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CHECK report for flowWorkspace on malbec1

This page was generated on 2019-04-16 11:49:11 -0400 (Tue, 16 Apr 2019).

Package 554/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowWorkspace 3.30.2
Greg Finak ,Mike Jiang
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/flowWorkspace
Branch: RELEASE_3_8
Last Commit: eac7b2d
Last Changed Date: 2019-01-04 13:33:27 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowWorkspace
Version: 3.30.2
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings flowWorkspace_3.30.2.tar.gz
StartedAt: 2019-04-15 23:59:48 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-16 00:01:53 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 125.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flowWorkspace.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings flowWorkspace_3.30.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/flowWorkspace.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘3.30.2’
* 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 83.7Mb
  sub-directories of 1Mb or more:
    lib   54.3Mb
    libs  28.1Mb
* 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’
  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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.cpp_setIndices’ ‘.getNodeInd’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getGate,GatingSetList-character: warning in unlist(res, recur = FALSE):
  partial argument match of 'recur' to 'recursive'
.addGatingHierarchies: no visible global function definition for ‘is’
.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’
.dropRedundantNodes : <anonymous>: no visible global function
  definition for ‘is’
.getSingleCellExpression: no visible binding for global variable
  ‘parallel’
.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’
.parse.pData: no visible binding for global variable ‘.’
.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 ‘.’
.preprocessor: no visible binding for global variable ‘groupName’
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’
dropRedundantNodes : <anonymous>: no visible global function definition
  for ‘is’
flowWorkspace.par.init: no visible global function definition for
  ‘gray’
getMergedStats: no visible binding for global variable ‘sampleName’
mkformula: no visible global function definition for ‘as.formula’
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,GatingHierarchy-character: no visible global function
  definition for ‘new’
GatingSet,character-character: no visible global function definition
  for ‘new’
GatingSet,flowSet-ANY: no visible global function definition for ‘new’
Rm,character-GatingSetList-character: no visible global function
  definition for ‘selectMethod’
[,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 ‘new’
add,GatingHierarchy-logicalFilterResult: no visible global function
  definition for ‘selectMethod’
add,GatingSet-filtersList: no visible global function definition for
  ‘selectMethod’
add,GatingSet-list: no visible global function definition for
  ‘selectMethod’
add,GatingSetList-filter: no visible global function definition for
  ‘selectMethod’
add,GatingSetList-filterList: no visible global function definition for
  ‘selectMethod’
add,GatingSetList-filters: no visible global function definition for
  ‘selectMethod’
add,GatingSetList-filtersList: no visible global function definition
  for ‘selectMethod’
add,GatingSetList-list: no visible global function definition for
  ‘selectMethod’
getPopStats,GatingHierarchy: no visible binding for global variable
  ‘node’
keyword,GatingSetList-character: no visible global function definition
  for ‘selectMethod’
keyword,GatingSetList-missing: no visible global function definition
  for ‘selectMethod’
openWorkspace,character: no visible global function definition for
  ‘new’
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’
rbind2,GatingSetList-missing: no visible global function definition for
  ‘new’
rbind2,GatingSetList-missing: no visible binding for global variable
  ‘slot’
recompute,GatingSetList: no visible global function definition for
  ‘selectMethod’
show,flowJoWorkspace: no visible global function definition for ‘.’
show,flowJoWorkspace: no visible binding for global variable
  ‘groupName’
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 desc extends gray
  groupName is median new node old openCyto.count parallel 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'add,GatingSet,list-method'
  ‘cluster_method_name’

Undocumented arguments in documentation object 'plot_diff_tree'
  ‘path’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.8-bioc/R/library/flowWorkspace/libs/flowWorkspace.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘__assert_fail’, possibly from ‘assert’ (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: 1 WARNING, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.



Installation output

flowWorkspace.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL flowWorkspace
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘flowWorkspace’ ...
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: Using the following compilation and linking flags for flowWorkspace
configure:    PKG_CPPFLAGS=-I/usr/include/libxml2
configure:    PKG_LIBS=-lxml2
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c R_API.cpp -o R_API.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: 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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.8-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-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: 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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.8-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-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c R_GatingSet.cpp -o R_GatingSet.o
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:433:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                              ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: 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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.8-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-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.8-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++)
                     ^
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:0,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/workspace.hpp: In member function ‘void workspace::toArray(std::__cxx11::string, std::vector<double>&, std::vector<double>&)’:
../inst/include/flowWorkspace/workspace.hpp:108:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned i=0;i<nLen;i++)
                       ^
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp: In member function ‘virtual trans_local xFlowJoWorkspace::getTransformation(wsRootNode, const compensation&, PARAM_VEC&, trans_global_vec*, biexpTrans*, linTrans*, bool)’:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:802:12: warning: unused variable ‘minRange’ [-Wunused-variable]
     double minRange=atof(transNode.getProperty("minRange").c_str());
            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp: In member function ‘CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)’:
/home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:1314:94: warning: ‘quad’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),interpolated(false),quadrant(_quad){
                                                                                              ^
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:410:10: note: ‘quad’ was declared here
     QUAD quad;
          ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: 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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.8-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-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.8-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++/5/memory:81:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c getDescendants.cpp -o getDescendants.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getDescendants.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getDescendants.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getDescendants.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getDescendants.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getDescendants.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getDescendants.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getDescendants.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.8-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-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getDescendants.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getDescendants.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.8-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-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from getSingleCellExpression.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c setCounts.cpp -o setCounts.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from setCounts.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: 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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from setCounts.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from setCounts.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from setCounts.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from setCounts.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from setCounts.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from setCounts.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.8-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-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from setCounts.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.8-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++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from setCounts.cpp:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.8-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-3.8-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.8-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-3.8-bioc/R/library/flowWorkspace/lib"
ar rs "/home/biocbuild/bbs-3.8-bioc/R/library/flowWorkspace/lib/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getSingleCellExpression.o setCounts.o
ar: creating /home/biocbuild/bbs-3.8-bioc/R/library/flowWorkspace/lib/libflowWorkspace.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getSingleCellExpression.o setCounts.o /home/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/lib/GatingSet.pb.o /home/biocbuild/bbs-3.8-bioc/R/library/RProtoBufLib/lib/libprotobuf.a -lxml2 -L/home/biocbuild/bbs-3.8-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-3.8-bioc/R/library/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
* DONE (flowWorkspace)

Tests output

flowWorkspace.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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)
Loading required package: flowCore
Loading required package: 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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")'.

mac version of flowJo workspace recognized.
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 781 SKIPPED: 3 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/InternalTestSuite.R")
> 
> 
> proc.time()
   user  system elapsed 
 42.444   0.916  35.208 

Example timings

flowWorkspace.Rcheck/flowWorkspace-Ex.timings

nameusersystemelapsed
GatingHierarchy-class2.5200.0842.701
GatingSet-class1.2520.0481.301
GatingSet-methods000
GatingSetList-class0.0040.0000.000
add000
asinh_Gml20.0000.0000.001
asinhtGml2_trans0.0040.0000.001
booleanFilter-class0.0000.0000.003
checkRedundantNodes0.0000.0000.001
clone000
compensate000
dropRedundantChannels000
dropRedundantNodes000
estimateLogicle.GatingHierarchy0.0000.0000.001
extract_cluster_pop_name_from_node0.0000.0000.001
flowJo.fasinh0.0000.0000.001
flowJo.flog0.0040.0000.001
flowJoTrans0.0000.0000.002
flowJoWorkspace-class0.1840.0000.089
flowJo_biexp_trans0.6600.0120.673
flowJo_fasinh_trans0.0000.0000.001
flowWorkspace.par.get000
flow_breaks0.5040.0120.517
getCompensationMatrices000
getData-methods000
getDescendants0.0080.0040.013
getGate000
getIndices-GatingSet-name-method000
getIndices000
getKeywords0.1400.0160.192
getMergedStats000
getParent000
getPopStats000
getSampleGroups000
getSamples000
getSingleCellExpression000
getStats000
getTransformations000
groupByChannels000
groupByTree000
insertGate000
keyword000
logicleGml2_trans0.0040.0000.001
logicle_trans0.0000.0000.001
loglevel000
logtGml2_trans0.0000.0000.001
markernames0.0000.0000.001
mkformula0.0000.0000.001
moveNode0.0600.0000.059
openWorkspace000
parseWorkspace000
plot-methods0.0000.0000.001
plotGate-methods000
plotPopCV000
plot_diff_tree000
prettyAxis000
sampleNames000
save_gs000
set.count.xml000
setGate000
setNode-methods0.0000.0000.001
transform000
transformerList0.0080.0040.008
updateChannels000
updateIndices-GatingHierarchy-character-logical-method0.6440.1120.522