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CHECK report for flowWorkspace on malbec2

This page was generated on 2018-10-17 08:23:37 -0400 (Wed, 17 Oct 2018).

Package 525/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowWorkspace 3.28.2
Greg Finak ,Mike Jiang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/flowWorkspace
Branch: RELEASE_3_7
Last Commit: bd5ee4c
Last Changed Date: 2018-09-12 18:32:05 -0400 (Wed, 12 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowWorkspace
Version: 3.28.2
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings flowWorkspace_3.28.2.tar.gz
StartedAt: 2018-10-16 00:28:52 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 00:30:29 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 97.4 seconds
RetCode: 0
Status:  OK 
CheckDir: flowWorkspace.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:flowWorkspace.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings flowWorkspace_3.28.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘3.28.2’
* 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 82.7Mb
  sub-directories of 1Mb or more:
    lib   53.6Mb
    libs  27.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' values for
  ‘BH’ ‘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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.7-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: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.

Installation output

flowWorkspace.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL flowWorkspace
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I/usr/local/include   -fpic  -g -O2 -c R_API.cpp -o R_API.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I/usr/local/include   -fpic  -g -O2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-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;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I/usr/local/include   -fpic  -g -O2 -c R_GatingSet.cpp -o R_GatingSet.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-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-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-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;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I/usr/local/include   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-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;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I/usr/local/include   -fpic  -g -O2 -c getDescendants.cpp -o getDescendants.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
/home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I/usr/local/include   -fpic  -g -O2 -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
/home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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;
                            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include" -I/usr/local/include   -fpic  -g -O2 -c setCounts.cpp -o setCounts.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
/home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.7-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;
                            ^
mkdir -p "/home/biocbuild/bbs-3.7-bioc/R/library/flowWorkspace/lib"
ar rs "/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/flowWorkspace/lib/libflowWorkspace.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/RProtoBufLib/lib/GatingSet.pb.o /home/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/lib/libprotobuf.a -lxml2 -L/home/biocbuild/bbs-3.7-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-3.7-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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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

mac version of flowJo workspace recognized.
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 776 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 
 24.744   0.696  25.299

Example timings

flowWorkspace.Rcheck/flowWorkspace-Ex.timings

nameusersystemelapsed
GatingHierarchy-class1.9200.0962.121
GatingSet-class0.8840.0440.931
GatingSet-methods000
GatingSetList-class0.0000.0000.003
add0.0000.0000.002
asinh_Gml20.0000.0000.001
asinhtGml2_trans0.0000.0000.001
booleanFilter-class0.0040.0000.002
checkRedundantNodes000
clone000
compensate000
dropRedundantChannels0.0000.0000.001
dropRedundantNodes0.0000.0000.001
estimateLogicle.GatingHierarchy000
flowJo.fasinh0.0000.0000.001
flowJo.flog0.0040.0000.002
flowJoTrans0.0000.0000.001
flowJoWorkspace-class0.0280.0000.028
flowJo_biexp_trans0.4840.0120.497
flowJo_fasinh_trans0.0040.0000.001
flowWorkspace.par.get0.0000.0000.001
flow_breaks0.5000.0200.518
getCompensationMatrices000
getData-methods0.0040.0000.001
getDescendants0.0120.0000.013
getGate0.0040.0000.001
getIndices-GatingSet-name-method000
getIndices0.0000.0000.001
getKeywords0.1560.0120.169
getMergedStats000
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