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CHECK report for CytoML on tokay2

This page was generated on 2020-10-17 11:56:24 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CytoML PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 415/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoML 2.0.5
Mike Jiang , Jake Wagner
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CytoML
Branch: RELEASE_3_11
Last Commit: b52baea
Last Changed Date: 2020-06-15 14:08:10 -0400 (Mon, 15 Jun 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CytoML
Version: 2.0.5
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoML.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CytoML_2.0.5.tar.gz
StartedAt: 2020-10-17 03:07:37 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:15:21 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 464.2 seconds
RetCode: 0
Status:  OK  
CheckDir: CytoML.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoML.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CytoML_2.0.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CytoML.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '2.0.5'
* 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 ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'CytoML' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 23.5Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    lib       2.4Mb
    libs     15.1Mb
* 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'
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 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 ... OK
* 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) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-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 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'C:/Users/biocbuild/bbs-3.11-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 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 7 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/CytoML.Rcheck/00check.log'
for details.

Installation output

CytoML.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CytoML_2.0.5.tar.gz && rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CytoML.buildbin-libdir CytoML_2.0.5.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CytoML_2.0.5.zip && rm CytoML_2.0.5.tar.gz CytoML_2.0.5.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 6604k  100 6604k    0     0  43.8M      0 --:--:-- --:--:-- --:--:-- 45.7M

install for i386

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

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


** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I'C:/Users/biocbuild/bbs-3.11-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:439:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                               
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/as_literal.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function.hpp:30,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-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>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 ../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:519:20: 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"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I'C:/Users/biocbuild/bbs-3.11-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:439:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                               
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/as_literal.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function.hpp:30,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-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:
C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-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:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-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:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-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:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-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:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-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:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-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:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-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:
C:/Users/biocbuild/bbs-3.11-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>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 ../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:519:20: 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++)
                  ~~^~~~~~~~~~~~~~~~~~~
mkdir -p "C:/Users/biocbuild/bbs-3.11-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/lib/i386"
"C:/rtools40/mingw32/bin/"ar rs "C:/Users/biocbuild/bbs-3.11-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/lib/i386/libflowWorkspace.a" RcppExports.o parseFlowJoWorkspace.o
C:\rtools40\mingw32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.11-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/lib/i386/libflowWorkspace.a
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o CytoML.dll tmp.def RcppExports.o parseFlowJoWorkspace.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath c:/libxml2//i386/lib/libxml2.a C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/lib/i386/libcytolib.a C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/lib/i386/libprotobuf-lite.a -LC:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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_compensations                    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
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I'C:/Users/biocbuild/bbs-3.11-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:439:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                               
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/as_literal.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function.hpp:30,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.11-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>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 ../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:519:20: 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"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/include' -I'C:/Users/biocbuild/bbs-3.11-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:439:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                               
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/range/as_literal.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/function.hpp:30,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-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:
C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-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:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-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:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-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:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-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:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-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:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-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:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-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:
C:/Users/biocbuild/bbs-3.11-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>&&)':
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: 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 C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:140,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-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 ../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:519:20: 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++)
                  ~~^~~~~~~~~~~~~~~~~~~
mkdir -p "C:/Users/biocbuild/bbs-3.11-bioc/meat/CytoML.buildbin-libdir/CytoML/lib/x64"
"C:/rtools40/mingw64/bin/"ar rs "C:/Users/biocbuild/bbs-3.11-bioc/meat/CytoML.buildbin-libdir/CytoML/lib/x64/libflowWorkspace.a" RcppExports.o parseFlowJoWorkspace.o
C:\rtools40\mingw64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.11-bioc/meat/CytoML.buildbin-libdir/CytoML/lib/x64/libflowWorkspace.a
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o CytoML.dll tmp.def RcppExports.o parseFlowJoWorkspace.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath c:/libxml2//x64/lib/libxml2.a C:/Users/biocbuild/bbs-3.11-bioc/R/library/cytolib/lib/x64/libcytolib.a C:/Users/biocbuild/bbs-3.11-bioc/R/library/RProtoBufLib/lib/x64/libprotobuf-lite.a -LC:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/CytoML.buildbin-libdir/CytoML/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CytoML' as CytoML_2.0.5.zip
* DONE (CytoML)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CytoML' successfully unpacked and MD5 sums checked

Tests output

CytoML.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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

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

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

> library(testthat)
> library(CytoML)
> 
> 
> 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).
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-H. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter SSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

== testthat results  ===========================================================
[ OK: 66 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 0 ]
> 
> #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 
  58.46    4.14   68.14

CytoML.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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

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

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

> library(testthat)
> library(CytoML)
> 
> 
> 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).
Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-H. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter SSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

Failed to use spillover/spectrum matrix Spill_defaultCompensation for compensated parameter FSC-A. It seems that the matrix was not properly defined in the Gating-ML file.

== testthat results  ===========================================================
[ OK: 66 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 0 ]
> 
> #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 
  54.84    2.87  138.57

Example timings

CytoML.Rcheck/examples_i386/CytoML-Ex.timings

nameusersystemelapsed
CytoML.par.get000
cytobank_to_gatingset000
extend0.100.030.12
fj_ws_get_keywords000
fj_ws_get_sample_groups000
fj_ws_get_samples000
flowjo_to_gatingset000
flowjo_workspace-class0.060.000.51
gatingset_to_cytobank2.020.252.69
gatingset_to_flowjo000
getChildren-graphGML-character-method000
getNodes-graphGML-method000
gs_compare_cytobank_counts2.410.193.73
open_diva_xml000
open_flowjo_xml000
plot-graphGML-missing-method000
range.GatingHierarchy000
read.gatingML.cytobank000

CytoML.Rcheck/examples_x64/CytoML-Ex.timings

nameusersystemelapsed
CytoML.par.get000
cytobank_to_gatingset000
extend0.080.030.11
fj_ws_get_keywords000
fj_ws_get_sample_groups000
fj_ws_get_samples000
flowjo_to_gatingset000
flowjo_workspace-class0.030.040.33
gatingset_to_cytobank1.750.151.94
gatingset_to_flowjo000
getChildren-graphGML-character-method000
getNodes-graphGML-method000
gs_compare_cytobank_counts2.500.132.70
open_diva_xml000
open_flowjo_xml000
plot-graphGML-missing-method000
range.GatingHierarchy000
read.gatingML.cytobank000