date: 2021-06-08 14:56:28 -0400 (Tue, 08 Jun 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    ERROR  
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: CytoML
Version: 2.5.3
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoML.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CytoML_2.5.3.tar.gz
StartedAt: 2021-07-30 23:58:51 -0400 (Fri, 30 Jul 2021)
EndedAt: 2021-07-31 00:03:48 -0400 (Sat, 31 Jul 2021)
EllapsedTime: 297.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: CytoML.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoML.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CytoML_2.5.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/CytoML.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CytoML/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CytoML' version '2.5.3'
* 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 'CytoML' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 25.5Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs     19.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  'RUnit' 'corpcor' 'openCyto' 'stats'
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  'ggcyto:::merge.quad.gates' 'lattice:::updateList'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addCustomInfo: no visible global function definition for
  'gh_get_transformations'
addGate: no visible binding for global variable 'id'
addGate: no visible binding for global variable 'gate_id'
addGate: no visible binding for global variable 'fcs'
addGate: no visible binding for global variable 'fcs_file_id'
addGate: no visible binding for global variable 'gate_def'
addGate: no visible binding for global variable 'name'
ce_get_panels: no visible binding for global variable 'panel'
ce_get_panels: no visible binding for global variable 'n'
constructTree: no visible binding for global variable 'id'
constructTree: no visible binding for global variable 'name'
createTransformIdentifier: no visible global function definition for
  'slotNames'
cytobank_to_gatingset.cytobank_experiment: no visible binding for
  global variable 'desc'
diva_to_gatingset: no visible binding for global variable 'specimen'
diva_to_gatingset: no visible binding for global variable
  'sampleSelected'
diva_to_gatingset: no visible global function definition for
  'gh_apply_to_new_fcs'
export_comp_trans: no visible global function definition for
  'gh_get_compensations'
export_comp_trans: no visible global function definition for
  'gh_get_transformations'
export_gates_cytobank: no visible global function definition for
  'gs_get_pop_paths'
export_gates_cytobank: no visible global function definition for
  'gs_pop_get_gate'
extend.polygonGate: no visible binding for global variable '..dim'
extend.polygonGate : <anonymous>: no visible binding for global
  variable 'y'
extend.polygonGate : <anonymous>: no visible binding for global
  variable 'x'
extend.polygonGate: no visible binding for global variable 'id'
extend.polygonGate: no visible binding for global variable 'x'
extend.polygonGate: no visible binding for global variable 'y'
extend.polygonGate: no visible binding for global variable 'is.smaller'
flinTr: no visible global function definition for 'lintGml2'
fratioTr: no visible global function definition for 'ratiotGml2'
generate_trans: no visible global function definition for
  'flowjo_log_trans'
gs_compare_cytobank_counts: no visible binding for global variable
  'population'
gs_compare_cytobank_counts: no visible binding for global variable
  'parent'
gs_compare_cytobank_counts: no visible binding for global variable
  'parent_count'
gs_compare_cytobank_counts: no visible global function definition for
  '.'
gs_compare_cytobank_counts: no visible binding for global variable
  'fcs_filename'
hyperlogTr: no visible global function definition for 'hyperlogtGml2'
open_cytobank_experiment: no visible global function definition for
  'unzip'
range.GatingHierarchy: no visible global function definition for
  'gh_get_transformations'
read.gatingML.cytobank: no visible binding for global variable 'id'
read.gatingML.cytobank: no visible binding for global variable
  'comp_ref'
transDg1polynomial: no visible global function definition for
  'dg1polynomial'
transEH: no visible global function definition for 'EHtrans'
transExponential: no visible global function definition for
  'exponential'
transHyperLog: no visible global function definition for 'hyperlog'
transHyperbolicSin: no visible global function definition for 'sinht'
transInvSplitScale: no visible global function definition for
  'invsplitscale'
transInverseHyperbolicSin: no visible global function definition for
  'asinht'
transLogarithm: no visible global function definition for 'logarithm'
transQuadratic: no visible global function definition for 'quadratic'
transRatio: no visible global function definition for 'ratio'
transSplitScale: no visible global function definition for 'splitscale'
transSquareroot: no visible global function definition for 'squareroot'
write.gatingML: no visible global function definition for 'sessionInfo'
xmlVertexNode : <anonymous>: no visible global function definition for
  'format_float'
identifyNode,http...www.isac.net.org.std.Gating.ML.v1.5.gating_DecisionTreeGate:
  no visible binding for global variable 'expressionFilter'
identifyNode,http...www.isac.net.org.std.Gating.ML.v1.5.gating_PolytopeGate:
  no visible global function definition for 'polytopeGate'
identifyNode,http...www.isac.net.org.std.Gating.ML.v2.0.transformations_spectrumMatrix:
  no visible global function definition for 'pseudoinverse'
show,flowjo_workspace: no visible binding for global variable
  'groupName'
show,flowjo_workspace: no visible binding for global variable 'groupID'
Undefined global functions or variables:
  . ..dim EHtrans asinht comp_ref desc dg1polynomial exponential
  expressionFilter fcs fcs_file_id fcs_filename flowjo_log_trans
  format_float gate_def gate_id gh_apply_to_new_fcs
  gh_get_compensations gh_get_transformations groupID groupName
  gs_get_pop_paths gs_pop_get_gate hyperlog hyperlogtGml2 id
  invsplitscale is.smaller lintGml2 logarithm n name panel parent
  parent_count polytopeGate population pseudoinverse quadratic ratio
  ratiotGml2 sampleSelected sessionInfo sinht slotNames specimen
  splitscale squareroot unzip x y
Consider adding
  importFrom("methods", "slotNames")
  importFrom("utils", "sessionInfo", "unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'parseWorkspace'
  'backend_dir' 'backend'
Documented arguments not in \usage in documentation object 'parseWorkspace':
  'h5_dir'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... 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.in'
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.14-bioc/R/library/CytoML/libs/i386/CytoML.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'D:/biocbuild/bbs-3.14-bioc/R/library/CytoML/libs/x64/CytoML.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  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' ... ERROR
Running examples in 'CytoML-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gs_compare_cytobank_counts
> ### Title: compare the counts to cytobank's exported csv so that the
> ###   parsing result can be verified.
> ### Aliases: gs_compare_cytobank_counts
> 
> ### ** Examples
> 
> 
> acsfile <- system.file("extdata/cytobank_experiment.acs", package = "CytoML")
> ce <- open_cytobank_experiment(acsfile)
Unpacking ACS file...
> gs <- cytobank_to_gatingset(ce)
not debris
singlets
CD3
CD4
CD8
CD8_Q2
Q3
Q4
Q2
Q1
HLA range
CD38 range
not debris
singlets
CD3
CD8
CD8_Q2
CD4
Q1
Q2
Q4
Q3
CD38 range
HLA range
done!
> ## verify the stats are correct
> statsfile <- ce$attachments[1]
> dt_merged <- gs_compare_cytobank_counts(gs, statsfile, id.vars = "population", skip = "FCS Filename")
terminate called after throwing an instance of 'std::domain_error'
  what():  not debris not found in gating tree of CytoTrol_CytoTrol_1.fcs
** running examples for arch 'x64' ... ERROR
Running examples in 'CytoML-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gs_compare_cytobank_counts
> ### Title: compare the counts to cytobank's exported csv so that the
> ###   parsing result can be verified.
> ### Aliases: gs_compare_cytobank_counts
> 
> ### ** Examples
> 
> 
> acsfile <- system.file("extdata/cytobank_experiment.acs", package = "CytoML")
> ce <- open_cytobank_experiment(acsfile)
Unpacking ACS file...
> gs <- cytobank_to_gatingset(ce)
not debris
singlets
CD3
CD4
CD8
CD8_Q2
Q3
Q4
Q2
Q1
HLA range
CD38 range
not debris
singlets
CD3
CD8
CD8_Q2
CD4
Q1
Q2
Q4
Q3
CD38 range
HLA range
done!
> ## verify the stats are correct
> statsfile <- ce$attachments[1]
> dt_merged <- gs_compare_cytobank_counts(gs, statsfile, id.vars = "population", skip = "FCS Filename")
terminate called without an active exception
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > win32_flag = .Platform$OS.type == "windows" && .Machine$sizeof.pointer != 8
  > if(!win32_flag)
  +   test_check("CytoML")
  As part of improvements to flowWorkspace, some behavior of
  GatingSet objects has changed. For details, please read the section
  titled "The cytoframe and cytoset classes" in the package vignette:
  
    vignette("flowWorkspace-Introduction", "flowWorkspace")
  Loading required package: ggplot2
  Loading required package: ncdfFlow
  Loading required package: RcppArmadillo
  Loading required package: BH
  INFO: Could not find files for the given pattern(s).
  INFO: Could not find files for the given pattern(s).
  terminate called without an active exception
* 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 ERRORs, 2 WARNINGs, 6 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/CytoML.Rcheck/00check.log'
for details.


Installation output

CytoML.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CytoML_2.5.3.tar.gz && rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CytoML.buildbin-libdir CytoML_2.5.3.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CytoML_2.5.3.zip && rm CytoML_2.5.3.tar.gz CytoML_2.5.3.zip
###
##############################################################################
##############################################################################


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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 6621k  100 6621k    0     0  11.8M      0 --:--:-- --:--:-- --:--:-- 11.8M

install for i386

* installing *source* package 'CytoML' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
rm -f RcppExports.o parseFlowJoWorkspace.o CytoML.dll
"D:/biocbuild/bbs-3.14-bioc/R/bin/i386/Rscript.exe" "../tools/winlibs.R" 2.9.8
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.8/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                               
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
D:/biocbuild/bbs-3.14-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 D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.14-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){
      ~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.14-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){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.14-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 D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
D:/biocbuild/bbs-3.14-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 ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function 'std::vector<CytoML::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)':
../inst/include/CytoML/flowJoWorkspace.hpp:605:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int j = 0; j < sample_ids.size(); j++)
                  ~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.8/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12,
                 from parseFlowJoWorkspace.cpp:9:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                               
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
D:/biocbuild/bbs-3.14-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 D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.14-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){
      ~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.14-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){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.14-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 D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
D:/biocbuild/bbs-3.14-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 ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function 'std::vector<CytoML::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)':
../inst/include/CytoML/flowJoWorkspace.hpp:605:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int j = 0; j < sample_ids.size(); j++)
                  ~~^~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o CytoML.dll tmp.def RcppExports.o parseFlowJoWorkspace.o -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lRlapack -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -L../windows/libxml2-2.9.8/lib/i386 -lxml2 -llzma -liconv -lz D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/lib/i386/libcytolib.a D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/lib/i386/GatingSet.pb.o -LD:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/lib/i386 -lprotobuf -LD:/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -LD:/biocbuild/bbs-3.14-bioc/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 -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CytoML'
    finding HTML links ... done
    CytoML-deprecated                       html  
    CytoML.par.get                          html  
    CytoML.par.init                         html  
    addCustomInfo                           html  
    ce_get_channels                         html  
    ce_get_compensations                    html  
    ce_get_markers                          html  
    ce_get_panels                           html  
    ce_get_samples                          html  
    ce_get_transformations                  html  
    compensate-GatingSet-graphGML-method    html  
    constructTree                           html  
    cytobank_experiment-methods             html  
    cytobank_to_gatingset                   html  
    diva_get_samples                        html  
    diva_to_gatingset                       html  
    diva_workspace-class                    html  
    finding level-2 HTML links ... done

    extend                                  html  
    fj_ws_get_keywords                      html  
    fj_ws_get_sample_groups                 html  
    fj_ws_get_samples                       html  
    flowjo_to_gatingset                     html  
    flowjo_workspace-class                  html  
    gatingset_to_cytobank                   html  
    gatingset_to_flowjo                     html  
    getChildren-graphGML-character-method   html  
    getCompensationMatrices.graphGML        html  
    getGate-graphGML-character-method       html  
    getNodes-graphGML-method                html  
    getParent-graphGML-character-method     html  
    getTransformations.graphGML             html  
    graphGML-class                          html  
    gs_compare_cytobank_counts              html  
    matchPath                               html  
    open_cytobank_experiment                html  
    open_diva_xml                           html  
    open_flowjo_xml                         html  
    parse.gateInfo                          html  
    plot-graphGML-missing-method            html  
    range.GatingHierarchy                   html  
    read.gatingML.cytobank                  html  
    show-graphGML-method                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CytoML' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
rm -f RcppExports.o parseFlowJoWorkspace.o CytoML.dll
"D:/biocbuild/bbs-3.14-bioc/R/bin/x64/Rscript.exe" "../tools/winlibs.R" 2.9.8
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.8/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                               
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
D:/biocbuild/bbs-3.14-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 D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.14-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){
      ~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.14-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){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.14-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 D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
D:/biocbuild/bbs-3.14-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 ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function 'std::vector<CytoML::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)':
../inst/include/CytoML/flowJoWorkspace.hpp:605:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for(int j = 0; j < sample_ids.size(); j++)
                  ~~^~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.8/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/flowWorkspace/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12,
                 from parseFlowJoWorkspace.cpp:9:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                               
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
D:/biocbuild/bbs-3.14-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 D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/function.hpp:30,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
D:/biocbuild/bbs-3.14-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){
      ~~~~~~~~~~~~~~^~~~~~~~~~
D:/biocbuild/bbs-3.14-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){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
D:/biocbuild/bbs-3.14-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 D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:465:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:478:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:561:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:570:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:572:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/CytoML/wsNode.hpp:13,
                 from ../inst/include/CytoML/workspace_type.hpp:4,
                 from ../inst/include/CytoML/workspace.hpp:10,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/CytoML/workspace.hpp:14,
                 from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
                 from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
D:/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
D:/biocbuild/bbs-3.14-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 ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/CytoML/openWorkspace.hpp:11,
                 from parseFlowJoWorkspace.cpp:9:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function 'std::vector<CytoML::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)':
../inst/include/CytoML/flowJoWorkspace.hpp:605:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for(int j = 0; j < sample_ids.size(); j++)
                  ~~^~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o CytoML.dll tmp.def RcppExports.o parseFlowJoWorkspace.o -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -L../windows/libxml2-2.9.8/lib/x64 -lxml2 -llzma -liconv -lz D:/biocbuild/bbs-3.14-bioc/R/library/cytolib/lib/x64/libcytolib.a D:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o -LD:/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/lib/x64 -lprotobuf -LD:/biocbuild/bbs-3.14-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LD:/biocbuild/bbs-3.14-bioc/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 -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/CytoML.buildbin-libdir/CytoML/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CytoML' as CytoML_2.5.3.zip
* DONE (CytoML)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'CytoML' successfully unpacked and MD5 sums checked

Tests output

CytoML.Rcheck/tests_i386/testthat.Rout


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

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

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

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

> library(testthat)
> library(CytoML)
> 
> win32_flag = .Platform$OS.type == "windows" && .Machine$sizeof.pointer != 8
> if(!win32_flag)
+   test_check("CytoML")
> 
> #devtools::test()
> 
> # test_file("~/rglab/workspace/CytoML/tests/testthat/flowjo2gs_internalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/Cytobank2GatingSet-InternalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/GatingSet2flowJo-InternalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/diva2gs-InternalTestSuite.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-cytobank.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-diva2gs.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-extend.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-GatingSet2flowJo.R")
> # test_file("~/rglab/workspace/CytoML/tests/testthat/test-flowjo2gs.R")
> 
> proc.time()
   user  system elapsed 
   2.50    0.25    2.73 

CytoML.Rcheck/tests_x64/testthat.Rout.fail


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

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> library(testthat)
> library(CytoML)
> 
> win32_flag = .Platform$OS.type == "windows" && .Machine$sizeof.pointer != 8
> if(!win32_flag)
+   test_check("CytoML")
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:

  vignette("flowWorkspace-Introduction", "flowWorkspace")
Loading required package: ggplot2
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
INFO: Could not find files for the given pattern(s).
INFO: Could not find files for the given pattern(s).
terminate called without an active exception

Example timings

CytoML.Rcheck/examples_i386/CytoML-Ex.timings

nameusersystemelapsed
CytoML.par.get000
cytobank_to_gatingset000
extend0.080.000.08
fj_ws_get_keywords0.000.010.01
fj_ws_get_sample_groups000
fj_ws_get_samples000
flowjo_to_gatingset000
flowjo_workspace-class0.060.000.10
gatingset_to_cytobank0.800.140.95
gatingset_to_flowjo000
getChildren-graphGML-character-method000
getNodes-graphGML-method000

CytoML.Rcheck/examples_x64/CytoML-Ex.timings

nameusersystemelapsed
CytoML.par.get000
cytobank_to_gatingset000
extend0.060.000.06
fj_ws_get_keywords000
fj_ws_get_sample_groups000
fj_ws_get_samples000
flowjo_to_gatingset000
flowjo_workspace-class0.030.020.05
gatingset_to_cytobank0.890.121.02
gatingset_to_flowjo000
getChildren-graphGML-character-method000
getNodes-graphGML-method000