Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:06:19 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for CytoML on palomino4


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

raw results

Package 456/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoML 2.9.0  (landing page)
Mike Jiang
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/CytoML
git_branch: master
git_last_commit: eee88b7
git_last_commit_date: 2022-04-26 11:33:22 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'openCyto' which is not available
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  NO, package depends on 'openCyto' which is not available

Summary

Package: CytoML
Version: 2.9.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoML.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings CytoML_2.9.0.tar.gz
StartedAt: 2022-06-24 00:44:41 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 00:48:10 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 208.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CytoML.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CytoML.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings CytoML_2.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/CytoML.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CytoML/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CytoML' version '2.9.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'CytoML' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 14.6Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      8.7Mb
* 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
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  'RUnit' 'corpcor' 'openCyto' 'stats'
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  'ggcyto:::merge.quad.gates' 'lattice:::updateList'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addCustomInfo: no visible global function definition for
  'gh_get_transformations'
addGate: no visible binding for global variable 'id'
addGate: no visible binding for global variable 'gate_id'
addGate: no visible binding for global variable 'fcs'
addGate: no visible binding for global variable 'fcs_file_id'
addGate: no visible binding for global variable 'gate_def'
addGate: no visible binding for global variable 'name'
ce_get_panels: no visible binding for global variable 'panel'
ce_get_panels: no visible binding for global variable 'n'
constructTree: no visible binding for global variable 'id'
constructTree: no visible binding for global variable 'name'
createTransformIdentifier: no visible global function definition for
  'slotNames'
cytobank_to_gatingset.cytobank_experiment: no visible binding for
  global variable 'desc'
diva_to_gatingset: no visible binding for global variable 'specimen'
diva_to_gatingset: no visible binding for global variable
  'sampleSelected'
diva_to_gatingset: no visible global function definition for
  'gh_apply_to_new_fcs'
export_comp_trans: no visible global function definition for
  'gh_get_compensations'
export_comp_trans: no visible global function definition for
  'gh_get_transformations'
export_gates_cytobank: no visible global function definition for
  'gs_get_pop_paths'
export_gates_cytobank: no visible global function definition for
  'gs_pop_get_gate'
extend.polygonGate: no visible binding for global variable '..dim'
extend.polygonGate : <anonymous>: no visible binding for global
  variable 'y'
extend.polygonGate : <anonymous>: no visible binding for global
  variable 'x'
extend.polygonGate: no visible binding for global variable 'id'
extend.polygonGate: no visible binding for global variable 'x'
extend.polygonGate: no visible binding for global variable 'y'
extend.polygonGate: no visible binding for global variable 'is.smaller'
flinTr: no visible global function definition for 'lintGml2'
fratioTr: no visible global function definition for 'ratiotGml2'
generate_trans: no visible global function definition for
  'flowjo_log_trans'
gs_compare_cytobank_counts: no visible binding for global variable
  'population'
gs_compare_cytobank_counts: no visible binding for global variable
  'parent'
gs_compare_cytobank_counts: no visible binding for global variable
  'parent_count'
gs_compare_cytobank_counts: no visible global function definition for
  '.'
gs_compare_cytobank_counts: no visible binding for global variable
  'fcs_filename'
hyperlogTr: no visible global function definition for 'hyperlogtGml2'
open_cytobank_experiment: no visible global function definition for
  'unzip'
range.GatingHierarchy: no visible global function definition for
  'gh_get_transformations'
read.gatingML.cytobank: no visible binding for global variable 'id'
read.gatingML.cytobank: no visible binding for global variable
  'comp_ref'
transDg1polynomial: no visible global function definition for
  'dg1polynomial'
transEH: no visible global function definition for 'EHtrans'
transExponential: no visible global function definition for
  'exponential'
transHyperLog: no visible global function definition for 'hyperlog'
transHyperbolicSin: no visible global function definition for 'sinht'
transInvSplitScale: no visible global function definition for
  'invsplitscale'
transInverseHyperbolicSin: no visible global function definition for
  'asinht'
transLogarithm: no visible global function definition for 'logarithm'
transQuadratic: no visible global function definition for 'quadratic'
transRatio: no visible global function definition for 'ratio'
transSplitScale: no visible global function definition for 'splitscale'
transSquareroot: no visible global function definition for 'squareroot'
write.gatingML: no visible global function definition for 'sessionInfo'
xmlVertexNode : <anonymous>: no visible global function definition for
  'format_float'
identifyNode,http...www.isac.net.org.std.Gating.ML.v1.5.gating_DecisionTreeGate:
  no visible binding for global variable 'expressionFilter'
identifyNode,http...www.isac.net.org.std.Gating.ML.v1.5.gating_PolytopeGate:
  no visible global function definition for 'polytopeGate'
identifyNode,http...www.isac.net.org.std.Gating.ML.v2.0.transformations_spectrumMatrix:
  no visible global function definition for 'pseudoinverse'
show,flowjo_workspace: no visible binding for global variable
  'groupName'
show,flowjo_workspace: no visible binding for global variable 'groupID'
Undefined global functions or variables:
  . ..dim EHtrans asinht comp_ref desc dg1polynomial exponential
  expressionFilter fcs fcs_file_id fcs_filename flowjo_log_trans
  format_float gate_def gate_id gh_apply_to_new_fcs
  gh_get_compensations gh_get_transformations groupID groupName
  gs_get_pop_paths gs_pop_get_gate hyperlog hyperlogtGml2 id
  invsplitscale is.smaller lintGml2 logarithm n name panel parent
  parent_count polytopeGate population pseudoinverse quadratic ratio
  ratiotGml2 sampleSelected sessionInfo sinht slotNames specimen
  splitscale squareroot unzip x y
Consider adding
  importFrom("methods", "slotNames")
  importFrom("utils", "sessionInfo", "unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'parseWorkspace'
  'backend_dir' 'backend'
Documented arguments not in \usage in documentation object 'parseWorkspace':
  'h5_dir'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... WARNING
  apparently using $(BLAS_LIBS) without following $(FLIBS) in 'src/Makevars.in'
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/CytoML/libs/x64/CytoML.dll':
  Found '_assert', possibly from 'assert' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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: 2 WARNINGs, 6 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/CytoML.Rcheck/00check.log'
for details.



Installation output

CytoML.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/CytoML_2.9.0.tar.gz && rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CytoML.buildbin-libdir CytoML_2.9.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL CytoML_2.9.0.zip && rm CytoML_2.9.0.tar.gz CytoML_2.9.0.zip
###
##############################################################################
##############################################################################


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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 6621k  100 6621k    0     0  7802k      0 --:--:-- --:--:-- --:--:-- 7808k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'CytoML' ...
** using staged installation

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


** libs
rm -f RcppExports.o parseFlowJoWorkspace.o CytoML.dll
"F:/biocbuild/bbs-3.16-bioc/R/bin/x64/Rscript.exe" "../tools/winlibs.R" 2.9.10
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.10/include/libxml2 -DLIBXML_STATIC -fpermissive -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment]
  435 |     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
      |                               
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function.hpp:30,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   58 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   62 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   68 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  507 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  520 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  603 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  612 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
F:/biocbuild/bbs-3.16-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>&&)':
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
                 from ../inst/include/CytoML.h:4,
                 from RcppExports.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   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:605:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  605 |   for(int j = 0; j < sample_ids.size(); j++)
      |                  ~~^~~~~~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.10/include/libxml2 -DLIBXML_STATIC -fpermissive -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12,
                 from parseFlowJoWorkspace.cpp:9:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment]
  435 |     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
      |                               
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-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:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function.hpp:30,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-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:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-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:
F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   58 |   if(valVec.size() != 1+n+n*n){
      |      ~~~~~~~~~~~~~~^~~~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   62 |    if(valVec.size() == 1+n+2*n*n){
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   68 |     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-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:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
   74 |     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
      |                               ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-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:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-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:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-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:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  507 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-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:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  520 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-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:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  603 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-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:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  612 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:606,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from F:/biocbuild/bbs-3.16-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:
F:/biocbuild/bbs-3.16-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>&&)':
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\memory:83,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from F:/biocbuild/bbs-3.16-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:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
   57 |   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:605:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  605 |   for(int j = 0; j < sample_ids.size(); j++)
      |                  ~~^~~~~~~~~~~~~~~~~~~
g++ -shared -s -static-libgcc -o CytoML.dll tmp.def RcppExports.o parseFlowJoWorkspace.o -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -L../windows/libxml2-2.9.10/lib/x64-ucrt -lxml2 -llzma -liconv -lz F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/lib/x64/libcytolib.a F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o -LF:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/lib/x64 -lprotobuf -LF:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LF:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/lib/x64-ucrt -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lsz -laec -lz -lpsapi -lws2_32 -lbcrypt -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* MD5 sums
packaged installation of 'CytoML' as CytoML_2.9.0.zip
* DONE (CytoML)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'CytoML' successfully unpacked and MD5 sums checked

Tests output

CytoML.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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)
> 
> win32_flag = .Platform$OS.type == "windows" && .Machine$sizeof.pointer != 8
> if(!win32_flag)
+   test_check("CytoML")
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:

  vignette("flowWorkspace-Introduction", "flowWorkspace")
Loading required package: ggplot2
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
INFO: Could not find files for the given pattern(s).
INFO: Could not find files for the given pattern(s).
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.

[ FAIL 0 | WARN 2 | SKIP 5 | PASS 66 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• (check_docker_status()[1] == "docker_ok" || check_binary_status() ==  (1)
• dir.exists("~/rglab/workspace/flowWorkspace/wsTestSuite") is not TRUE (1)
• dir.exists(path) is not TRUE (1)
• file.exists(acsfile) is not TRUE (2)

[ FAIL 0 | WARN 2 | SKIP 5 | PASS 66 ]
Warning message:
replacing previous import 'flowViz::contour' by 'graphics::contour' when loading 'flowStats' 
> 
> #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 
  45.95    2.87   50.57 

Example timings

CytoML.Rcheck/CytoML-Ex.timings

nameusersystemelapsed
CytoML.par.get000
cytobank_to_gatingset000
extend0.110.000.11
fj_ws_get_keywords000
fj_ws_get_sample_groups000
fj_ws_get_samples000
flowjo_to_gatingset000
flowjo_workspace-class0.050.000.19
gatingset_to_cytobank1.430.011.45
gatingset_to_flowjo000
getChildren-graphGML-character-method000
getNodes-graphGML-method000
gs_compare_cytobank_counts2.190.102.45
open_diva_xml000
open_flowjo_xml000
plot-graphGML-missing-method000
range.GatingHierarchy000
read.gatingML.cytobank000