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CHECK report for cytolib on malbec1

This page was generated on 2018-04-12 13:16:35 -0400 (Thu, 12 Apr 2018).

Package 324/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cytolib 1.0.1
Mike Jiang
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/cytolib
Branch: RELEASE_3_6
Last Commit: cc476f0
Last Changed Date: 2017-11-03 18:44:20 -0400 (Fri, 03 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: cytolib
Version: 1.0.1
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings cytolib_1.0.1.tar.gz
StartedAt: 2018-04-11 22:41:20 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:42:44 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 84.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: cytolib.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings cytolib_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/cytolib.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cytolib/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cytolib’ version ‘1.0.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory ‘src’ contains:
  GatingSet.proto GatingSet_pb2.py
These are unlikely file names for src files.
* 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 ‘cytolib’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 41.7Mb
  sub-directories of 1Mb or more:
    lib   21.9Mb
    libs  18.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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
File ‘cytolib/libs/cytolib.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Objects: ‘GatingHierarchy.o’, ‘GatingSet.o’, ‘gate.o’,
      ‘nodeProperties.o’, ‘transformation.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/cytolib.Rcheck/00check.log’
for details.

Installation output

cytolib.Rcheck/00install.out

* installing *source* package ‘cytolib’ ...
** libs
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/flowData.hpp:20,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from GatingHierarchy.cpp:8:
/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-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c GatingSet.cpp -o GatingSet.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.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-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.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-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/flowData.hpp:20,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.cpp:9:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/cytolib/populationTree.hpp:11,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:13,
                 from ../inst/include/cytolib/GatingSet.hpp:12,
                 from GatingSet.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-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c GatingSet.pb.cc -o GatingSet.pb.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c POPINDICES.cpp -o POPINDICES.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/flowData.hpp:20,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from POPINDICES.cpp:8:
/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-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c calibrationTable.cpp -o calibrationTable.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from calibrationTable.cpp:8:
/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-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c compensation.cpp -o compensation.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/transformation.hpp:24,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from ../inst/include/cytolib/compensation.hpp:10,
                 from compensation.cpp:8:
/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-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c delimitedMessage.cpp -o delimitedMessage.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c ellipse2points.cpp -o ellipse2points.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.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-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.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-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/flowData.hpp:20,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.cpp:1:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/ellipse2points.hpp:10,
                 from ellipse2points.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-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c flowData.cpp -o flowData.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/flowData.hpp:20,
                 from flowData.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from flowData.cpp:8:
/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-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c gate.cpp -o gate.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.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-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.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-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/flowData.hpp:20,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.cpp:10:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from gate.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-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c global.cpp -o global.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c nodeProperties.cpp -o nodeProperties.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/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-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/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-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/flowData.hpp:20,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/flowData.hpp:19,
                 from ../inst/include/cytolib/gate.hpp:14,
                 from ../inst/include/cytolib/POPINDICES.hpp:15,
                 from ../inst/include/cytolib/nodeProperties.hpp:11,
                 from nodeProperties.cpp:7:
/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-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c spline.cpp -o spline.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DROUT -I../inst/include/ -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/include" -I/usr/local/include   -fpic  -g -O2 -c transformation.cpp -o transformation.o
In file included from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/property_map/property_map.hpp:601,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/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-3.6-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/function.hpp:30,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from ../inst/include/cytolib/transformation.hpp:24,
                 from transformation.cpp:8:
/home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/BH/include/boost/functional/hash/extensions.hpp:37,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash/hash.hpp:594,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/functional/hash.hpp:6,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered/unordered_set.hpp:18,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/unordered_set.hpp:17,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:21,
                 from /home/biocbuild/bbs-3.6-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
                 from ../inst/include/cytolib/calibrationTable.hpp:18,
                 from ../inst/include/cytolib/transformation.hpp:23,
                 from transformation.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
mkdir -p "/home/biocbuild/bbs-3.6-bioc/meat/cytolib.Rcheck/cytolib/lib"
ar rs "/home/biocbuild/bbs-3.6-bioc/meat/cytolib.Rcheck/cytolib/lib/libcytolib.a" GatingHierarchy.o GatingSet.o GatingSet.pb.o POPINDICES.o calibrationTable.o compensation.o delimitedMessage.o ellipse2points.o flowData.o gate.o global.o nodeProperties.o spline.o transformation.o
ar: creating /home/biocbuild/bbs-3.6-bioc/meat/cytolib.Rcheck/cytolib/lib/libcytolib.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o cytolib.so GatingHierarchy.o GatingSet.o GatingSet.pb.o POPINDICES.o calibrationTable.o compensation.o delimitedMessage.o ellipse2points.o flowData.o gate.o global.o nodeProperties.o spline.o transformation.o /home/biocbuild/bbs-3.6-bioc/R/library/RProtoBufLib/lib/libprotobuf.a -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/cytolib.Rcheck/cytolib/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cytolib)

Tests output

Example timings

cytolib.Rcheck/cytolib-Ex.timings

nameusersystemelapsed
LdFlags0.0080.0040.011