Package: flowWorkspace

Version: 3.34.1

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings flowWorkspace_3.34.1.tar.gz

StartedAt: 2020-04-15 01:01:23 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:03:30 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 127.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowWorkspace.Rcheck

Warnings: 3

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings flowWorkspace_3.34.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘3.34.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowWorkspace’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 87.5Mb
  sub-directories of 1Mb or more:
    lib   57.0Mb
    libs  29.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Versioned 'LinkingTo' values for
  ‘BH’ ‘RProtoBufLib’ ‘cytolib’
are only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘RBGL’ ‘grDevices’ ‘graphics’ ‘utils’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘flowCore:::.estimateLogicle’ ‘flowCore:::checkClass’
  ‘flowCore:::copyFlowSet’ ‘flowCore:::guid’
  ‘flowCore:::logicle_transform’ ‘flowCore:::updateTransformKeywords’
  ‘graph:::.makeEdgeKeys’ ‘lattice:::updateList’
  ‘ncdfFlow:::.isValidSamples’ ‘stats:::.splinefun’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.addGatingHierarchies: no visible global function definition for ‘is’
.addGatingHierarchies : <anonymous>: no visible global function
  definition for ‘fj_ws_get_keywords’
.computeCV : <anonymous>: no visible binding for global variable
  ‘xml.count’
.computeCV : <anonymous>: no visible binding for global variable
  ‘openCyto.count’
.computeCV : <anonymous> : <anonymous>: no visible global function
  definition for ‘IQR’
.computeCV : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
.computeCV_gh : <anonymous>: no visible global function definition for
  ‘IQR’
.computeCV_gh : <anonymous>: no visible global function definition for
  ‘median’
.graph_handler : asGraphNEL: no visible global function definition for
  ‘new’
.graph_handler : asGraphNEL: no visible global function definition for
  ‘validObject’
.load_gs: no visible global function definition for ‘new’
.load_gs: no visible global function definition for ‘.hasSlot’
.load_gs: no visible global function definition for ‘slot’
.load_gs: no visible global function definition for ‘is’
.mergeGates : <anonymous>: no visible global function definition for
  ‘extends’
.plotGate: no visible global function definition for ‘new’
.plotGate: no visible global function definition for ‘as.formula’
.preplot: no visible global function definition for ‘as’
.preprocessMap: no visible binding for global variable ‘old’
.preprocessMap: no visible binding for global variable ‘.’
GatingSetList: no visible global function definition for ‘as’
GatingSetList: no visible global function definition for ‘validObject’
booleanFilter: no visible global function definition for ‘new’
booleanFilter: no visible global function definition for ‘is’
char2booleanFilter: no visible global function definition for ‘new’
flowWorkspace.par.init: no visible global function definition for
  ‘gray’
gh_apply_to_new_fcs: no visible global function definition for ‘new’
gh_pop_compare_stats: no visible binding for global variable ‘node’
gh_pop_get_count: no visible binding for global variable ‘count’
gh_pop_get_proportion: no visible binding for global variable ‘percent’
gh_pop_get_stats_tfilter: no visible global function definition for
  ‘is’
gs_get_singlecell_expression: no visible global function definition for
  ‘is’
gs_get_singlecell_expression: no visible binding for global variable
  ‘parallel’
gs_pop_add: no visible global function definition for ‘is’
gs_pop_get_count_fast: no visible global function definition for ‘is’
gs_pop_get_count_with_meta: no visible binding for global variable
  ‘sampleName’
gs_pop_set_gate: no visible global function definition for ‘is’
gs_remove_redundant_nodes : <anonymous>: no visible global function
  definition for ‘is’
gslist_to_gs: no visible global function definition for ‘new’
gslist_to_gs: no visible binding for global variable ‘slot’
mkformula: no visible global function definition for ‘as.formula’
parse_transformer: no visible global function definition for ‘is’
pop.MFI: no visible binding for global variable ‘desc’
save_gslist: no visible binding for global variable ‘slot’
transformerList: no visible global function definition for ‘is’
transformerList: no visible binding for global variable ‘is’
GatingSet,flowSet-ANY: no visible global function definition for ‘new’
[,GatingSet-ANY: no visible global function definition for ‘new’
[,GatingSet-ANY: no visible global function definition for ‘extends’
[,GatingSetList-ANY: no visible global function definition for
  ‘callNextMethod’
[,GatingSetList-ANY: no visible global function definition for ‘as’
[[,GatingSet-character: no visible global function definition for ‘as’
flowData,GatingSet: no visible binding for global variable ‘obj’
gs_cyto_data,GatingSet: no visible global function definition for ‘is’
keyword,GatingSetList-character: no visible global function definition
  for ‘selectMethod’
keyword,GatingSetList-missing: no visible global function definition
  for ‘selectMethod’
pData<-,GatingSetList-data.frame: no visible global function definition
  for ‘callNextMethod’
pData<-,GatingSetList-data.frame: no visible global function definition
  for ‘as’
plotGate,GatingSetList-character: no visible global function definition
  for ‘selectMethod’
recompute,GatingSetList: no visible global function definition for
  ‘selectMethod’
setNode,GatingSet-character-ANY: no visible global function definition
  for ‘is’
transform,GatingSet: no visible global function definition for ‘is’
transform,GatingSet : <anonymous>: no visible global function
  definition for ‘is’
Undefined global functions or variables:
  . .hasSlot IQR as as.formula callNextMethod count desc extends
  fj_ws_get_keywords gray is median new node obj old openCyto.count
  parallel percent sampleName selectMethod slot validObject xml.count
Consider adding
  importFrom("grDevices", "gray")
  importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
             "is", "new", "selectMethod", "slot", "validObject")
  importFrom("stats", "IQR", "as.formula", "median")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘getChildren’ ‘getData’ ‘getGate’ ‘getNodes’ ‘getParent’
  ‘getPopStats’ ‘gh_pop_get_stats_tfilter’ ‘gs_cyto_data<-’
  ‘gs_pop_get_stats_tfilter’
Undocumented S4 methods:
  generic 'flowData<-' and siglist 'GatingSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'GatingSet-class':
Slots for class 'GatingSet'
  Code: FCSPath axis compensation data flag guid name pointer
        transformation
  Docs: FCSPath axis compensation data flag guid pointer transformation

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

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

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

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

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

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.10-bioc/R/library/flowWorkspace/libs/flowWorkspace.so’:
  Found ‘__assert_fail’, possibly from ‘assert’ (C)
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (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: 3 WARNINGs, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL flowWorkspace
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DROUT -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c R_API.cpp -o R_API.o
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.10-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>&&)’:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function ‘virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable ‘thisMin’ [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ~~^~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DROUT -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.10-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>&&)’:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function ‘virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable ‘thisMin’ [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ~~^~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DROUT -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c R_GatingSet.cpp -o R_GatingSet.o
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.10-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>&&)’:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function ‘virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable ‘thisMin’ [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ~~^~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DROUT -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-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>&&)’:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function ‘virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable ‘thisMin’ [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ~~^~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DROUT -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c getDescendants.cpp -o getDescendants.o
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.10-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>&&)’:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function ‘virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable ‘thisMin’ [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ~~^~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DROUT -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c getPopStats.cpp -o getPopStats.o
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.10-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>&&)’:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function ‘virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable ‘thisMin’ [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ~~^~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DROUT -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.10-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>&&)’:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function ‘virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable ‘thisMin’ [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ~~^~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DROUT -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c setCounts.cpp -o setCounts.o
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.10-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>&&)’:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.10-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/gate.hpp:14:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp: In member function ‘virtual void logTrans::transforming(EVENT_DATA_TYPE*, int)’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable ‘thisMin’ [-Wunused-variable]
    EVENT_DATA_TYPE thisMin=0;//input.min();
                    ^~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                   ~~^~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.10-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                   ~~^~~~~~~~~
mkdir -p "/home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib"
ar rs "/home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o
ar: creating /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib/libflowWorkspace.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o /home/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/lib/GatingSet.pb.o /home/biocbuild/bbs-3.10-bioc/R/library/RProtoBufLib/lib/libprotobuf.a -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowWorkspace.so; fi
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowWorkspace)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

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

> library(testthat)
> library(flowWorkspace)
> library(flowCore)
> library(ncdfFlow)
Loading required package: RcppArmadillo
Loading required package: BH
> 
> test_check("flowWorkspace")

Attaching package: 'dplyr'

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

    between, first, last

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

    filter

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

    filter

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

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

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

    combine, intersect, setdiff, union

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

    normalize

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

    IQR, mad, sd, var, xtabs

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

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

Welcome to Bioconductor

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

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 903 | SKIPPED: 3 | WARNINGS: 40 | FAILED: 0 ]
> 
> #devtools::test("~/rglab/workspace/flowWorkspace")
> #devtools::check_man()
> #test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-archive.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/test-parseWorkspace.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/GatingHierarchy-testSuite.R")
> # test_file("/home/wjiang2/rglab/workspace/flowWorkspace/tests/testthat/GatingSet-testSuite.R")
> 
> proc.time()
   user  system elapsed 
 60.160   2.020  43.777 

name	user	system	elapsed
GatingHierarchy-class	0	0	0
GatingSet-class	0	0	0
GatingSet-methods	0.000	0.000	0.001
GatingSetList-class	0.000	0.000	0.001
asinh_Gml2	0	0	0
asinhtGml2_trans	0.004	0.000	0.003
booleanFilter-class	0.004	0.000	0.003
compensate	0	0	0
estimateLogicle.GatingHierarchy	0.000	0.000	0.001
extract_cluster_pop_name_from_node	0.000	0.000	0.001
flowJo_flog	0.000	0.000	0.001
flowWorkspace.par.get	0.004	0.000	0.002
flow_breaks	0.704	0.044	0.763
flowjo_biexp	0.000	0.000	0.002
flowjo_biexp_trans	0.556	0.028	0.583
flowjo_fasinh	0.004	0.000	0.000
flowjo_fasinh_trans	0.000	0.000	0.001
gh_copy_gate	0.228	0.004	0.230
gh_get_compensations	0.000	0.000	0.001
gh_get_transformations	0.000	0.000	0.001
gh_pop_get_descendants	0.020	0.000	0.017
gh_pop_get_gate	0	0	0
gh_pop_get_indices	0	0	0
gh_pop_move	0.072	0.008	0.077
gh_pop_set_indices	0.824	0.144	0.754
gh_pop_set_xml_count	0.004	0.000	0.000
gs_check_redundant_nodes	0	0	0
gs_clone	0	0	0
gs_get_pop_paths	0	0	0
gs_get_singlecell_expression	0.000	0.000	0.001
gs_plot_diff_tree	0	0	0
gs_plot_pop_count_cv	0	0	0
gs_pop_add	0.004	0.000	0.000
gs_pop_get_children	0	0	0
gs_pop_get_count_fast	0	0	0
gs_pop_get_data	0	0	0
gs_pop_get_stats	0.000	0.000	0.001
gs_pop_set_gate	0	0	0
gs_pop_set_name	0	0	0
gs_pop_set_visibility	0	0	0
gs_remove_redundant_channels	0	0	0
gs_remove_redundant_nodes	0	0	0
gs_split_by_channels	0	0	0
gs_split_by_tree	0	0	0
gs_update_channels	0	0	0
keyword	0	0	0
logicleGml2_trans	0.000	0.000	0.001
logicle_trans	0.000	0.000	0.001
loglevel	0	0	0
logtGml2_trans	0	0	0
markernames	0	0	0
mkformula	0.000	0.000	0.002
plot-methods	0	0	0
plotGate-methods	0.004	0.000	0.000
prettyAxis	0	0	0
rotate_gate	0	0	0
sampleNames	0	0	0
save_gs	0	0	0
scale_gate	0	0	0
shift_gate	0.000	0.000	0.001
swap_data_cols	0.700	0.024	0.725
transform	0.000	0.000	0.001
transform_gate	0.000	0.000	0.001
transformerList	0.028	0.004	0.030